Biology subjects

Holopainen, M.

Publications and source records attributed to Holopainen, M..

6 recordsLinked to original sources

bioRxiv2024

Functional omics of ORP7 in primary endothelial cells.

BackgroundMany members of the oxysterol binding protein related protein (ORP) family have been characterized in detail over the past decades, but the lipid transport and other functions of ORP7 still remain elusive. What is known about ORP7 points toward an endoplasmic reticulum and plasma membrane-localized protein, which also interacts with GABARAPL2 and unlipidated LC3B, suggesting a further autophagosomal/lysosomal association. Functional roles of ORP7 have been suggested in cholesterol efflux, hypercholesterolemia, and macroautophagy. We performed a hypothesis-free omics analysis of chemical ORP7 inhibition utilizing transcriptomics and lipidomics as well as proximity biotinylation interactomics to characterize ORP7 functions in a primary cell type, human umbilical vein endothelial cells (HUVECs). Moreover, assays on metrics such as angiogenesis, cholesterol efflux and lipid droplet quantification were conducted. ResultsPharmacological inhibition of ORP7 lead to an increase in gene expression related to lipid metabolism and inflammation, while genes associated with cell cycle and cell division were downregulated. Lipidomic analysis revealed increases in ceramides, lysophosphaditylcholines, as well as saturated and monounsaturated triacylglycerols. Significant decreases were seen in all cholesteryl ester and in some unsaturated triacylglycerol species, compatible with the detected decrease of mean lipid droplet area. Along with the reduced lipid stores, ABCG1-mediated cholesterol efflux and angiogenesis decreased. Interactomics revealed an interaction of ORP7 with AKT1, a central metabolic regulator. ConclusionsThe transcriptomics results suggest an increase in prostanoid as well as oxysterol synthesis, which could be related to the observed upregulation of proinflammatory genes. We envision that the defective angiogenesis in HUVECs subjected to ORP7 inhibition could be the result of an unfavorable plasma membrane lipid composition and/or reduced potential for cell division. To conclude, the present study suggests multifaceted functions of ORP7 in lipid homeostasis, angiogenic tube formation and gene expression of lipid metabolism, inflammation and cell cycle in primary endothelial cells, possibly through AKT1 interaction.

molecular biology↗

bioRxiv2023

Seasonal and genetic effects on lipid profiles of juvenile Atlantic salmon

Seasonality can influence many physiological traits requiring optimal energetic capacity for life-history stage transitions. In Atlantic salmon, high-energy status is essential for the initiation of maturation. Atlantic salmon lipid reserves are predominantly found in the viscera and myosepta in the muscle while the liver is essential for maintaining lipid metabolism. A genomic study found a region including a transcription co-factor-coding gene, vgll3, linked to Atlantic salmon maturation timing, which acts as an inhibitor of adipogenesis in mice, and mediates maturation via condition factor in Atlantic salmon. Here we investigate the influence of season and vgll3 genotypes associating with early (EE) and late (LL) maturation on lipid profiles in the muscle and liver in juvenile Atlantic salmon. We reared Atlantic salmon for two years until the occurrence of sexually mature males and sampled muscle and liver at two time points: spring and autumn of the second year. We found no seasonal or genotype effect in lipid profiles in muscle of immature males and females. However, in the liver we did detect a triacylglycerol (TG) enrichment and a genotype specific direction of change in membrane lipids, phosphatidylcholine (PC) and phosphatidylethanolamine (PE), from spring to autumn. Specifically, from spring to autumn membrane lipid concentrations increased in vgll3*EE individuals and decreased in vgll3*LL individuals. This could be explained with two possible scenarios 1) a seasonally more stable capacity of endoplasmic reticulum (ER) functions in vgll3*EE individuals compared to vgll3*LL individuals or 2) vgll3*LL individuals storing larger lipid droplets from spring to autumn in the liver compared to vgll3*EE individuals at the expense of ER capacity. This genotype specific seasonal direction of change in membrane lipid concentrations provides more indirect evidence that a mechanism linking vgll3 with lipid metabolism and storage exists. HighlightsO_LISeasonal lipid species profile separation in muscle and liver in juvenile Atlantic salmon C_LIO_LIGenotype specific direction of change of membrane lipids from spring to autumn C_LIO_LIIndirect evidence that a mechanism linking vgll3 with lipid metabolism and storage exists C_LI

evolutionary biology↗

bioRxiv2021

Unveiling effects of growth conditions on crown architecture and growth potential of Scots pine trees

Trees adapt to their growing conditions by regulating the sizes of their parts and their relationships. For example, removal or death of adjacent trees increases the growing space and the amount of light received by the remaining trees enabling their crowns to expand. Knowledge about the effects of silvicultural practices on crown size and shape as well as about the quality of branches affecting the shape of a crown is, however, still limited. Thus, the aim was to study the crown structure of individual Scots pine trees in forest stands with varying stem densities due to past forest management practices. Furthermore, we wanted to understand how crown and stem attributes as well as tree growth affects stem area at the height of maximum crown diameter (SAHMC), which could be used as a proxy for tree growth potential. We used terrestrial laser scanning (TLS) to generate attributes characterizing crown size and shape. The results showed that increasing stem density decreased Scots pine crown size. TLS provided more detailed attributes for crown characterization compared to traditional field measurements. Furthermore, decreasing stem density increased SAHMC and strong relationships (Spearman correlations >0.5) were found between SAHMC and crown and stem size as well as stem growth. Thus, this study provided quantitative and more comprehensive characterization of Scots pine crowns and their growth potential.

ecology↗

bioRxiv2021

Small mitochondrial protein NERCLIN regulates cardiolipin homeostasis and mitochondrial ultrastructure.

Cardiolipin (CL) is an essential phospholipid for mitochondrial structure and function. Here we present a small mitochondrial protein, NERCLIN, as a negative regulator of CL homeostasis and mitochondrial ultrastructure. Primate-specific NERCLIN is expressed ubiquitously from GRPEL2 locus on a tightly regulated low level, but induced by heat stress. NERCLIN overexpression severely disrupts mitochondrial cristae structure and induces mitochondrial fragmentation. Proximity labeling suggested interactions of NERCLIN with CL synthesis and prohibitin complexes on the matrix side of the inner mitochondrial membrane. Lipid analysis indicated that NERCLIN regulates mitochondrial CL content. The regulation may occur directly through interaction with PTPMT1, a proximal partner on the CL synthesis pathway, as its product phosphatidylglycerol was also reduced by NERCLIN. We propose that NERCLIN contributes to stress-induced adaptation of mitochondrial dynamics and turnover by regulating the mitochondrial CL content. Our findings add NERCLIN to the group of recently identified small mitochondrial proteins with important regulatory functions.

cell biology↗

bioRxiv2020

Detailed point cloud data on stem size and shape of Scots pine trees

Quantitative assessment of the effects of forest management on tree size and shape has been challenging as there has been a lack of methodologies for characterizing differences and possible changes comprehensively in space and time. Terrestrial laser scanning (TLS) and photogrammetric point clouds provide three-dimensional (3D) information on tree stem reconstructions required for characterizing differences between stem shapes and growth allocation. This data set includes 3D reconstructions of stems of Scots pine (Pinus sylvestris L.) trees from sample plots with different thinning treatments. The thinning treatments include two intensities of thinning, three thinning types as well as control (i.e. no thinning treatment since the establishment). The data set can be used in developing point clouds processing algorithms for single tree stem reconstruction and for investigating variation in stem size and shape of Scots pine trees. Additionally, it offers possibilities in characterizing the effects of various thinning treatments on stem size and shape of Scots pine trees from boreal forests. Data setZenodo https://zenodo.org/record/3701271 Data set licenseAttribution 4.0 International (CC BY 4.0)

ecology↗

bioRxiv2020

Assessing the effects of stand dynamics on stem growth allocation of individual Scots pine trees

Forest management alters the growing conditions and thus further development of trees. However, quantitative assessment of forest management on tree growth has been demanding as methodologies for capturing changes comprehensively in space and time have been lacking. Terrestrial laser scanning (TLS) has shown to be capable of providing three-dimensional (3D) tree stem reconstructions required for revealing differences between stem shapes and sizes. In this study, we used 3D reconstructions of tree stems from TLS and an unmanned aerial vehicle (UAV) to investigate how varying thinning treatments and the following growth effects affected stem shape and size of Scots pine (Pinus sylvestris L.) trees. The results showed that intensive thinning resulted in more stem volume and therefore total biomass allocation and carbon uptake compared to the moderate thinning. Relationship between tree height and diameter at breast height (i.e. slenderness) varied between both thinning intensity and type (i.e. from below and above) indicating differing response to thinning and allocation of stem growth of Scots pine trees. Furthermore, intensive thinning, especially from below, produced less variation in relative stem attributes characterizing stem shape and size. Thus, it can be concluded that thinning intensity, type, and the following growth effects have an impact on post-thinning stem shape and size of Scots pine trees. Our study presented detailed measurements on post-thinning stem growth of Scots pines that have been laborious or impracticable before the emergence of detailed 3D technologies. Moreover, the stem reconstructions from TLS and UAV provided variety of attributes characterizing stem shape and size that have not traditionally been feasible to obtain. The study demonstrated that detailed 3D technologies, such as TLS and UAV, provide information that can be used to generate new knowledge for supporting forest management and silviculture as well as improving ecological understanding of boreal forests.

ecology↗