Biology subjects

Frey, D.

Publications and source records attributed to Frey, D..

4 recordsLinked to original sources

bioRxiv2023

Distribution of the invasive Anisandrus maiche (Coleoptera: Scolytinae) in Switzerland, first record in Europe of its ambrosia fungus Ambrosiella cleistominuta, and its new association with Xylosandrus crassiusculus

In 2022, two independent insect surveys in canton Ticino (southern Switzerland) revealed the widespread occurrence of the invasive ambrosia beetle Anisandrus maiche from southern to central-upper Ticino. This species is native to east Asia and has previously been found as a non-native invasive species in the United States, Canada, western Russia, Ukraine and, in 2021, in northern Italy. Here, we present the results of several trapping studies using different trap types (bottle traps, funnel traps and Polytrap intercept traps) and attractants and a map of the distribution of the species. In total, 685 specimens of A. maiche, all female, were trapped, and the identity of selected individuals was confirmed by morphological and molecular identification based on three mitochondrial and nuclear markers (COI, 28S and CAD). Traps checked from early April to early September 2022 in intervals of two to four weeks showed that flights of A. maiche occurred mainly from June to mid-August. Isolation of fungal associates of A. maiche from beetles trapped alive revealed the presence of four fungal species, including the ambrosia fungus Ambrosiella cleistominuta, the known mutualists of A. maiche. The identity of A. cleistominuta was confirmed by comparing DNA sequences of its nuclear, internal transcribed spacer (ITS) gene with reference sequences in NCBI and BOLDSYSTEMS. This represents the first record of A. cleistominuta in Europe. Ambrosiella cleistominuta was also found in association with another non-native invasive ambrosia beetle, Xylosandrus crassiusculus, at a botanic garden in central Ticino. As ambrosia beetles usually show a high degree of fidelity with only one mutualistic fungus (in the case of X. crassiusculus normally Ambrosiella roeperi), this association is highly unusual and probably the result of lateral transfer among these non-native invasive species. Of the other fungal associates isolated from A. maiche in Ticino, Fusarium lateritium is of note as there is a possibility that A. maiche could act as a vector of this plant pathogen. We highlight several research needs that should be addressed to gain insight into the potential impact of these non-native species and to overcome problems with heteroplasmy in COI sequences in studies of invasion and population genetics of ambrosia beetles.

ecology↗

bioRxiv2022

An approach to rapid distributed manufacturing of broad spectrum anti-viral griffithsin using cell-free systems to mitigate pandemics

This study describes the cell-free biomanufacturing of a broad-spectrum antiviral protein, griffithsin (GRFT) such that it can be produced with consistent purity and potency in less than 24 hours. We demonstrate GRFT production using two independent cell-free systems, one plant and one microbial. Griffithsin purity and quality were verified using standard regulatory metrics. Efficacy was demonstrated in vitro against SARS-CoV-2 and HIV-1 and was nearly identical to that of GRFT expressed in vivo. The proposed production process is efficient and can be readily scaled up and deployed anywhere in the world where a viral pathogen might emerge. The current emergence of viral variants has resulted in frequent updating of existing vaccines and loss of efficacy for front-line monoclonal antibody therapies. Proteins such as GRFT with its efficacious and broad virus neutralizing capability provide a compelling pandemic mitigation strategy to promptly suppress viral emergence at the source of an outbreak.

bioengineering↗

bioRxiv2022

A Coiled-Coil-Based Design Strategy for the Thermostabilization of G-Protein-Coupled Receptors

The most common methods for generating crystallizable GPCRs are scanning alanine mutagenesis and fusion to crystallization-facilitating partner proteins. The major goal of our work was to create a new GPCR tool that would provide receptor stability and additional soluble surface for crystallization. Towards this aim, we selected the two-stranded antiparallel coiled coil as a domain fold that satisfies both criteria. A selection of antiparallel coiled coils was used for structure-guided substitution of intracellular loop of the {beta}3 adrenergic receptor. Unexpectedly, only the two GPCR variants containing thermostable coiled coils were expressed. We showed that one GPCR chimera is stable upon purification in detergent, retains ligand-binding properties, and can be crystallized. However, the quality of the crystals was not suitable for structure determination. To supply additional surface for promoting crystal contacts, we replaced in a structure-based approach the loop of the antiparallel coiled coil by T4L. Although expression is currently not suitable for structural work, we found that the engineered GPCR is even more stable than the coiled-coil variant. Our approach should be of interest for applications that benefit from stable GPCRs.

biophysics↗

bioRxiv2019

A framework for testing different imputation methods for tabular datasets

Background and purposeHandling missing values is a prevalent challenge in the analysis of clinical data. The rise of data-driven models demands an efficient use of the available data. Methods to impute missing values are thus crucial. Here, we developed a publicly available framework to test different imputation methods and compared their impact in a typical stroke clinical dataset as a use case.\n\nMethodsA clinical dataset based on the 1000Plus stroke study with 380 completed-entries patients was used. 13 common clinical parameters including numerical and categorical values were selected. Missing values in a missing-at-random (MAR) and missing-completely-at-random (MCAR) fashion from 0% to 60% were simulated and consequently imputed using the mean, hot-deck, multiple imputation by chained equations, expectation maximization method and listwise deletion. The performance was assessed by the root mean squared error, the absolute bias and the performance of a linear model for discharge mRS prediction.\n\nResultsListwise deletion was the worst performing method and started to be significantly worse than any imputation method from 2% (MAR) and 3% (MCAR) missing values on. The underlying missing value mechanism seemed to have a crucial influence on the identified best performing imputation method. Consequently no single imputation method outperformed all others. A significant performance drop of the linear model started from 11% (MAR+MCAR) and 18% (MCAR) missing values.\n\nConclusionsIn the presented case study of a typical clinical stroke dataset we confirmed that listwise deletion should be avoided for dealing with missing values. Our findings indicate that the underlying missing value mechanism and other dataset characteristics strongly influence the best choice of imputation method. For future studies with similar data structure, we thus suggest to use the developed framework in this study to select the most suitable imputation method for a given dataset prior to analysis.

neuroscience↗