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Jalkanen, J.

Publications and source records attributed to Jalkanen, J..

4 recordsLinked to original sources

Defining ecologically realistic biodiversity offset multipliers with the Response-based Habitat Hectare Assessment of Biodiversity Gains (REHAB)

In biodiversity offsetting, balancing biodiversity losses with gains can be achieved by using multipliers that define the ratio between the magnitude of biodiversity loss and the area required to deliver equivalent biodiversity gains. Although there is broad scientific consensus that multipliers should be calibrated to deliver no net loss or a net gain for biodiversity, they are often applied without quantitative assessment of the ecological outcomes of offset actions. Here we operationalise the Response-based Habitat Hectare Assessment of Biodiversity Gains (REHAB), a framework where multipliers are informed by an understanding of habitat-specific ecological responses to offset action. To support Finlands national biodiversity offsetting scheme, we harnessed the knowledge of 111 experts to compile ecological attributes and condition matrices for all 388 Finnish habitat types and derive 346 offset action multipliers that represent ecological response functions for 216 habitat type-specific offset actions including restoration, management and passive recovery. Our analysis reveals substantial variation in response-functions, resulting in offset multipliers between 1.3-4,000 across offset actions and habitat types. We find that the fixed multipliers commonly used in offset schemes would result in net loss in 60% of the cases if action- habitat specific responses were not considered. This variability underscores that fixed multipliers cannot deliver reliable biodiversity outcomes and should be avoided in offsetting schemes. The REHAB framework has already been integrated into Finlands national offsetting policy. Other potential areas of application include informing ecosystem restoration planning and assessing biodiversity gains linked to credit issuance in emerging nature-credit markets.

ecology↗

Transcriptomic Profiling of scWAT Reveals Reduced Lipid-Associated Macrophage Signatures in Long-Term Endurance- and Resistance-Trained Athletes

Regular exercise training is associated with systemic and tissue-specific performance and health benefits, yet long-term molecular adaptations in subcutaneous abdominal white adipose tissue (scWAT) remain unclear. We analyzed the resting scWAT transcriptome of 89 adults (35-50 years) who were long-term (>15 years) endurance- or strength-trained, or untrained. Long-term training was linked to enrichment of ribosomal, mitochondrial, and aerobic metabolism-related pathways, while immune-related pathways were enriched in untrained individuals. A distinct sex dimorphic scWAT was identified: untrained females exhibited a more metabolically favorable, trained-like transcriptomic profile, and untrained males an untrained-like profile. In trained males, the inflammatory gene signature was lower than in untrained males. We also identified 11 genes specific to lipid-associated macrophages with lower expression in trained individuals, particularly in all endurance-trained individuals and strength-trained females. These findings highlight sex-specific, exercise-induced adaptations in scWAT relevant to metabolic health, and underscore the importance of including both sexes in scWAT research.

physiology↗

QClus: Robust and reliable preprocessing method for human heart snRNA-seq

Single nuclei RNA sequencing (snRNA-seq) remains a challenge for many human tissues, as incomplete removal of background signal masks cell-type-specific signals and interferes with downstream analyses. Here, we present QClus, a droplet-filtering algorithm targeted toward challenging samples, using cardiac tissue as an example. QClus uses specific metrics such as cell-type-specific marker gene expression to cluster nuclei and filter empty and highly contaminated droplets, providing reliable cleaning of samples with varying number of nuclei and contamination levels. In a benchmarking analysis against seven alternative methods across six datasets consisting of 252 samples and over 1.9 million nuclei, QClus achieved the highest quality in the greatest number of samples over all evaluated quality metrics and recorded no processing failures, while robustly retaining numbers of nuclei within the expected range. QClus combines high quality, automation, and robustness with flexibility and user-adjustability, catering to diverse experimental needs and datasets.

genomics↗

Single-cell dissection of live human hearts in ischemic heart disease and heart failure reveals cell-type-specific driver genes and pathways

Ischemic heart disease is globally the leading cause of death. It plays a central role in the electrical and structural remodeling of the right atrium, predisposing to arrhythmias, heart failure, and sudden death. Here, we provide the first dissection of the gene expression changes in the live right atrial tissue, using single-nuclei RNA-seq and spatial transcriptomics. We investigate matched samples of the tissue and pericardial fluid and reveal substantial differences in disease- associated gene expression in all cell types, leading to inflammatory microvascular dysfunction and changes in the tissue composition. Our study demonstrates the importance of creating high- resolution cellular maps and partitioning disease signals beyond epicardial coronary arteries and ischemic left ventricle to identify candidate mechanisms leading to more severe types of human cardiovascular disease. One-Sentence SummarySingle-cell dissection of ex vivo heart biopsies and pericardial fluid in ischemic heart disease and heart failure

molecular biology↗