Biology subjects

Nyman, T.

Publications and source records attributed to Nyman, T..

6 recordsLinked to original sources

bioRxiv2026

Effects of Tempo, Dynamics, and String on Physical Exposure in Professional Violinists

1.This study examined how tempo, dynamics, and string influence upper-extremity physical exposure in professional violinists and how exposure variability is distributed among musical characteristics, between-subject differences, and residual variability. Twelve violinists performed seven standardized scales while bilateral upper-arm and wrist kinematics and shoulder and forearm muscle activity were recorded. Linear mixed-effects models showed that faster tempo increased right upper-arm velocity and bilateral forearm activity while reducing right upper-arm and wrist ranges of motion. Louder dynamics increased bilateral forearm and right trapezius activity and right-wrist ranges of motion. Higher-posture strings increased right upper-arm elevation and right shoulder muscle activity. Variance analysis identified exposures predominantly related to musical characteristics, jointly related to musical characteristics and between-subject differences, predominantly related to between-subject differences, or mainly unexplained. These findings support future exposure prediction from musical characteristics and targeted prevention through repertoire-based workload management, structured recovery, and individualized technique-focused strategies. 2. HighlightsO_LITempo, dynamics, and string produced distinct upper-extremity exposures. C_LIO_LIFaster tempo and louder dynamics increased bilateral forearm muscle activity. C_LIO_LIHigher-posture strings increased right upper-arm elevation and shoulder activity. C_LIO_LIDistinct musical, between-subject, and residual variance patterns were identified. C_LIO_LIFindings support repertoire-based and individualized PRMSD prevention. C_LI

bioengineering↗

bioRxiv2024

Identification of unique and potent inhibitors of SARS-CoV-2 main protease from DNA-encoded chemical libraries

In vitro screening of large compounds libraries with automated high-throughput screening is expensive, time consuming and requires dedicated infrastructures. Conversely, the selection of DNA-encoded chemical libraries (DECL) can be rapidly performed with routine equipment available in most laboratories. In this study we identified novel inhibitors of SARS-CoV-2 main protease (Mpro) through the affinity-based selection of the DELopen library (open access for academics), containing 4.2 billion compounds. The identified inhibitors were peptide-like compounds containing an N-terminal electrophilic group able to form a covalent bond with the nucleophilic Cys145 of Mpro, as confirmed by x-ray crystallography. This DECL selection campaign enabled the discovery of the unoptimized compound SLL11 displaying an IC50 of 30 nM, proving that the rapid exploration of large chemical spaces enabled by DECL technology, allows for the direct identification of potent inhibitors avoiding several rounds of iterative medicinal chemistry. Compound MP1, a close analogue of SLL11, showed antiviral activity against SARS-CoV-2 in the low micromolar range when tested in Caco-2 and Calu-3 (EC50 = 2.3 {micro}M) cell lines. As peptide-like compounds can suffer from low cell permeability and metabolic stability, the cyclization of the compounds as well as the substitution of selected residues with D-enantiomers will be explored in the future to improve the antiviral activity of these novel compounds.

microbiology↗

bioRxiv2022

Museum specimens of a landlocked pinniped reveal recent loss of genetic diversity and unexpected population connections

AimThe Saimaa ringed seal (Pusa hispida saimensis) is endemic to Lake Saimaa in Finland. The subspecies is thought to have originated when parts of the ringed seal population of the Baltic region were trapped in lakes emerging due to post-glacial bedrock rebound around 9,000 years ago. During the 20th century, the population experienced a drastic human-induced bottleneck. Today encompassing a little over 400 seals with extremely low genetic diversity, it is classified as endangered. Our main aim was to evaluate the role of the 20th century bottleneck in the erosion of genetic diversity in the Saimaa seal population. We also evaluated connections with other ringed seals from the Baltic Sea, Lake Ladoga, North America, Svalbard and the White Sea. LocationLake Saimaa, Finland, together with the Baltic Sea and the Arctic Ocean. MethodsWe sequenced sections of the mitochondrial control region from 60 up to 125 years old museum specimens of the Saimaa ringed seal. The generated dataset was combined with publicly available sequences. We studied how genetic variation has changed through time in this subspecies, and how it is phylogenetically related to other ringed seal populations. ResultsWe observed temporal fluctuations in haplotype frequencies and loss of haplotypes accompanied by a recent reduction in female effective population size. In apparent contrast with the traditionally held view of the Baltic origin of the population, the Saimaa ringed seal mtDNA variation shows also affinities to North American ringed seals. Main conclusionsOur results suggest that the Saimaa ringed seal has experienced recent genetic drift associated with small population size. The results further suggest that extant Baltic ringed seals do not represent well the ancestral population of the Saimaa ringed seal, which calls for re-evaluation of the deep history of this subspecies.

evolutionary biology↗

bioRxiv2021

Adipose gene expression profiles reveal novel insights into the adaptation of northern Eurasian semi-domestic reindeer (Rangifer tarandus)

Reindeer (Rangifer tarandus) are semi-domesticated animals adapted to the challenging arctic conditions of northern Eurasia. Adipose tissues play a crucial role in animals living in northern environments by altering gene expression in their tissues to regulate energy homeostasis and thermogenic activity. Here, we performed transcriptome profiling by RNA sequencing of adipose tissues from three different anatomical depots: metacarpal (bone marrow), perirenal, and prescapular fat in Finnish and Even reindeer (in Sakha) during two seasonal time points (spring and winter). On average 36.5 million pair-ended clean reads were obtained for each sample, and a total of 16,362 genes were expressed in our data. Gene expression profiles in metacarpal tissue were distinct and clustered separately from perirenal and prescapular adipose tissues. Notably, metacarpal adipose tissue appeared to have a significant role in the regulation of the energy metabolism of reindeer in spring when their nutritional condition is poor after winter. During spring, when the animals are in less optimal condition, genes associated with the immune system (e.g., CCL2, CCL11, CXCL14, IGSF3, IGHM, IGLC7, IGKC, JCHAIN, and IGSF10) were upregulated in the perirenal and prescapular adipose tissue, while genes involved in energy metabolism (e.g., ACOT2, APOA1, ANGPTL1, ANGPTL8, ELOVL7, MSMO1, PFKFB1, and ST3GAL6) were upregulated in metacarpal tissue. Even reindeer harboured relatively fewer significantly differentially expressed genes than Finnish reindeer, irrespective of the season, possibly owing to climatic and management differences. Moreover, blood and tissue parameters reflecting general physiological and metabolic status showed less seasonal variation in Even reindeer than in Finnish reindeer. This study identified adipose candidate genes potentially involved in immune response, fat deposition, energy metabolism, development, cell growth, and organogenesis. Taken together, this study provides new information on the mechanisms by which reindeer adapt to less optimal arctic conditions.

genomics↗

bioRxiv2020

Patterns of microbiome variation among infrapopulations of permanent bloodsucking parasites

While interspecific variation in microbiome composition can often be readily explained by factors such as host species identity, there is still limited knowledge of how microbiomes vary at scales lower than the species level (e.g., between individuals or populations). Here, we evaluated variation in microbiome composition of individual parasites among infrapopulations (i.e., populations of parasites of the same species living on a single host individual). To address this question, we used genome-resolved and shotgun metagenomic data of 17 infrapopulations (balanced design) of the permanent, bloodsucking seal louse Echinophthirius horridus sampled from individual Saimaa ringed seals Pusa hispida saimensis. Both genome-resolved and read-based metagenomic classification approaches consistently show that parasite infrapopulation identity is a significant factor that explains both qualitative and quantitative patterns of microbiome variation at the intraspecific level. This study contributes to the general understanding of the factors driving patterns of intraspecific variation in microbiome composition, especially of bloodsucking parasites, and has implications for understanding how well-known processes occurring at higher taxonomic levels, such as phylosymbiosis, might arise in these systems.

ecology↗

bioRxiv2020

Climate, species richness, and body size drive geographical variation in resource specialization of herbivorous butterflies

AimIt is generally assumed that the degree of resource specialization in herbivorous insects increases towards lower latitudes. However, latitudinal patterns in herbivore diet breadth at large spatial scales remain poorly understood. In this work, we investigated drivers of latitudinal variation in lepidopteran "fundamental" resource specialization, which we defined as the host breadth when not limited by interspecific interactions at the same trophic level. LocationThe Japanese archipelago (22{degrees}N-45{degrees}N), including hemiboreal, temperate, and subtropical zones. TaxonHerbivorous butterflies. MethodsSpecies-specific fundamental host breadth was calculated based on pooled geographical occurrence and host-use records. We investigated the latitudinal pattern and significant drivers of the degree of specialization in regional species pools at a 10-km grid level. As potential drivers, we focused on geography, current climate, and diversity and body size of butterflies. Through Bayesian structural equation modeling, we investigated the complicated relationships between these variables and community-level resource specialization represented by three different indices of host breadth. ResultsWe found that fundamental resource specialization of butterfly communities increases toward higher latitudes. This pattern is contrary to the presumed general trend found in studies based on realized resource specialization within local communities. We found that the observed pattern is driven mainly by factors related to climate, butterfly diversity, and body size in each community. Above all, annual mean temperature most strongly drove community-level fundamental host breadth of butterflies. Main conclusionsOur findings suggest that fundamental resource specialization may show different latitudinal patterns from the conventional prediction based on knowledge of realized resource specialization. Our results emphasize the importance of the current climate as a major factor regulating butterfly morphology and fundamental host breadth, regardless of whether the impact is direct or indirect.

ecology↗