Gillian H. Dean, N. Ivalú Cacho, Alejandro Zuluaga Trochez, Gregory J. Pec
In 2020, at the beginning of the COVID-19 pandemic, Applications in Plant Sciences (APPS) published a special issue titled “Conducting botanical research with limited resources: Low-cost methods in the plant sciences” (Dean et al., 2020). The goal of that collection was to highlight robust, low-cost methods that could be used by researchers in under-resourced settings. Plant scientists face resource limitations for many reasons. In some countries, inadequate national funding is a major issue, as well as limited long-term investment in research infrastructure. At the same time, factors contributing to low-resource settings are also experienced by researchers in countries where research funding is more abundant. For example, although national research programs in the Global North are generally well funded, these funds may be difficult to access for investigators who hold positions at smaller institutions, such as predominantly undergraduate institutions.
Regardless of geographic location, lack of training and access to expensive and specialized equipment can be limiting, and funding to acquire expensive equipment often does not include salary for maintenance and operation by trained personnel after the initial purchase and set up. In addition, research may be performed by new investigators such as undergraduate or graduate students, or when established labs wish to explore new areas of research or techniques without committing significant resources.
Globally, substantial and significant scientific research is performed in these under-resourced settings. The COVID-19 pandemic exacerbated this situation by disrupting supply chains and forcing researchers to work from home or in isolation at their workplace, resulting in dynamic adaptations in their approaches to generating or collecting data. Suddenly confronted with an inability to travel, many scientists looked to their local environment to leverage their skills to continue research closer to home. In light of these challenges, this APPS special issue, titled “Resilient botany: Innovation in the face of limited mobility and resources,” showcases the creative ways that plant scientists carried on with research during a global pandemic. The papers in this issue encompass a variety of fields and scales of research, ranging from investigations of plant structure at the microscopic level to utilizing big data to understand biodiversity, but they all have one thing in common: they are all accessible to researchers and practitioners challenged by funding or travel restrictions.
It has been well documented that cataloging global biodiversity is a daunting task that will take a concerted effort by many scientists and community scientists, especially given that much of the world's biodiversity is located in areas with under-resourced research communities. A large amount of data is already contained in herbaria, and digitizing this information is an impor
{"title":"Resilient botany: Innovation in the face of limited mobility and resources","authors":"Gillian H. Dean, N. Ivalú Cacho, Alejandro Zuluaga Trochez, Gregory J. Pec","doi":"10.1002/aps3.11577","DOIUrl":"https://doi.org/10.1002/aps3.11577","url":null,"abstract":"<p>In 2020, at the beginning of the COVID-19 pandemic, <i>Applications in Plant Sciences</i> (<i>APPS</i>) published a special issue titled “Conducting botanical research with limited resources: Low-cost methods in the plant sciences” (Dean et al., <span>2020</span>). The goal of that collection was to highlight robust, low-cost methods that could be used by researchers in under-resourced settings. Plant scientists face resource limitations for many reasons. In some countries, inadequate national funding is a major issue, as well as limited long-term investment in research infrastructure. At the same time, factors contributing to low-resource settings are also experienced by researchers in countries where research funding is more abundant. For example, although national research programs in the Global North are generally well funded, these funds may be difficult to access for investigators who hold positions at smaller institutions, such as predominantly undergraduate institutions.</p><p>Regardless of geographic location, lack of training and access to expensive and specialized equipment can be limiting, and funding to acquire expensive equipment often does not include salary for maintenance and operation by trained personnel after the initial purchase and set up. In addition, research may be performed by new investigators such as undergraduate or graduate students, or when established labs wish to explore new areas of research or techniques without committing significant resources.</p><p>Globally, substantial and significant scientific research is performed in these under-resourced settings. The COVID-19 pandemic exacerbated this situation by disrupting supply chains and forcing researchers to work from home or in isolation at their workplace, resulting in dynamic adaptations in their approaches to generating or collecting data. Suddenly confronted with an inability to travel, many scientists looked to their local environment to leverage their skills to continue research closer to home. In light of these challenges, this <i>APPS</i> special issue, titled “Resilient botany: Innovation in the face of limited mobility and resources,” showcases the creative ways that plant scientists carried on with research during a global pandemic. The papers in this issue encompass a variety of fields and scales of research, ranging from investigations of plant structure at the microscopic level to utilizing big data to understand biodiversity, but they all have one thing in common: they are all accessible to researchers and practitioners challenged by funding or travel restrictions.</p><p>It has been well documented that cataloging global biodiversity is a daunting task that will take a concerted effort by many scientists and community scientists, especially given that much of the world's biodiversity is located in areas with under-resourced research communities. A large amount of data is already contained in herbaria, and digitizing this information is an impor","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11577","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140559577","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}
Natalie N. Patten, Michelle L. Gaynor, Douglas E. Soltis, Pamela S. Soltis
Premise
Digitized biodiversity data offer extensive information; however, obtaining and processing biodiversity data can be daunting. Complexities arise during data cleaning, such as identifying and removing problematic records. To address these issues, we created the R package Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs).
Methods and Results
The gatoRs workflow includes functions that streamline downloading records from the Global Biodiversity Information Facility (GBIF) and Integrated Digitized Biocollections (iDigBio). We also created functions to clean downloaded specimen records. Unlike previous R packages, gatoRs accounts for differences in download structure between GBIF and iDigBio and allows for user control via interactive cleaning steps.
Conclusions
Our pipeline enables the scientific community to process biodiversity data efficiently and is accessible to the R coding novice. We anticipate that gatoRs will be useful for both established and beginning users. Furthermore, we expect our package will facilitate the introduction of biodiversity-related concepts into the classroom via the use of herbarium specimens.
前提条件数字化的生物多样性数据提供了大量信息；然而，获取和处理生物多样性数据的工作可能非常艰巨。数据清理过程中会出现一些复杂问题，如识别和删除有问题的记录。为了解决这些问题，我们创建了基于 R 的地理与分类出现清理（Geographic And Taxonomic Occurrence R-based Scrubbing，gatoRs）软件包。方法与结果 gatoRs 工作流程包括简化从全球生物多样性信息基金（GBIF）和综合数字化生物收集（iDigBio）下载记录的功能。我们还创建了清理下载标本记录的函数。与以前的 R 软件包不同，gatoRs 考虑到了 GBIF 和 iDigBio 下载结构的差异，并允许用户通过交互式清理步骤进行控制。我们预计，gatoRs 对成熟用户和初学者都很有用。此外，我们还希望我们的软件包能通过标本馆标本的使用，促进将生物多样性相关概念引入课堂。
{"title":"Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs): An R package and workflow for processing biodiversity data","authors":"Natalie N. Patten, Michelle L. Gaynor, Douglas E. Soltis, Pamela S. Soltis","doi":"10.1002/aps3.11575","DOIUrl":"10.1002/aps3.11575","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Digitized biodiversity data offer extensive information; however, obtaining and processing biodiversity data can be daunting. Complexities arise during data cleaning, such as identifying and removing problematic records. To address these issues, we created the R package Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>The gatoRs workflow includes functions that streamline downloading records from the Global Biodiversity Information Facility (GBIF) and Integrated Digitized Biocollections (iDigBio). We also created functions to clean downloaded specimen records. Unlike previous R packages, gatoRs accounts for differences in download structure between GBIF and iDigBio and allows for user control via interactive cleaning steps.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Our pipeline enables the scientific community to process biodiversity data efficiently and is accessible to the R coding novice. We anticipate that gatoRs will be useful for both established and beginning users. Furthermore, we expect our package will facilitate the introduction of biodiversity-related concepts into the classroom via the use of herbarium specimens.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11575","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140200249","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}
Hugo Jaimes, Alejandra Londoño, Carolina Saavedra-Diaz, Jhon Henry Trujillo-Montenegro, Jershon López-Gerena, John J. Riascos, Fernando S. Aguilar
Premise
Detecting single-nucleotide polymorphisms (SNPs) in a cost-effective way is fundamental in any plant breeding pipeline. Here, we compare three genotyping techniques for their ability to reproduce the allele dosage of SNPs of interest in sugarcane (Saccharum spp.).
Methods
To identify a reproducible technique to estimate allele dosage for the validation of SNP markers, the correlation between Flex-Seq, kompetitive allele-specific PCR (KASP), and genotyping-by-sequencing and restriction site–associated DNA sequencing (GBS+RADseq) was determined for a set of 76 SNPs. To find alternative methodologies for allele dosage estimation, the KASP and Flex-Seq techniques were compared for the same set of SNPs. For the three techniques, a population of 53 genotypes from the diverse sugarcane panel of the Centro de Investigación de la Caña de Azúcar (Cenicaña), Colombia, was selected.
Results
The average Pearson correlation coefficients between GBS+RADseq and Flex-Seq, GBS+RADseq and KASP, and Flex-Seq and KASP were 0.62 ± 0.27, 0.38 ± 0.27, and 0.38 ± 0.30, respectively.
Discussion
Flex-Seq reproduced the allele dosages determined using GBS+RADseq with good levels of precision because of its depth of sequencing and ability to target specific positions in the genome. Additionally, Flex-Seq outperformed KASP by allowing the conversion of a higher number of SNPs and a more accurate estimation of the allele dosage. Flex-Seq has therefore become the genotyping methodology of choice for marker validation at Cenicaña.
{"title":"Sequencing vs. amplification for the estimation of allele dosages in sugarcane (Saccharum spp.)","authors":"Hugo Jaimes, Alejandra Londoño, Carolina Saavedra-Diaz, Jhon Henry Trujillo-Montenegro, Jershon López-Gerena, John J. Riascos, Fernando S. Aguilar","doi":"10.1002/aps3.11574","DOIUrl":"10.1002/aps3.11574","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Detecting single-nucleotide polymorphisms (SNPs) in a cost-effective way is fundamental in any plant breeding pipeline. Here, we compare three genotyping techniques for their ability to reproduce the allele dosage of SNPs of interest in sugarcane (<i>Saccharum</i> spp.).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>To identify a reproducible technique to estimate allele dosage for the validation of SNP markers, the correlation between Flex-Seq, kompetitive allele-specific PCR (KASP), and genotyping-by-sequencing and restriction site–associated DNA sequencing (GBS+RADseq) was determined for a set of 76 SNPs. To find alternative methodologies for allele dosage estimation, the KASP and Flex-Seq techniques were compared for the same set of SNPs. For the three techniques, a population of 53 genotypes from the diverse sugarcane panel of the Centro de Investigación de la Caña de Azúcar (Cenicaña), Colombia, was selected.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The average Pearson correlation coefficients between GBS+RADseq and Flex-Seq, GBS+RADseq and KASP, and Flex-Seq and KASP were 0.62 ± 0.27, 0.38 ± 0.27, and 0.38 ± 0.30, respectively.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Flex-Seq reproduced the allele dosages determined using GBS+RADseq with good levels of precision because of its depth of sequencing and ability to target specific positions in the genome. Additionally, Flex-Seq outperformed KASP by allowing the conversion of a higher number of SNPs and a more accurate estimation of the allele dosage. Flex-Seq has therefore become the genotyping methodology of choice for marker validation at Cenicaña.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11574","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140148152","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}
Sara E. Hansen, Michael J. Monfils, Rachel A. Hackett, Ryan T. Goebel, Anna K. Monfils
Premise
Species distribution models (SDMs) are widely utilized to guide conservation decisions. The complexity of available data and SDM methodologies necessitates considerations of how data are chosen and processed for modeling to enhance model accuracy and support biological interpretations and ecological applications.
Methods
We built SDMs for the invasive aquatic plant European frog-bit using aggregated and field data that span multiple scales, data sources, and data types. We tested how model results were affected by five modeler decision points: the exclusion of (1) missing and (2) correlated data and the (3) scale (large-scale aggregated data or systematic field data), (4) source (specimens or observations), and (5) type (presence-background or presence-absence) of occurrence data.
Results
Decisions about the exclusion of missing and correlated data, as well as the scale and type of occurrence data, significantly affected metrics of model performance. The source and type of occurrence data led to differences in the importance of specific explanatory variables as drivers of species distribution and predicted probability of suitable habitat.
Discussion
Our findings relative to European frog-bit illustrate how specific data selection and processing decisions can influence the outcomes and interpretation of SDMs. Data-centric protocols that incorporate data exploration into model building can help ensure models are reproducible and can be accurately interpreted in light of biological questions.
{"title":"Data-centric species distribution modeling: Impacts of modeler decisions in a case study of invasive European frog-bit","authors":"Sara E. Hansen, Michael J. Monfils, Rachel A. Hackett, Ryan T. Goebel, Anna K. Monfils","doi":"10.1002/aps3.11573","DOIUrl":"10.1002/aps3.11573","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Species distribution models (SDMs) are widely utilized to guide conservation decisions. The complexity of available data and SDM methodologies necessitates considerations of how data are chosen and processed for modeling to enhance model accuracy and support biological interpretations and ecological applications.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We built SDMs for the invasive aquatic plant European frog-bit using aggregated and field data that span multiple scales, data sources, and data types. We tested how model results were affected by five modeler decision points: the exclusion of (1) missing and (2) correlated data and the (3) scale (large-scale aggregated data or systematic field data), (4) source (specimens or observations), and (5) type (presence-background or presence-absence) of occurrence data.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Decisions about the exclusion of missing and correlated data, as well as the scale and type of occurrence data, significantly affected metrics of model performance. The source and type of occurrence data led to differences in the importance of specific explanatory variables as drivers of species distribution and predicted probability of suitable habitat.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our findings relative to European frog-bit illustrate how specific data selection and processing decisions can influence the outcomes and interpretation of SDMs. Data-centric protocols that incorporate data exploration into model building can help ensure models are reproducible and can be accurately interpreted in light of biological questions.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11573","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140126498","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}
During the COVID-19 pandemic lockdown, all laboratory work was suspended, and we were obliged to work from home, causing delays in our research. As the disruption to supply chains made it difficult to obtain our regular lab supplies, we were obliged to search for substitutes. We became familiar with a plastic material known as biaxially oriented polypropylene (BOPP) that is widely used in the food industry for wrapping or storing fruits, vegetables, and meat. BOPP is easily dissolved in organic solvents such as xylenes, acetone, or thinner, but these reagents are very toxic, flammable, and can cause nausea in some users. After testing several alternatives, we found a polyurethane remover that proved to be an effective and relatively harmless BOPP solvent.
Methods and Results
By dissolving thin slices of BOPP in a polyurethane solvent, we obtained a clean fluid that we used to obtain leaf surface prints that could be mounted on microscope slides with a coverslip. This fluid produced excellent bark and wood sections and can be used to obtain wood or charcoal surface prints. Our attempts to use it as a mounting medium were unsuccessful.
Conclusions
BOPP dissolved in a polyurethane remover is a handy, versatile resource for plant microtechniques. In addition to its economic advantages, it is useful in terms of reducing plastic pollution.
{"title":"Using disposable food packaging materials as printing, embedding, and sectioning media in the plant anatomy lab","authors":"Guillermo Angeles, Carolina Madero-Vega","doi":"10.1002/aps3.11570","DOIUrl":"10.1002/aps3.11570","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>During the COVID-19 pandemic lockdown, all laboratory work was suspended, and we were obliged to work from home, causing delays in our research. As the disruption to supply chains made it difficult to obtain our regular lab supplies, we were obliged to search for substitutes. We became familiar with a plastic material known as biaxially oriented polypropylene (BOPP) that is widely used in the food industry for wrapping or storing fruits, vegetables, and meat. BOPP is easily dissolved in organic solvents such as xylenes, acetone, or thinner, but these reagents are very toxic, flammable, and can cause nausea in some users. After testing several alternatives, we found a polyurethane remover that proved to be an effective and relatively harmless BOPP solvent.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>By dissolving thin slices of BOPP in a polyurethane solvent, we obtained a clean fluid that we used to obtain leaf surface prints that could be mounted on microscope slides with a coverslip. This fluid produced excellent bark and wood sections and can be used to obtain wood or charcoal surface prints. Our attempts to use it as a mounting medium were unsuccessful.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>BOPP dissolved in a polyurethane remover is a handy, versatile resource for plant microtechniques. In addition to its economic advantages, it is useful in terms of reducing plastic pollution.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11570","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139981077","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}
Jessica A. Savage, Sydney J. Hudzinski, Mady R. Olson
Premise
With growing interest in the impact of false springs on plant reproduction, there is the need to develop reliable, high-throughput methods for assessing floral freezing damage. Here we present a method for use with floral tissue that will facilitate more comparative work on floral freezing tolerance in the future.
Methods and Results
We examined the effectiveness of a modified electrolyte leakage protocol to assess floral freezing damage. By comparing data from temperature response curves to an estimate of visual tissue damage, we optimized the protocol for different floral types and improved the signal-to-noise ratio for floral data.
Conclusions
Our modified protocol provides a quick and straightforward method for quantifying floral freezing damage that can be standardized across floral types. This method allows for cross-species comparisons and can be a powerful tool for studying broad patterns in floral freezing tolerance.
{"title":"Use of electrolyte leakage to assess floral damage after freezing","authors":"Jessica A. Savage, Sydney J. Hudzinski, Mady R. Olson","doi":"10.1002/aps3.11569","DOIUrl":"10.1002/aps3.11569","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>With growing interest in the impact of false springs on plant reproduction, there is the need to develop reliable, high-throughput methods for assessing floral freezing damage. Here we present a method for use with floral tissue that will facilitate more comparative work on floral freezing tolerance in the future.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We examined the effectiveness of a modified electrolyte leakage protocol to assess floral freezing damage. By comparing data from temperature response curves to an estimate of visual tissue damage, we optimized the protocol for different floral types and improved the signal-to-noise ratio for floral data.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Our modified protocol provides a quick and straightforward method for quantifying floral freezing damage that can be standardized across floral types. This method allows for cross-species comparisons and can be a powerful tool for studying broad patterns in floral freezing tolerance.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11569","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139923334","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}
The editors gratefully acknowledge our reviewers, who have generously given their time and expertise to review manuscripts submitted to Applications in Plant Sciences. The list includes those who reviewed manuscripts from December 31, 2022, to December 31, 2023. Thank you for helping APPS maintain a prompt and fair peer-review process.
Dewi Pramanik, Lotta Vaskimo, K. Joost Batenburg, Alexander Kostenko, Kevin Droppert, Erik Smets, Barbara Gravendeel
Premise
Most studies of the movement of orchid fruits and roots during plant development have focused on morphological observations; however, further genetic analysis is required to understand the molecular mechanisms underlying this phenomenon. A precise tool is required to observe these movements and harvest tissue at the correct position and time for transcriptomics research.
Methods
We utilized three-dimensional (3D) micro–computed tomography (CT) scans to capture the movement of fast-growing Erycina pusilla roots, and built an integrated bioinformatics pipeline to process 3D images into 3D time-lapse videos. To record the movement of slowly developing E. pusilla and Phalaenopsis equestris fruits, two-dimensional (2D) photographs were used.
Results
The E. pusilla roots twisted and resupinated multiple times from early development. The first period occurred in the early developmental stage (77–84 days after germination [DAG]) and the subsequent period occurred later in development (140–154 DAG). While E. pusilla fruits twisted 45° from 56–63 days after pollination (DAP), the fruits of P. equestris only began to resupinate a week before dehiscence (133 DAP) and ended a week after dehiscence (161 DAP).
Discussion
Our methods revealed that each orchid root and fruit had an independent direction and degree of torsion from the initial to the final position. Our innovative approaches produced detailed spatial and temporal information on the resupination of roots and fruits during orchid development.
{"title":"Orchid fruit and root movement analyzed using 2D photographs and a bioinformatics pipeline for processing sequential 3D scans","authors":"Dewi Pramanik, Lotta Vaskimo, K. Joost Batenburg, Alexander Kostenko, Kevin Droppert, Erik Smets, Barbara Gravendeel","doi":"10.1002/aps3.11567","DOIUrl":"https://doi.org/10.1002/aps3.11567","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Most studies of the movement of orchid fruits and roots during plant development have focused on morphological observations; however, further genetic analysis is required to understand the molecular mechanisms underlying this phenomenon. A precise tool is required to observe these movements and harvest tissue at the correct position and time for transcriptomics research.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We utilized three-dimensional (3D) micro–computed tomography (CT) scans to capture the movement of fast-growing <i>Erycina pusilla</i> roots, and built an integrated bioinformatics pipeline to process 3D images into 3D time-lapse videos. To record the movement of slowly developing <i>E. pusilla</i> and <i>Phalaenopsis equestris</i> fruits, two-dimensional (2D) photographs were used.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The <i>E. pusilla</i> roots twisted and resupinated multiple times from early development. The first period occurred in the early developmental stage (77–84 days after germination [DAG]) and the subsequent period occurred later in development (140–154 DAG). While <i>E. pusilla</i> fruits twisted 45° from 56–63 days after pollination (DAP), the fruits of <i>P. equestris</i> only began to resupinate a week before dehiscence (133 DAP) and ended a week after dehiscence (161 DAP).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our methods revealed that each orchid root and fruit had an independent direction and degree of torsion from the initial to the final position. Our innovative approaches produced detailed spatial and temporal information on the resupination of roots and fruits during orchid development.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11567","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139750012","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}
Benjamin A. Lloyd, Richard S. Barclay, Regan E. Dunn, Ellen D. Currano, Ayuni I. Mohamaad, Kymbre Skersies, Surangi W. Punyasena
Premise
Leaf epidermal cell morphology is closely tied to the evolutionary history of plants and their growth environments and is therefore of interest to many plant biologists. However, cell measurement can be time consuming and restrictive with current methods. CuticleTrace is a suite of Fiji and R-based functions that streamlines and automates the segmentation and measurement of epidermal pavement cells across a wide range of cell morphologies and image qualities.
Methods and Results
We evaluated CuticleTrace-generated measurements against those from alternate automated methods and expert and undergraduate hand tracings across a taxonomically diverse 50-image data set of variable image qualities. We observed ~93% statistical agreement between CuticleTrace and expert hand-traced measurements, outperforming alternate methods.
Conclusions
CuticleTrace is a broadly applicable, modular, and customizable tool that integrates data visualization and cell shape measurement with image segmentation, lowering the barrier to high-throughput studies of epidermal morphology by vastly decreasing the labor investment required to generate high-quality cell shape data sets.
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In this study, we use simulations to determine how pollen flow and sampling constraints can influence the genetic conservation found in seed collections.
Methods
We simulated genotypes of parental individuals and crossed the parentals based on three different ranges of pollen flow (panmictic, limited, and highly limited) to create new seed sets for sampling. We tested a variety of sampling scenarios modeled on those occurring in nature and calculated the proportion of alleles conserved in each scenario.
Results
We found that pollen flow greatly influences collection outcomes, with panmictic pollen flow resulting in seed sets containing 21.6% more alleles than limited pollen flow and 48.6% more alleles than highly limited pollen flow, although this impact diminishes when large numbers of maternal plants are sampled. Simulations of realistic seed sampling (sampling more seed from some plants and fewer from others) showed a relatively minor impact (<2.5%) on genetic diversity conserved compared to ideal sampling (uniform sampling across all maternal plants).
Discussion
We conclude that future work must consider limited pollen flow, but collectors can be flexible with their sampling in the field as long as many unique maternal plants are sampled. Simulations remain a fruitful method to advance ex situ sampling guidelines.
在这项研究中，我们通过模拟来确定花粉流动和取样限制如何影响种子采集中的遗传保护。
{"title":"Simulating pollen flow and field sampling constraints helps revise seed sampling recommendations for conserving genetic diversity","authors":"Kaylee J. Rosenberger, Sean Hoban","doi":"10.1002/aps3.11561","DOIUrl":"10.1002/aps3.11561","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>In this study, we use simulations to determine how pollen flow and sampling constraints can influence the genetic conservation found in seed collections.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We simulated genotypes of parental individuals and crossed the parentals based on three different ranges of pollen flow (panmictic, limited, and highly limited) to create new seed sets for sampling. We tested a variety of sampling scenarios modeled on those occurring in nature and calculated the proportion of alleles conserved in each scenario.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We found that pollen flow greatly influences collection outcomes, with panmictic pollen flow resulting in seed sets containing 21.6% more alleles than limited pollen flow and 48.6% more alleles than highly limited pollen flow, although this impact diminishes when large numbers of maternal plants are sampled. Simulations of realistic seed sampling (sampling more seed from some plants and fewer from others) showed a relatively minor impact (<2.5%) on genetic diversity conserved compared to ideal sampling (uniform sampling across all maternal plants).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>We conclude that future work must consider limited pollen flow, but collectors can be flexible with their sampling in the field as long as many unique maternal plants are sampled. Simulations remain a fruitful method to advance ex situ sampling guidelines.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11561","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139662266","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}
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