Applications in Plant Sciences最新文献

{"title":"Advancing plant metabolic research by using large language models to expand databases and extract labeled data","authors":"Rachel Knapp,&nbsp;Braidon Johnson,&nbsp;Lucas Busta","doi":"10.1002/aps3.70007","DOIUrl":"10.1002/aps3.70007","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Recently, plant science has seen transformative advances in scalable data collection for sequence and chemical data. These large datasets, combined with machine learning, have demonstrated that conducting plant metabolic research on large scales yields remarkable insights. A key next step in increasing scale has been revealed with the advent of accessible large language models, which, even in their early stages, can distill structured data from the literature. This brings us closer to creating specialized databases that consolidate virtually all published knowledge on a topic.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Here, we first test different combinations of prompt engineering techniques and language models in the identification of validated enzyme–product pairs. Next, we evaluate the application of automated prompt engineering and retrieval-augmented generation to identify compound–species associations. Finally, we build and determine the accuracy of a multimodal language model–based pipeline that transcribes images of tables into machine-readable formats.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>When tuned for each specific task, these methods perform with high (80–90%) or modest (50%) accuracies for enzyme–product pair identification and table image transcription, but with lower false-negative rates than previous methods (decreasing from 55% to 40%) for compound–species pair identification.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>We enumerate several suggestions for researchers working with language models, among which is the importance of the user's domain-specific expertise and knowledge.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 4","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144768090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new spin on chemotaxonomy: Using non-proteogenic amino acids as a test case","authors":"Makenzie Gibson,&nbsp;William Thives Santos,&nbsp;Alan R. Oyler,&nbsp;Lucas Busta,&nbsp;Craig A. Schenck","doi":"10.1002/aps3.70006","DOIUrl":"10.1002/aps3.70006","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Specialized metabolites serve various roles for plants and humans. Unlike core metabolites, specialized metabolites are restricted to certain plant lineages; thus, in addition to their ecological functions, specialized metabolites can serve as diagnostic markers of plant lineages.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We investigated the phylogenetic distribution of plant metabolites using non-proteogenic amino acids (NPAA). Species–NPAA associations for eight NPAAs were identified from the existing literature and placed within a phylogenetic context using R packages and the Interactive Tree of Life. To confirm and extend the literature-based NPAA distribution, we selected azetidine-2-carboxylic acid (Aze) and screened over 70 diverse plants using gas chromatography–mass spectrometry (GC-MS).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Literature searches identified 163 NPAA-relevant articles, which were manually inspected to identify 822 species–NPAA associations. NPAAs were mapped at the order and genus level, revealing that some NPAAs are restricted to single orders, whereas others are present across divergent taxa. The observed distribution of Aze across plants and ancestral state reconstruction suggests a convergent evolutionary history.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Although reliance on chemotaxonomy has decreased in recent years, there is still value in placing metabolites within a phylogenetic context to understand the evolutionary processes of plant chemical diversification. This approach can be applied to metabolites present in any organism and compared at a range of taxonomic levels.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 4","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144767905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A low-cost protocol for the optical method of vulnerability curves to calculate P50","authors":"Georgina González-Rebeles,&nbsp;Miguel Ángel Alonso-Arevalo,&nbsp;Eulogio López,&nbsp;Rodrigo Méndez-Alonzo","doi":"10.1002/aps3.70004","DOIUrl":"10.1002/aps3.70004","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The quantification of plant drought resistance, particularly embolism formation, within and across species, is critical for ecosystem management and agriculture. We developed a cost-effective protocol to measure the water potential at which 50% of hydraulic conductivity (<i>P</i>₅₀) is lost in stems, using affordable and accessible materials in comparison to the traditional optical method.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>Our protocol uses inexpensive USB microscopes, which are secured along with the plants to a pegboard base to avoid movement. A Python program automatized the image acquisition. This method was applied to quantify <i>P</i>₅₀ in an exotic species (<i>Nicotiana glauca</i>) and native species (<i>Rhus integrifolia</i>) of the Mediterranean vegetation in Baja California, Mexico.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>The intra- and interspecific patterns of variation in stem <i>P</i>₅₀ of <i>N. glauca</i> and <i>R. integrifolia</i> were obtained using the low-cost optical method with widely available and affordable materials that can be easily replicated for other species.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143884020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The PteridoPortal: A publicly accessible collection of over three million records of extant and extinct pteridophytes","authors":"Carl J. Rothfels,&nbsp;Jaemin Lee,&nbsp;Michael A. Sundue,&nbsp;Alan R. Smith,&nbsp;Amy Kasameyer,&nbsp;Joyce Gross,&nbsp;Garth Holman,&nbsp;Shusheng Hu,&nbsp;Matt von Konrat,&nbsp;Emily B. Sessa,&nbsp;Kimberly Watson,&nbsp;Alan Weakley,&nbsp;Libing Zhang,&nbsp;Patricia Gensel,&nbsp;Michael Hassler,&nbsp;Katelin D. Pearson,&nbsp;Ed Gilbert,&nbsp;Robyn J. Burnham,&nbsp;Richard K. Rabeler,&nbsp;Patrick Sweeney,&nbsp;Alejandra Vasco,&nbsp;Weston Testo,&nbsp;David E. Giblin,&nbsp;Stefanie M. Ickert-Bond,&nbsp;Margaret Landis,&nbsp;Melanie Link-Perez,&nbsp;Tatyana Livshultz,&nbsp;Ian Miller,&nbsp;Christopher Neefus,&nbsp;Kathleen Pigg,&nbsp;Mitchell Power,&nbsp;Alan Prather,&nbsp;Tiana Rehman,&nbsp;Lena Struwe,&nbsp;Michael Vincent,&nbsp;George Weiblen,&nbsp;Timothy Whitfeld,&nbsp;Michael D. Windham,&nbsp;George Yatskievych,&nbsp;Aaron Liston,&nbsp;Elizabeth Makings,&nbsp;Kathleen M. Pryer,&nbsp;Caroline Strömberg,&nbsp;Eve Atri,&nbsp;Jason Best,&nbsp;Ian Glasspool,&nbsp;Layne Huiet,&nbsp;Elizabeth Johnson,&nbsp;Megan R. King,&nbsp;Az Klymiuk,&nbsp;Richard Lupia,&nbsp;Lucas C. Majure,&nbsp;Carol Ann McCormick,&nbsp;Richard McCourt,&nbsp;Shanna Oberreiter,&nbsp;Kent D. Perkins,&nbsp;Yarency Rodriguez,&nbsp;Chelsea Smith,&nbsp;James Solomon,&nbsp;Jordan Teisher,&nbsp;Donna Ford-Werntz,&nbsp;Petra Fuehrding-Potschkat,&nbsp;Holly Little,&nbsp;Tom A. Ranker,&nbsp;Eric Schuettpelz,&nbsp;Carrie M. Tribble,&nbsp;Diane M. Erwin,&nbsp;Cindy V. Looy","doi":"10.1002/aps3.70003","DOIUrl":"10.1002/aps3.70003","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Pteridophytes—vascular land plants that disperse by spores—are a powerful system for studying plant evolution, particularly with respect to the impact of abiotic factors on evolutionary trajectories through deep time. However, our ability to use pteridophytes to investigate such questions—or to capitalize on the ecological and conservation-related applications of the group—has been impaired by the relative isolation of the neo- and paleobotanical research communities and by the absence of large-scale biodiversity data sources.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Here we present the Pteridophyte Collections Consortium (PCC), an interdisciplinary community uniting neo- and paleobotanists, and the associated PteridoPortal, a publicly accessible online portal that serves over three million pteridophyte records, including herbarium specimens, paleontological museum specimens, and iNaturalist observations. We demonstrate the utility of the PteridoPortal through discussion of three example PteridoPortal-enabled research projects.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The data within the PteridoPortal are global in scope and are queryable in a flexible manner. The PteridoPortal contains a taxonomic thesaurus (a digital version of a Linnaean classification) that includes both extant and extinct pteridophytes in a common phylogenetic framework. The PteridoPortal allows applications such as greatly accelerated classic floristics, entirely new “next-generation” floristic approaches, and the study of environmentally mediated evolution of functional morphology across deep time.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>The PCC and PteridoPortal provide a comprehensive resource enabling novel research into plant evolution, ecology, and conservation across deep time, facilitating rapid floristic analyses and other biodiversity-related investigations, and providing new opportunities for education and community engagement.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143884192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A comprehensive illustrated protocol for clearing, mounting, and imaging leaf venation networks","authors":"Isabella Niewiadomski,&nbsp;Monica Antonio,&nbsp;Luiza Maria T. Aparecido,&nbsp;Mickey Boakye,&nbsp;Sonoma Carlos,&nbsp;Andrea Echevarria,&nbsp;Adrian Fontao,&nbsp;Joseph Mann,&nbsp;Ilaíne Silveira Matos,&nbsp;Norma Salinas,&nbsp;Bradley Vu,&nbsp;Benjamin Wong Blonder","doi":"10.1002/aps3.70002","DOIUrl":"10.1002/aps3.70002","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Leaf venation network architecture can provide insights into plant evolution, ecology, and physiology. Venation networks are typically assessed through histological methods, but existing protocols provide limited guidance on processing large or challenging leaves.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and results</h3>\u0000 \u0000 <p>We present an illustrated protocol for visualizing whole leaf venation networks, including sample preparation, clearing, staining, mounting, imaging, and archiving steps. The protocol also includes supply lists, troubleshooting procedures, safety considerations, and examples of successful and unsuccessful outcomes. The protocol is suitable for a wide range of leaf sizes and morphologies and has been used with all major plant groups.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusion</h3>\u0000 \u0000 <p>We provide a workflow for obtaining high-quality mounts and images of venation networks of a wide range of species, using readily available materials.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143884061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of plant metabolomics data using identification-free approaches","authors":"Xinyu Yuan,&nbsp;Nathaniel S. S. Smith,&nbsp;Gaurav D. Moghe","doi":"10.1002/aps3.70001","DOIUrl":"10.1002/aps3.70001","url":null,"abstract":"<p>Plant metabolomes are structurally diverse. One of the most popular techniques for sampling this diversity is liquid chromatography–mass spectrometry (LC-MS), which typically detects thousands of peaks from single organ extracts, many representing true metabolites. These peaks are usually annotated using in-house retention time or spectral libraries, in silico fragmentation libraries, and increasingly through computational techniques such as machine learning. Despite these advances, over 85% of LC-MS peaks remain unidentified, posing a major challenge for data analysis and biological interpretation. This bottleneck limits our ability to fully understand the diversity, functions, and evolution of plant metabolites. In this review, we first summarize current approaches for metabolite identification, highlighting their challenges and limitations. We further focus on alternative strategies that bypass the need for metabolite identification, allowing researchers to interpret global metabolic patterns and pinpoint key metabolite signals. These methods include molecular networking, distance-based approaches, information theory–based metrics, and discriminant analysis. Additionally, we explore their practical applications in plant science and highlight a set of useful tools to support researchers in analyzing complex plant metabolomics data. By adopting these approaches, researchers can enhance their ability to uncover new insights into plant metabolism.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 4","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144767428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhancing plant morphological trait identification in herbarium collections through deep learning–based segmentation","authors":"Hanane Ariouat,&nbsp;Youcef Sklab,&nbsp;Edi Prifti,&nbsp;Jean-Daniel Zucker,&nbsp;Eric Chenin","doi":"10.1002/aps3.70000","DOIUrl":"10.1002/aps3.70000","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Deep learning has become increasingly important in the analysis of digitized herbarium collections, which comprise millions of scans that provide valuable resources for studying plant evolution and biodiversity. However, leveraging deep learning algorithms to analyze these scans presents significant challenges, partly due to the heterogeneous nature of the non-plant material that forms the background of the scans. We hypothesize that removing such backgrounds can improve the performance of these algorithms.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We propose a novel method based on deep learning to segment and generate plant masks from herbarium scans and subsequently remove the non-plant backgrounds. The semi-automatic preprocessing stages involve the identification and removal of non-plant elements, substantially reducing the manual effort required to prepare the training dataset.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The results highlight the importance of effective image segmentation, which achieved an F1 score of up to 96.6%. Moreover, when used in classification models for plant morphological trait identification, the images resulting from segmentation improved classification accuracy by up to 3% and F1 score by up to 7% compared to non-segmented images.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our approach isolates plant elements in herbarium scans by removing background elements to improve classification tasks. We demonstrate that image segmentation significantly enhances the performance of plant morphological trait identification models.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70000","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143883986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Looking to the past to inform the future: What eDNA from herbarium specimens can tell us about plant–animal interactions","authors":"Christopher Waters,&nbsp;Carla Hurt,&nbsp;Shawn Krosnick","doi":"10.1002/aps3.11633","DOIUrl":"10.1002/aps3.11633","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The importance of natural history collections in modern ecological and genetic research cannot be overstated. Herbarium specimens provide historical information that can be used to investigate community ecology, phenology, and population genetics. In this study, environmental DNA (eDNA) metabarcoding and next-generation sequencing were used to test the efficacy of detecting historical plant–animal interactions from herbarium specimen flowers.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>A modified eDNA isolation method and standard Illumina sequencing protocols were used. Animal eDNA was amplified using both cytochrome c oxidase subunit I (COI) and 16S primers to increase detection probability. The relationship between specimen age (0–69 years) and target taxa read depth was also investigated.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We generated and identified over 1.5 million sequences of animal taxa belonging to 29 clades (families or orders). These methods enabled the detection of taxa including birds, mammals, hymenopterans, lepidopterans, coleopterans, and taxa belonging to “intrafloral” communities. While herbarium specimens overall yielded less identifiable eDNA compared to fresh material, the age of the herbarium specimen negligibly affected the amount of target and/or non-target eDNA detected in flowers.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>With careful consideration of the types of data that may be obtained through sampling eDNA from herbarium specimens, these methods could prove valuable to future research on plant–animal interactions.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11633","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143883790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optogenetic control of transgene expression in Marchantia polymorpha","authors":"Anya Lillemor Lindström Battle,&nbsp;Lee James Sweetlove","doi":"10.1002/aps3.11632","DOIUrl":"10.1002/aps3.11632","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The model liverwort <i>Marchantia polymorpha</i> is an emerging testbed species for plant metabolic engineering but lacks well-characterized inducible promoters, which are necessary to minimize biochemical and physiological disruption when over-accumulating target products. Here, we demonstrate the functionality of the light-inducible plant-usable light-switch elements (PULSE) optogenetic system in <i>Marchantia</i> and exemplify its use through the light-inducible overproduction of the bioplastic poly-3-hydroxybutyrate (PHB).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>The PULSE system was used to drive expression of luciferase as a reporter and characterize its induction in transgenic <i>M. polymorpha</i>. Additionally, PULSE was used to drive expression of the PHB biosynthetic pathway; the accumulation of PHB under light-inducible control was compared to constitutive overexpression.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>PULSE was fully functional and minimally leaky in <i>M. polymorpha</i>. The presence of the PULSE construct, even in the absence of induction, resulted in a developmental phenotype. Constitutive and inducible expression resulted in similar PHB accumulation levels.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>PHB biosynthesis in plants is known to adversely affect plant health, but placing its production under optogenetic control alleviated negative effects on biomass accumulation in some instances. The work presented here represents a significant expansion of the toolbox for the metabolic engineering of <i>M. polymorpha</i>.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 4","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11632","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144767969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"mvh: An R tool to assemble and organize virtual herbaria from openly available specimen images","authors":"Thais Vasconcelos,&nbsp;James D. Boyko","doi":"10.1002/aps3.11631","DOIUrl":"10.1002/aps3.11631","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Recent advances in imaging herbarium specimens have enhanced their use in biodiversity studies. However, user-friendly tools that facilitate the assembly of customized sets of herbarium specimen images on personal devices are still lacking.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>Here we present the R package mvh (“my virtual herbarium”), which includes functions designed to search and download metadata and openly available images associated with herbarium specimens based on taxon or geography. We tested the functionalities of mvh by searching metadata associated with five sets of 10 vascular plant species and five sets of 10 terrestrial coordinates. The download function had a success rate of 99%, downloading 291 out of the 293 images found in the search. Possible reasons for download failure are discussed.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>As long as an internet connection is available, mvh simplifies the assembly and organization of virtual herbaria, thereby facilitating the investigation of novel empirical questions as well as trends in digitization efforts.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11631","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143883941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}