Min-Soo Choi

Summary: Methods in metabolomics have grown exponentially in recent years, providing new insight into the ecological function and evolutionary impact of diverse plant metabolites. Metabolomics requires a command of numerous tools, the outputs of which are typically integrated through in‐house custom code that presents a workflow bottleneck and a barrier to entry for researchers in ecology, evolution, and behavior who may benefit from adding a metabolomics perspective to their research. We introduce eCOMET , an R package for integrating and harmonizing the outputs of common metabolomics bioinformatics tools and conducting statistical analyses and data visualization methods useful for ecological metabolomics. Our package combines metabolome feature metadata with quantification tables (e.g. mzmine ), feature dissimilarity matrices (e.g. modified cosine and DreaMS ), and feature annotations (e.g. SIRIUS ) into a cohesive R data object to facilitate downstream analyses, including the calculation of diversity and disparity metrics and differential accumulation analysis. We provide two tutorials, each explores herbivore‐induced Arabidopsis thaliana metabolome and 10 co‐occurring tropical trees species metabolomes. Our goal is to make metabolomics accessible to a wider range of researchers in ecology, evolution, and behavior to unlock the potential of ecological metabolomics to generate novel insight into these fields.

Summary: Methods in metabolomics have grown exponentially in recent years, providing new insight into the ecological function and evolutionary impact of diverse plant metabolites. Metabolomics requires a command of numerous tools, the outputs of which are typically integrated through in-house, custom code that presents a workflow bottleneck and a barrier to entry for researchers in ecology, evolution, and behavior who may benefit from adding a metabolomics perspective to their research. We introduce eCOMET , an R package for integrating and harmonizing the outputs of common metabolomics bioinformatics tools and conducting statistical analyses and data visualization methods useful for ecological metabolomics. Our package combines metabolome feature metadata with quantification tables (e.g., mzmine ), feature dissimilarity matrices (e.g., modified cosine and DreaMS ), and feature annotations (e.g., SIRIUS ) into a cohesive R data object to facilitate downstream analyses, including the calculation of diversity and disparity metrics and differential accumulation analysis. Our goal is to make metabolomics accessible to a wider range of researchers in ecology, evolution, and behavior to unlock the potential of ecological metabolomics to generate novel insight in these fields.

King George Island, one of the most rapidly warming regions in maritime Antarctica, has experienced pronounced expansion of ice-free areas and proliferation of cryptogamic vegetation in recent decades. This accelerated ecological greening has been accompanied by repeated reports of Arrhenia , Galerina , and Omphalina species. However, despite their frequent occurrence, comprehensive taxonomic assessments of these Antarctic mushrooms remain limited and unresolved. We applied an integrative systematic framework combining morphological examination, multilocus phylogenetic reconstruction, species delimitation analyses, and chemical analyses to 50 mushroom specimens collected from vegetated ice-free areas of King George Island. By integrating polyphasic evidence, we confirmed four species ( Arrhenia antarctica , Galerina fallax , Galerina venenata , and Omphalina frigida ) and resolved several historical taxonomic uncertainties related to these species. This study provides the first phylogenetic analysis of Arrhenia antarctica , a first mushroom species documented from Antarctica. Additionally, regarding Antarctic Omphalina , for which several new species have recently been reported from Antarctica, we verified that the real species diversity has been inflated and have rectified it. Lastly, LC-MS/MS analysis confirmed amanitin production in materials identified as Galerina pseudomycenopsis , thereby clarifying previous taxonomic ambiguity within the Galerina marginata species complex by synonymizing Galerina pseudomycenopsis with Galerina venenata . Divergence-time estimation further suggests that Antarctic lineages diversified before current climate warming, likely in association with repeated glacial-interglacial cycles that reshaped ice-free habitats in Antarctica. By clarifying species identities and integrating multilocus phylogenetics with temporal inference, this study revises the taxonomy of key Antarctic mushrooms and provides a robust framework for future investigation in their diversity, ecological roles, and potential adaptive mechanisms associated with Antarctic greening in extreme environments.

The genus Aristolochia is renowned for its kettle‐like trap flowers that temporarily retain visiting insects, primarily using trapping trichomes. Most Aristolochia species attract fly pollinators through floral mimicry, by imitating their oviposition sites and/or food sources. In this study, we investigated the potential mimicry system of Isotrema manshuriense, a species formerly classified as Aristolochia manshuriensis that lacks trapping trichomes. We identified its pollinators and analysed its multimodal floral cues. Anthesis was divided into three sexual phases: female phase, interphase, and male phase. Insects entrapped in flowers were collected and identified. Limb secretion from female‐phase flowers was analysed using GC–MS for metabolite profiling. Visual and olfactory cues of female‐ and male‐phase flowers were investigated by measuring the spectral reflectance of spatial flower parts. External and internal floral volatile compounds were analysed during the day and at night. Floral scent profiles were compared to those of other species and potential models through non‐metric multidimensional scaling. Most flower visitors were female flies, with pollinators in the Fanniidae, Anthomyiidae, and Lonchaeidae. There was no significant difference in number of retained insects between female‐ and male‐phase flowers. Limb secretion contained various amino acids and organic acids. Spatial and temporal variations were observed in perianth coloration, including UV reflectance, and floral scent composition. Notably, external floral scents resembled those of cucurbit fruits, whereas internal scents were more similar to those of rewarding flowers. I. manshuriense exhibits unique floral traits, distinct from other brood site‐mimicking Isotrema and Aristolochia species, while sharing the saprophagous nature of pollinators. This suggests that I. manshuriense incorporates multiple models, positioning flowers as phenotypic intermediates between generalized food sources and oviposition sites.

The plant cell wall not only serves as a physical barrier against pathogens but, when damaged, also functions as a source of cell wall-derived molecules that play crucial roles in plant immunity as damage-associated molecular patterns (DAMPs). While oligogalacturonides from homogalacturonan are well-studied DAMPs, the immune-signaling potential of other cell wall components remains largely unexplored. Conventional genetic and biochemical approaches aimed at identifying ligand-receptor pairs in plant immunity have been limited by the vast diversity of potential ligand molecules and functional redundancy of putative receptors. Here, we developed a high-throughput screening pipeline that simultaneously examines multiple interactions between plant cell wall-derived glycans and >350 extracellular domains (ECDs) of receptor kinases and receptor like proteins in Arabidopsis, resulting in the screening of >40,000 interactions. We discovered a group of leucine-rich repeat receptor kinases named ARMs (AWARENESS of RG-I MAINTENANCES) that interact with rhamnogalacturonan-I (RG-I), a major component of pectin. RG-I treatment induced pattern-triggered immunity responses, with distinct kinetics compared to oligogalacturonide responses. We identified RG-I oligosaccharide structures required for interaction with ARM receptors and immune activation, and found that ARM receptors are redundantly involved in plant immunity. Collectively, our approach provides a powerful platform for discovering glycan-receptor pairs in plants, facilitating a more comprehensive understanding of cell wall surveillance mechanisms in plant immunity.

Jeong-Min Kim, Min-Soo Choi, Juhee Lee, Yong-Chan Cho and Youngsung Joo. J Ecol Environ 2024;48:. https://doi.org/10.5141/jee.24.048

1. Many plants compensate for the damage caused by herbivorous insects through tolerance responses. Besides directly causing plant tissue loss and seed production reduction, herbivory causes phenological changes in the host plant. However, little is known about the fitness costs of phenological changes caused by tolerance responses to herbivorous attacks. 2. The girdling beetle Phytoecia rufiventris caused a short-term decrease in the number of flowers of the host plant Erigeron annuus . However, accelerated growth restored the number of flowers, but after a 2-week delay. With an objective to examine whether the tolerance response with such a delay fully compensates the fitness, we experimentally reproduced a 2-week delay in germination under greenhouse and field settings. Under both conditions, intraspecific competition resulted in serious defects in the growth and reproduction of E. annuus plants which of germination was delayed. However, delayed germination resulted in better growth when competition and herbivory were eliminated from the field. 3. Thus, we showed that the tolerance response to restore reproductive production does not fully compensate for the fitness loss caused by insect attack; rather, the delay in seed production in attacked plants leads to delayed germination and subsequent inferiority in intraspecific competition. 4. Synthesis. Our results imply that compensation for floral production after an herbivore attack does not fully restore offspring fitness in the presence of intraspecific competition and herbivory. Assessing the ecological consequences of defense traits in an appropriate layer of interaction is critical to interpreting adaptive values.

Autophagy serves as an important recycling route for the growth and survival of eukaryotic organisms in nutrient-deficient conditions. Since starvation induces massive changes in the metabolic flux that are coordinated by key metabolic enzymes, specific processing steps of autophagy may be linked with metabolic flux-monitoring enzymes. We attempted to identify carbon metabolic genes that modulate autophagy using VIGS screening of 45 glycolysis- and Calvin–Benson cycle-related genes in Arabidopsis (Arabidopsis thaliana). Here, we report that three consecutive triose-phosphate-processing enzymes involved in cytosolic glycolysis, triose-phosphate-isomerase (TPI), glyceraldehyde-3-phosphate dehydrogenase (GAPC), and phosphoglycerate kinase (PGK), designated TGP, negatively regulate autophagy. Depletion of TGP enzymes causes spontaneous autophagy induction and increases AUTOPHAGY-RELATED 1 (ATG1) kinase activity. TGP enzymes interact with ATG101, a regulatory component of the ATG1 kinase complex. Spontaneous autophagy induction and abnormal growth under insufficient sugar in TGP mutants are suppressed by crossing with the atg101 mutant. Considering that triose-phosphates are photosynthates transported to the cytosol from active chloroplasts, the TGP enzymes would be strategically positioned to monitor the flow of photosynthetic sugars and modulate autophagy accordingly. Collectively, these results suggest that TGP enzymes negatively control autophagy acting upstream of the ATG1 complex, which is critical for seedling development.

본 연구의 목적은 코로나19 상황에서 중·고등학교 온라인 체육수업의 실태를 조사 분석하는데 있다. 이를 위해 G광역시 소재 5개구 10개 학교학생 1,180명을 대상으로 Google을 활용하여 온라인으로 설문조사를 실시하였다. 수집된 자료는 연구의 목적에 따라 SPSS 25.0 프로그램을 통해 분석하였다. 분석한 결과 중·고등학교 온라인 체육수업 참여실태는 첫째, 온라인 체육수업의 형태는 외부 영상 수업(EBS, 유튜브 등)의 비율이 55.6%이고, 체육교사 자체 제작 영상의 비율이 44.4%로 나타났다. 둘째, 온라인 체육수업 학습 방식과 관련하여 성별, 학년, 운동 빈도별 모두 가정내 PC를 가장 많이 활용하는 것으로 나타났고, 스마트폰과 태블릿 PC사용은 비슷하게 나타났다. 셋째, 온라인 체육수업 선호 형태와 관련하여 성별, 학년별, 운동빈도별 모두 유튜브 영상을 통해 학습하는 것을 선호하는 것으로 나타났으며 다음으로 체육교사 자체 제작영상을 선호하였다. 넷째, 온라인 체육수업의 어려움과 관련하여 남학생의 경우 협동활동, 수업집중, 학습량 과다, 궁금증 해결 등의 순으로 어려움을 느꼈고, 여학생의 경우 수업집중, 협동활동, 학습량과다, 궁금증 해결 등의 순으로 어려움을 느꼈다. 향후 코로나19 뿐만 아니라 다양한 질병 혹은 환경요인에 의해 온라인 수업의 비율은 높아질 것으로 판단되며 체육교사들은 이번 코로나19 사태를 계기로 다양하고 흥미있는 온라인 콘텐츠 제작에도 관심과 노력을 기울여야 할 것으로 판단된다.