Biology subjects

Moretti, E.

Publications and source records attributed to Moretti, E..

3 recordsLinked to original sources

bioRxiv2024

Sensitive tumor detection, accurate quantification, and cancer subtype classification using low-pass whole methylome sequencing of plasma DNA

The analysis of circulating tumor DNA (ctDNA) is increasingly used for monitoring disease in patients with metastatic cancer. Here, we introduce a robust and reproducible strategy combining low-pass whole methylome sequencing of plasma DNA with METER, a novel computational tool. Engaging prediction models trained on independent available datasets, METER enables the detection and quantification of tumor content (TC) and performs molecular cancer subtyping. Applied to plasma methylomes from early metastatic breast cancer patients, our method demonstrated reliable quantification, sensitive tumor detection below 3% of TC, and the ability to perform accurate Estrogen Receptor (ER) subtyping. METER provided clinically relevant predictions, underscored by associations with relevant prognostic factors, robust correlation with matched circulating tumor cells, and highly correlated with patients outcomes in challenging scenarios as TC<3%. Our strategy provides comprehensive and sensitive analysis of plasma samples, serving as a valuable yet cost-effective precision oncology tool.

cancer biology↗

bioRxiv2023

Gain efficiency with streamlined and automated data processing: Examples from high-throughput monoclonal antibody production

Data management and sample tracking in complex biological workflows are essential steps to ensure necessary documentation and guarantee the reusability of data and metadata. Currently, these steps pose challenges related to correct annotation and labeling, error detection, and safeguarding the quality of documentation. With growing acquisition of biological data and the expanding automatization of laboratory workflows, manual processing of samples is no longer favorable, as it is time- and resource-consuming, is prone to biases and errors, and lacks scalability and standardization. Thus, managing heterogeneous biological data calls for efficient and tailored systems, especially in laboratories run by biologists with limited computational expertise. Here, we showcase how to meet these challenges with a modular pipeline for data processing, facilitating the complex production of monoclonal antibodies from single B-cells. We present best practices for development of data processing pipelines concerned with extensive acquisition of biological data that undergoes continuous manipulation and analysis. Moreover, we assess the versatility of proposed design principles through a proof-of-concept data processing pipeline for automated induced pluripotent stem cell culture and differentiation. We show that our approach streamlines data management operations, speeds up experimental cycles and leads to enhanced reproducibility. Finally, adhering to the presented guidelines will promote compliance with FAIR principles upon publishing.

cell biology↗

bioRxiv2023

Meta-analysis of herbicide non-target effects on pest natural enemies

A critical component of integrated pest management is minimizing disruption of biological control by reducing use of pesticides with significant non-target effects on natural enemies. Insecticide non-target effects testing for natural enemies has become increasingly common, but research examining the non-target effects of herbicides on natural enemies is scarce and recommendations regarding herbicide selectivity are non-existent. We used meta-analysis to summarize laboratory bioassays testing non-target effects of herbicides on arthropod natural enemies and identify patterns in taxon susceptibility and active ingredient toxicity. Data was extracted from 103 papers representing 801 total observations. Herbicides increased natural enemy mortality and decreased longevity, reproduction, and predation. Mesostigmatan mites and hemipterans were the most sensitive to herbicides and spiders, neuropterans, and hymenopterans were the least sensitive. Mortality was higher in juvenile predators versus parasitoids, but did not differ between adults; parasitoid juveniles are likely better protected within the host. In terms of acute mortality, metribuzin, glufosinate, and oxyfluorfen were the most harmful herbicides. Only nicosulfuron, rimsulfuron, pendimethalin, phenmedipham, atrazine, and urea did not increase natural enemy mortality. The large effect size of glufosinate is particularly concerning, as it is the most likely replacement herbicide for glyphosate in many crops. Many active ingredients remain under-studied. Our analysis indicates that herbicides have a strong potential to disrupt biological control in cropping systems. Simple SummaryReducing the use of pesticides that harm natural enemies of crop pests is important to pest management. Currently, there is limited information on how herbicides might affect natural enemies. The researchers found that herbicides increased natural enemy mortality and reduced their longevity and efficacy as predators. Some potential glyphosate replacement herbicides were more harmful than glyphosate. There was little or no data available for many herbicides and beneficial insects, indicating that much more research is needed on this topic.

ecology↗