@article{petri_exploring_2025,
	title = {Exploring the world of small proteins in plant biology and bioengineering},
	volume = {41},
	issn = {0168-9525},
	url = {https://www.sciencedirect.com/science/article/pii/S0168952524002129},
	doi = {10.1016/j.tig.2024.09.004},
	abstract = {Small proteins are ubiquitous in all kingdoms of life. MicroProteins, initially characterized as small proteins with protein interaction domains that enable them to interact with larger multidomain proteins, frequently modulate the function of these proteins. The study of these small proteins has contributed to a greater comprehension of protein regulation. In addition to sequence homology, sequence-divergent small proteins have the potential to function as microProtein mimics, binding to structurally related proteins. Moreover, a multitude of other small proteins encoded by short open reading frames (sORFs) and peptides, derived from diverse sources such as long noncoding RNAs (lncRNAs) and miRNAs, contribute to a variety of biological processes. The potential of small proteins is evident, offering promising avenues for bioengineering that could revolutionize crop performance and reduce reliance on agrochemicals in future agriculture.},
	number = {2},
	urldate = {2025-02-07},
	journal = {Trends in Genetics},
	author = {Petri, Louise and Van Humbeeck, Anne and Niu, Huanying and Ter Waarbeek, Casper and Edwards, Ashleigh and Chiurazzi, Maurizio Junior and Vittozzi, Ylenia and Wenkel, Stephan},
	month = feb,
	year = {2025},
	keywords = {lncRNA, microProteins, sORFs, transcription factor},
	pages = {170--180},
}

Small proteins are ubiquitous in all kingdoms of life. MicroProteins, initially characterized as small proteins with protein interaction domains that enable them to interact with larger multidomain proteins, frequently modulate the function of these proteins. The study of these small proteins has contributed to a greater comprehension of protein regulation. In addition to sequence homology, sequence-divergent small proteins have the potential to function as microProtein mimics, binding to structurally related proteins. Moreover, a multitude of other small proteins encoded by short open reading frames (sORFs) and peptides, derived from diverse sources such as long noncoding RNAs (lncRNAs) and miRNAs, contribute to a variety of biological processes. The potential of small proteins is evident, offering promising avenues for bioengineering that could revolutionize crop performance and reduce reliance on agrochemicals in future agriculture.

@article{jeong_spectral_2025,
	title = {Spectral unmixing of hyperspectral images revealed pine wilt disease sensitive endmembers},
	volume = {177},
	copyright = {© 2025 Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70090},
	doi = {10.1111/ppl.70090},
	abstract = {Throughout the entire cycle of leaf phenological events, leaf colour undergoes changes that are influenced by either abiotic stress or biotic infection. These changes in colouration are closely linked to the quantity and quality of photosynthetic pigments, which directly impact the primary productivity of plants. Therefore, monitoring and quantifying leaf colouration changes are crucial for distinguishing damage caused by pine wilt nematodes from natural tree senescence. In this study, a hyperspectral camera sensor was employed for the non-invasive and non-destructive evaluation of needle colour changes in coniferous trees grown in field tests. Three distinct needle colour variations of six coniferous tree species were selected and monitored using a hyperspectral sensor: those displaying seasonal autumn colours, undergoing nematode-infected necrosis processes, and experiencing natural death. To mitigate the inherently mixed spectral properties of hyperspectral data, endmembers were extracted from individual images using the Purity Pixel Index algorithm under the assumption of linear mixing of endmembers. From a total of 1,321 endmembers extracted from 378 hyperspectral images of six pine species, eight endmembers were ultimately chosen to reconstruct hyperspectral images and generate abundance maps. Among these eight endmembers, four represent varying levels of photosynthetic pigment contents—ranging from very low to high. Consequently, these coniferous endmembers hold promise for assessing seasonal leaf phenology and the extent of damage in pine trees infected by pine wilt nematodes. This comprehensive approach underscores the effectiveness of spectral unmixing of hyperspectral images in advancing precision forestry through meticulous coniferous needle trait analysis.},
	language = {en},
	number = {1},
	urldate = {2025-02-07},
	journal = {Physiologia Plantarum},
	author = {Jeong, Seok Won and Lee, Il Hwan and Kim, Yang-Gil and Kang, Kyu-Suk and Shim, Donghwan and Hurry, Vaughan and Ivanov, Alexander G. and Park, Youn-Il},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70090},
	pages = {e70090},
}

Throughout the entire cycle of leaf phenological events, leaf colour undergoes changes that are influenced by either abiotic stress or biotic infection. These changes in colouration are closely linked to the quantity and quality of photosynthetic pigments, which directly impact the primary productivity of plants. Therefore, monitoring and quantifying leaf colouration changes are crucial for distinguishing damage caused by pine wilt nematodes from natural tree senescence. In this study, a hyperspectral camera sensor was employed for the non-invasive and non-destructive evaluation of needle colour changes in coniferous trees grown in field tests. Three distinct needle colour variations of six coniferous tree species were selected and monitored using a hyperspectral sensor: those displaying seasonal autumn colours, undergoing nematode-infected necrosis processes, and experiencing natural death. To mitigate the inherently mixed spectral properties of hyperspectral data, endmembers were extracted from individual images using the Purity Pixel Index algorithm under the assumption of linear mixing of endmembers. From a total of 1,321 endmembers extracted from 378 hyperspectral images of six pine species, eight endmembers were ultimately chosen to reconstruct hyperspectral images and generate abundance maps. Among these eight endmembers, four represent varying levels of photosynthetic pigment contents—ranging from very low to high. Consequently, these coniferous endmembers hold promise for assessing seasonal leaf phenology and the extent of damage in pine trees infected by pine wilt nematodes. This comprehensive approach underscores the effectiveness of spectral unmixing of hyperspectral images in advancing precision forestry through meticulous coniferous needle trait analysis.

@article{routier_investigating_2024,
	title = {Investigating the {Effect} of {Syringe} {Infiltration} on {Nicotiana} tabacum ({Tobacco})},
	volume = {5},
	issn = {2692-1952},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11752493/},
	doi = {10.1021/acsagscitech.4c00170},
	abstract = {, Plant infiltration techniques, particularly agroinfiltration,
have
transformed plant science and biotechnology by enabling transient
gene expression for genetic engineering of plants or genomic studies.
Recently, the use of infiltration has expanded to introduce nanomaterials
and polymers in plants to enable nonnative functionalities. Despite
its wide use, the impact of the infiltration process per se on plant physiology needs to be better understood. This study investigates
the effect of syringe infiltration, a commonly employed technique
in plants, using a typical infiltration buffer solution. Noninvasive
and real-time monitoring methods, including high-resolution thermal
imaging and a porometer/fluorometer, were used to study the physiological
responses and stress levels of the infiltrated plants. Our results
revealed localized cell damage at the infiltration site due to syringe
compression, but the overall cell viability and tissue integrity were
largely unaffected. Thermography showed a temporary temperature increase
of the leaves and stomatal conductance alterations postinfiltration,
with leaf recovery in 3–6 days. Additionally, fluorescence
measurements indicated a 6\% decrease in maximum quantum efficiency
(Fv/Fm) and
a 34\% decrease in photosystem II (ΦPSII) quantum yield, persisting
for 5 days after infiltration, suggesting sustained photosystem efficiency
changes. Our work highlights the need to consider the effect of infiltration
when performing biological studies and aims to facilitate the optimization
of protocols commonly used in plant science and biotechnology.},
	number = {1},
	urldate = {2025-01-31},
	journal = {ACS Agricultural Science \& Technology},
	author = {Routier, Cyril and Hermida-Carrera, Carmen and Stavrinidou, Eleni},
	month = dec,
	year = {2024},
	pmid = {39850806},
	pmcid = {PMC11752493},
	pages = {28--35},
}

, Plant infiltration techniques, particularly agroinfiltration, have transformed plant science and biotechnology by enabling transient gene expression for genetic engineering of plants or genomic studies. Recently, the use of infiltration has expanded to introduce nanomaterials and polymers in plants to enable nonnative functionalities. Despite its wide use, the impact of the infiltration process per se on plant physiology needs to be better understood. This study investigates the effect of syringe infiltration, a commonly employed technique in plants, using a typical infiltration buffer solution. Noninvasive and real-time monitoring methods, including high-resolution thermal imaging and a porometer/fluorometer, were used to study the physiological responses and stress levels of the infiltrated plants. Our results revealed localized cell damage at the infiltration site due to syringe compression, but the overall cell viability and tissue integrity were largely unaffected. Thermography showed a temporary temperature increase of the leaves and stomatal conductance alterations postinfiltration, with leaf recovery in 3–6 days. Additionally, fluorescence measurements indicated a 6% decrease in maximum quantum efficiency (Fv/Fm) and a 34% decrease in photosystem II (ΦPSII) quantum yield, persisting for 5 days after infiltration, suggesting sustained photosystem efficiency changes. Our work highlights the need to consider the effect of infiltration when performing biological studies and aims to facilitate the optimization of protocols commonly used in plant science and biotechnology.

@article{hogberg_improved_2024,
	title = {Improved methodology for tracing a pulse of {13C}-labelled tree photosynthate carbon to ectomycorrhizal roots, other soil biota and soil processes in the field},
	volume = {45},
	issn = {0829-318X},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11775467/},
	doi = {10.1093/treephys/tpae169},
	abstract = {Isotopic pulse-labelling of photosynthate allows tracing of carbon (C) from tree canopies to below-ground biota and calculations of its turnover in roots and recipient soil microorganisms. A high concentration of label is desirable but is difficult to achieve in field studies of intact ecosystem patches with trees. Moreover, root systems of trees overlap considerably in most forests, which requires a large labelled area to minimize the impact of C allocated below-ground by un-labelled trees. We describe a method which combines a high level of labelling at ambient concentrations of CO2, [CO2], with undisturbed root systems and a model to account for root C and root-derived C from un-labelled trees. We raised 5-m-tall chambers, each covering 50 m2 of ground (volume 250 m3) in a young boreal Pinus sylvestris L. forest with up to 5 m tall trees. Rather than a conventional single release of 13CO2, we used five consecutive releases, each followed by a draw-down period, thus avoiding high [CO2]. Hence, we elevated successively the 13CO2 from 1.1 to 23 atom\% after the first release to 61 atom\% after the fifth, while maintaining [CO2] below 500 p.p.m. during 4–4.5 h of labelling. The average abundance of 13CO2 was as high as 42 atom\%. We used the central 10 m2 of the 50 m2 area for sampling of roots and other soil biota. We modelled the dilution of labelled C across the plots by un-labelled C from roots of trees outside the area. In the central 10 m2 area, {\textasciitilde}85\% of roots and root-associated biota received C from labelled trees. In summary, we elevated the labelling of roots and associated soil biota four-fold compared with previous studies and described the commonly overlooked impact of roots from un-labelled trees outside the labelled area.},
	number = {1},
	urldate = {2025-01-31},
	journal = {Tree Physiology},
	author = {Högberg, Peter and Klatt, Christian and Franklin, Oskar and Henriksson, Nils and Lim, Hyungwoo and Inselsbacher, Erich and Hurry, Vaughan and Näsholm, Torgny and Högberg, Mona N},
	month = dec,
	year = {2024},
	pmid = {39731437},
	pmcid = {PMC11775467},
	pages = {tpae169},
}

Isotopic pulse-labelling of photosynthate allows tracing of carbon (C) from tree canopies to below-ground biota and calculations of its turnover in roots and recipient soil microorganisms. A high concentration of label is desirable but is difficult to achieve in field studies of intact ecosystem patches with trees. Moreover, root systems of trees overlap considerably in most forests, which requires a large labelled area to minimize the impact of C allocated below-ground by un-labelled trees. We describe a method which combines a high level of labelling at ambient concentrations of CO2, [CO2], with undisturbed root systems and a model to account for root C and root-derived C from un-labelled trees. We raised 5-m-tall chambers, each covering 50 m2 of ground (volume 250 m3) in a young boreal Pinus sylvestris L. forest with up to 5 m tall trees. Rather than a conventional single release of 13CO2, we used five consecutive releases, each followed by a draw-down period, thus avoiding high [CO2]. Hence, we elevated successively the 13CO2 from 1.1 to 23 atom% after the first release to 61 atom% after the fifth, while maintaining [CO2] below 500 p.p.m. during 4–4.5 h of labelling. The average abundance of 13CO2 was as high as 42 atom%. We used the central 10 m2 of the 50 m2 area for sampling of roots and other soil biota. We modelled the dilution of labelled C across the plots by un-labelled C from roots of trees outside the area. In the central 10 m2 area, ~85% of roots and root-associated biota received C from labelled trees. In summary, we elevated the labelling of roots and associated soil biota four-fold compared with previous studies and described the commonly overlooked impact of roots from un-labelled trees outside the labelled area.

@article{ding_insights_2025,
	title = {Insights into \textit{{PeERF168}} gene in slash pine terpene biosynthesis: {Integrating} high-throughput phenotyping, {GWAS}, and transgenic studies},
	volume = {300},
	issn = {0141-8130},
	shorttitle = {Insights into \textit{{PeERF168}} gene in slash pine terpene biosynthesis},
	url = {https://www.sciencedirect.com/science/article/pii/S0141813025002776},
	doi = {10.1016/j.ijbiomac.2025.139728},
	abstract = {Resin biosynthesis in conifer is a complex process, controlled by multiple quantitative trait loci (QTLs). Quantifying resin components is traditionally expensive and labor-intensive. In this study, we employed near infrared (NIR) spectroscopy to quantify resin components in Slash pine using 240 genotypes. A partial least squares regression model was applied to identify the characteristic bands responsed to variations in Alpha and Beta pinene levels. Genome-wide association study (GWAS) identified 35 significant SNPs involved in terpenoid precursor biosynthesis, transport, modification, and abiotic stress resistance. eQTL mapping co-localized four candidate genes: PeCHITINASE (c166891.graph\_c0), PeGLYCOSYLTRANSFERASE (c160167.graph\_c0), PeASIL2 (c324347.graph\_c0), and PeERF168 (c311225.graph\_c0). Mutations in two SNPs increased the expression of PeASIL2 and PeERF168, leading to higher levels of Alpha and Beta pinene. Further heterologous transformation experiments confirmed that the PeERF168 gene regulates the concentration of both monoterpenes and sesquiterpenes. These findings provide valuable insights into the molecular mechanisms of resin biosynthesis, facilitating cost-effective gene discovery through high-throughput resin component detection and genomics integration, with substantial potential to enhance molecular breeding and improve resin yield and quality.},
	urldate = {2025-01-31},
	journal = {International Journal of Biological Macromolecules},
	author = {Ding, Xianyin and Diao, Shu and Zhang, Yini and Luan, Qifu and Li, Yanjie and Jiang, Jingmin and Wu, Harry X.},
	month = apr,
	year = {2025},
	keywords = {GWAS, High-throughput phenotyping, Slash pine, Terpene biosynthesis, eQTL mapping},
	pages = {139728},
}

Resin biosynthesis in conifer is a complex process, controlled by multiple quantitative trait loci (QTLs). Quantifying resin components is traditionally expensive and labor-intensive. In this study, we employed near infrared (NIR) spectroscopy to quantify resin components in Slash pine using 240 genotypes. A partial least squares regression model was applied to identify the characteristic bands responsed to variations in Alpha and Beta pinene levels. Genome-wide association study (GWAS) identified 35 significant SNPs involved in terpenoid precursor biosynthesis, transport, modification, and abiotic stress resistance. eQTL mapping co-localized four candidate genes: PeCHITINASE (c166891.graph_c0), PeGLYCOSYLTRANSFERASE (c160167.graph_c0), PeASIL2 (c324347.graph_c0), and PeERF168 (c311225.graph_c0). Mutations in two SNPs increased the expression of PeASIL2 and PeERF168, leading to higher levels of Alpha and Beta pinene. Further heterologous transformation experiments confirmed that the PeERF168 gene regulates the concentration of both monoterpenes and sesquiterpenes. These findings provide valuable insights into the molecular mechanisms of resin biosynthesis, facilitating cost-effective gene discovery through high-throughput resin component detection and genomics integration, with substantial potential to enhance molecular breeding and improve resin yield and quality.