Biology subjects

Koehler, K.

Publications and source records attributed to Koehler, K..

7 recordsLinked to original sources

bioRxiv2026

Plasma metabolite responses to an oral protein tolerance test differ between young and sarcopenic participants and suggest altered anabolic sensitivity

BackgroundSarcopenia is associated with anabolic resistance, a blunted muscle protein synthesis response to protein ingestion. Here, we hypothesized that anabolic resistance may be associated with a delayed postprandial decline in circulating plasma amino acids following protein ingestion. We therefore wanted to investigate whether an oral protein tolerance test (OPTT) combined with untargeted plasma metabolomics can detect age-related or sarcopenia-related differences in amino acid time courses consistent with altered postprandial amino acid handling, which could potentially reflect reduced anabolic sensitivity. Moreover, we investigated whether metabolites other than amino acids reacted to the OPTT. MethodsTwelve young healthy adults (controls: 22-28 years) and 12 older adults with clinically diagnosed probable or confirmed sarcopenia (70-91 years) ingested 20 g of whey protein after an overnight fast. We collected venous blood at baseline, 1 h, and 2 h post-ingestion and analyzed the samples by untargeted LC-HRMS plasma metabolomics. Linear mixed-effects models were fitted for 2,968 metabolic features with Benjamini-Hochberg FDR correction. For each category (branched-chain amino acid, essential amino acid [EAA], total amino acid) we summed the within-subject log2 fold changes (FC) of the constituent amino acids. This composite is reported as the summed log2FC Results201 metabolites were structurally annotated including 58 amino acid-related metabolites and 97 lipids. Fourteen of 17 proteinogenic amino acids increased significantly after protein ingestion (FDR<0.05). In young controls, essential amino acids rose more steeply at 1 h than in sarcopenic individuals (+10.06 {+/-} 1.05 vs. +7.84 {+/-} 1.58 summed log2FC) and declined more between 1 and 2 h (-4.93 {+/-} 1.29 vs. -0.20 {+/-} 2.27 summed log2FC). Leucine exemplified this pattern best, rising 1.74 log2FC in controls and declining to 0.96 at 2 h, while remaining elevated at 1.61 log2FC in the sarcopenic group at 2 h (p=0.009). Beyond amino acids, whey protein lowered circulating free fatty acids in both groups (FA 18:2, FA 18:1, FA 16:0; all FDR<0.05). Medium- and long-chain acylcarnitines (Car 8:0, Car14:2) declined postprandially in controls but remained elevated in sarcopenic individuals (p<0.05), suggesting altered postprandial lipid metabolism. ConclusionIn this proof-of-concept study, an OPTT showed that plasma EAAs declined more slowly from their postprandial peak in older adults with sarcopenia than in young adults, consistent with altered postprandial amino acid handling that may reflect anabolic resistance. Whey protein ingestion additionally modulates lipid and acylcarnitine metabolism in an age-dependent manner, suggesting broader alterations in postprandial metabolic regulation in older adults with sarcopenia.

physiology↗

bioRxiv2026

Multi-Trait Meta-QTL Analysis Reveals Genomic Hotspot Classes for Strategic Maize Improvement

BackgroundDecades of maize (Zea mays L.) quantitative trait locus (QTL) mapping have produced fragmented results across hundreds of independent studies, characterized by broad confidence intervals, population-specific effects, and a predominantly single-trait scope. Comprehensive multi-trait integration remains limited in the public domain, yet it could improve our understanding of trait relationships for strategic maize breeding. We integrated 2,701 QTLs published over 30 years across five trait categories (grain yield and components (GYC); plant development and architecture (PDA); plant physiology and stress adaptation (PHS); grain quality and nutritional composition (GQN); and disease and pest resistance (DPR)) to identify functionally classified genomic hotspots and prioritize candidate genes for multi-trait breeding. ResultsBioMercator V4.2.3 consolidated 2,518 projectable QTLs into 187 high-confidence meta-QTLs (MQTLs), achieving a 4.0-fold (75%) reduction in mean genetic-map confidence interval width (47.6 to 11.8 cM); 128 of 187 MQTLs (68.4%) showed genome-wide association study (GWAS) co-localization, and 119 (63.6%) met the strict dual-platform criterion. Twenty-three genomic hotspots harbored 131 of 187 MQTLs (70.1%) and were classified by an ordered, data-driven rule into three categories: ten multi-trait hubs enabling simultaneous improvement through pleiotropic or tightly linked genes; seven pathway-focused clusters dominated by a single trait pathway, exemplified by the chromosome 8 kernel-yield cluster; and six major-effect loci, each carrying a member meta-QTL of large effect (phenotypic variance explained (PVE) of at least 28%), including the Rp1 common-rust locus (35% member-MQTL PVE) and the chromosome 9 Wx1/THP9 starch-and-protein locus (up to 52% member-MQTL PVE). Environmental classification distinguished MQTLs predominantly supported by optimal-condition QTLs (42%) from those supported by stress-condition QTLs (28%), the latter showing [~]1.7-fold greater mean contributing-QTL phenotypic variance (12.8% vs. 7.4%), consistent with conditional effect amplification under stress; within-population comparisons under contrasting water regimes showed a larger, [~]3.5-fold amplification. Network-based candidate gene prioritization with cross-cereal ortholog analysis identified priority candidates with confirmed orthologs in one or more comparison cereals (rice, sorghum, wheat, or barley), with conservation highest for developmental and metabolic genes and lowest for pathogen-resistance genes, identifying priority targets for functional genomics investment. ConclusionsThis functionally classified and environmentally characterized meta-QTL framework provides breeders with a structured resource for multi-trait hotspot selection, environment-appropriate allele deployment, and functional genomics prioritization, with broader applicability as a transferable template for other crops confronting fragmented QTL literature and complex multi-trait breeding objectives.

plant biology↗

bioRxiv2026

Copper transport is required for metabolism and persistence of Toxoplasma gondii

Copper is a conserved cofactor, required for essential processes including aerobic respiration. Pathogens subvert host copper; however the mechanisms of copper uptake are not well understood. Here, we identify and validate two copper transporters of Toxoplasma gondii and determine the role of copper in parasite metabolism and pathogenesis. We show that Ctr1 is required for copper uptake. Deletion leads to undetectable parasite-associated copper, a significant growth defect and a metabolic shift from mitochondrial respiration with to glycolysis. Absence of Crt1 was fully and rapidly rescued by exogenous copper, which we believe is transported through the lower-affinity transporter Ctr2. Ctr2 is dispensable in rapid growth, however, has a role in parasite persistence in chronic infection, both in vitro and in vivo. Together, these findings reveal for the first time a critical role for copper uptake in shaping metabolic plasticity, and highlights the importance of nutrient availability in regulating apicomplexan metabolism.

cell biology↗

bioRxiv2025

Long-read single-cell RNA sequencing uncovers cell-type specific transcript regulation in COVID-19

SARS-CoV-2 infection leads to extensive host transcriptomic changes, but the role of alternative splicing in shaping the immune response remains underexplored. Here, we present the first application of long-read single-cell RNA sequencing on nasopharyngeal swabs from COVID-19 patients and healthy controls to resolve transcript-level changes across cell types. Our analysis identified major epithelial cell types and pronounced immune infiltration, with cell-type annotations concordant with those from short-read data. By enabling isoform-level resolution, our nanopore sequencing approach revealed cell-type specific alternative splicing, undetectable with short-read sequencing. For example, although gene-level expression of the key immune and apoptosis regulators, IFNAR2 and FAIM, did not differ between COVID-19 patients and healthy controls we identified marked shifts in isoform usage. Between moderate and critical cases, we observed cell-type specific differential transcript usage in the T cell signaling kinase FYN and the immune-regulatory transcription factor IRF2. As some of these splicing alterations yield functionally distinct isoforms, we hypothesize that alternative splicing modulates immune signaling and apoptosis, fine-tuning the host response to SARS-CoV-2 infection. Our study demonstrates the unique power of long-read single-cell transcriptomics to uncover isoform-resolved regulatory changes, offering novel insights into the role of alternative splicing in shaping immune responses to viral infections.

genomics↗

bioRxiv2024

DERIVATION OF ELEPHANT INDUCED PLURIPOTENT STEM CELLS

The crisis of biodiversity loss in the anthropogenic era requires new tools for studying non-model organisms. Elephants, for example, are both an endangered species and excellent models studying complex phenotypes like size, social behavior, and longevity, but they remain severely understudied. Here we report the first derivation of elephant (Elephas maximus) induced pluripotent stem cells (emiPSCs) achieved via a two-step process of chemical-media induction and colony selection, followed by overexpression of elephant transcription factors OCT4, SOX2, KLF4, MYC {+/-} NANOG and LIN28A, and modulation of the TP53 pathway. Since the seminal discovery of reprogramming by Shinya Yamanaka, iPSCs from many species including the functionally extinct northern white rhinocerous have been reported, but emiPSCs have remained elusive. While for multiple species the reprogramming protocol was adopted with little changes compared to model organisms like mouse and human, our emiPSC protocol requires a longer timeline and inhibition of TP53 expansion genes that are hypothesized to confer unique cancer resistance in elephants. iPSCs unlock tremendous potential to explore cell fate determination, cell and tissue development, cell therapies, drug screening, disease modeling, cancer development, gametogenesis and beyond to further our understanding of this iconic megafauna. This study opens new frontiers in advanced non-model organism cellular models for genetic rescue and conservation.

cell biology↗

bioRxiv2020

Evaluation of Field Sampling Techniques for Environmental Microbial Exposure: Assessing Efficacy and Feasibility

Environmental exposures in schools, including microbial exposures, can lead to detrimental childhood health outcomes. We evaluated two sampling techniques - standard flocked swabs versus sterile electrostatic cloths - to quantify Staphylococcus bacterial burden from school surfaces. Electrostatic cloths demonstrated higher test sensitivity and yielded higher surface area-standardized colony forming units compared to swabs. Despite protocol standardization, consistently larger surface areas were sampled with electrostatic cloths. This suggest that electrostatic cloths were more effective and practical for fieldwork.

microbiology↗

bioRxiv2017

Compensation For Chronic Oxidative Stress In ALADIN Null Mice

BackgroundMutations in the AAAS gene coding for the nuclear pore complex protein ALADIN lead to the autosomal recessive disorder triple A syndrome. Triple A patients present with a characteristic phenotype including alacrima, achalasia and adrenal insufficiency. Patient fibroblasts show increased levels of oxidative stress and several in vitro studies demonstrated that the nucleoporin ALADIN is involved in the cellular oxidative stress response and in adrenal steroidogenesis. We showed that ALADIN knock-out mice lack a phenotype resembling human triple A syndrome. Thus, we hypothesized that application of chronic oxidative stress by ingestion of paraquat will generate triple A-like phenotype in ALADIN null mice.\n\nResultsWe demonstrate that ALADIN knock-out mice present with an unexpected compensated glutathione metabolism still lacking a phenotype resembling human triple A syndrome after application of chronic oxidative stress. We could not observe increased levels of oxidative stress and alterations in adrenal steroidogenesis in mice depleted for ALADIN.\n\nConclusionsThis study stresses the species-specific role of the nucleoporin ALADIN presenting a novel compensatory mechanism of the cellular glutathione redox response and shedding light on the role of ALADIN in the cell.

cell biology↗