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Szlachta, K.

Publications and source records attributed to Szlachta, K..

3 recordsLinked to original sources

Passage through submersible and Archimedes pumps results in decreased migration survival in coho salmon yearlings

Flood-control pumpstations compromise connectivity and survival for migratory fish globally, yet field evaluations of modern "fish-friendly" designs remain scarce. We evaluated out-migration survival and behavior of yearling coho salmon (Oncorhynchus kisutch) entrained through an open-Archimedes screw station (Hammersley) and a conventional radial station (Barrowtown) in the lower Fraser River floodplain, British Columbia. Using acoustic telemetry over two migration seasons (2024-2025), we tracked smolts across an 84-km corridor to New Westminster and modeled apparent survival using a Cormack-Jolly-Seber framework. Baseline natural mortality in downstream controls averaged 60% across years (cumulative survival: ~40%). Entrainment through the conventional radial station caused 87.5% mortality. The open-Archimedes station conferred an improvement over the conventional facility but still induced 11.5% mortality. Notably, pump-induced losses at the Archimedes pump were predominantly latent: while acute survival through immediate tailrace receivers was high (95-98%), survival deficits diverged downstream in the mainstem Fraser River. Entrainment also prolonged out-migration, causing up to a 10-day delay in 2024 driven by forebay holding and depressed downstream transit speeds. Our findings demonstrate that while open-Archimedes screws improve survival relative to legacy radial impellers, they still impose substantial latent mortality. In heavily altered basins where baseline smolt mortality is already high, additive losses from drainage infrastructure may exacerbate survival bottlenecks.

ecology↗

Seq2Karyotype (S2K): A Method for in-silico Karyotyping Using Single-Sample Whole-Genome Sequencing Data

DNA abnormalities characterized by cytogenetic imaging at the single cell resolution, i.e. karyotyping, have long served as cancer diagnostic and prognostic biomarkers. To enable in-silico karyotyping using unpaired whole-genome sequencing data, we developed Seq2Karyotype (S2K), a tool that fits karyotype models with clonality estimation based on read-depth and allelic imbalance in a bulk sample and supports visualization-guided refinement. Analysis on 19 adult and pediatric cancer cell lines revealed unexpected intratumoral heterogeneity involving multiple copy number variation (CNV) states including whole-genome duplication, which were validated by imaging and single-cell omics profiling. Analyses on patient samples showed high concordance with clinical cytogenetic reports for acute myeloid leukemia, and revealed evolutionary trajectories from multi-region metastatic neuroblastomas implicating reversion. These findings highlight extensive and dynamic intratumoral heterogeneity contributed by CNV in both cell line models and patient samples, which may inform future research on tumor evolution under selective pressure such as drug exposure.

bioinformatics↗

CNCC: An analysis tool to determine genome-wide DNA break end structure at single-nucleotide resolution

DNA double-stranded breaks (DSBs) are potentially deleterious events in a cell. The end structures (blunt, 3- and 5-overhangs) at sites of double-stranded breaks contribute to the fate of their repair and provide critical information for consequences of the damage. Here, we describe the use of a coverage-normalized cross correlation analysis (CNCC) to process high-precision genome-wide break mapping data, and determine genome-wide break end structure distributions at single-nucleotide resolution. For the first time, on a genome-wide scale, our analysis revealed the increase in the 5 to 3 end resection following etoposide treatment, and the global progression of the resection due to the removal of DNA topoisomerase II cleavage complexes. Further, our method distinguished the change in the pattern of DSB end structure with increasing doses of the drug. The ability of this method to determine DNA break end structures without a priori knowledge of break sequences or genomic position should have broad applications in understanding genome instability.

genomics↗