Biology subjects

Pfeiffer, P.

Publications and source records attributed to Pfeiffer, P..

5 recordsLinked to original sources

bioRxiv2026

Next-generation insect digitization: combining phenomics and genomics by subsequent synchrotron X-ray imaging and DNA sequencing

Recent technological advances allow for the large-scale acquisition of genetic and morphological data: high-throughput sequencing has transformed the field of genomics while synchrotron X-ray microtomography enables rapid, noninvasive 3D imaging. However, integrating these approaches for the same specimens is challenging because X-rays can fragment DNA, and DNA extraction damages internal morphology, particularly relevant for small bodied organisms, such as insects. We systematically tested multiple extraction protocols and irradiation conditions across three model insect species. We irradiated more than 1,000 specimens under varying conditions and tested DNA quality through DNA barcoding and UCE sequencing. Our results demonstrate that high-quality DNA and high-resolution tomograms can be obtained from the same individuals, provided that the parameters are carefully optimized and rapid SR-CT scanning precedes DNA extraction. In this respect, our findings establish practical guidelines for combining genomics and phenomics, paving the way for comprehensive integrative digitization of biodiversity.

genetics↗

bioRxiv2024

Towards routine proteome profiling of FFPE tissue: Insights from a 1,200 case pan-cancer study

Proteome profiling of formalin-fixed paraffin-embedded (FFPE) specimens has gained traction for the analysis of cancer tissue for the discovery of molecular biomarkers. However, reports so far focused on single cancer entities, comprised relatively few cases and did not assess the long-term performance of experimental workflows. Here, we did so by analyzing 1,220 tumors from six cancer entities processed over the course of three years. Key findings include the need for a new normalization method ensuring equal and reproducible sample loading for LC-MS/MS analysis across cohorts, showing that tumors can, on average, be profiled to a depth of >4,000 proteins and discovering that current software fails to process such large data sets. We report the first comprehensive pan-cancer proteome expression resource for FFPE material comprising 11,000 proteins which is of immediate utility to the scientific community by way of a web resource. It enables a range of analysis including quantitative comparisons of proteins between patients or cohorts or the discovery of protein fingerprints representing the tissue of origin, or proteins enriched in certain cancer entities.

pathology↗

bioRxiv2023

Environmental variables and species traits as drivers of wild bee pollination in intensive agroecosystems -a metabarcoding approach

Wild bees are known to be efficient pollinators of wild plants and cultivated crops and they are essential ecosystem service providers. However, wild bee populations have been suffering from significant declines in the last decades mainly due to the use of agrochemicals. Within this framework, we aimed to characterize wild bees pollination spectrum (i.e. the community of pollinated flowering plants) in intensive agroecosystems, and describe the environmental variables and wild bee species traits influencing the pollination. To do this, we conducted metabarcoding analyses of pollen loads from wild bees collected in sunflower crops in the French region of Nouvelle-Aquitaine. Our study revealed that wild bees visited flowering plants corresponding to 231 different Operational Taxonomic Units, classified in 38 families of which Asteraceae, Brassicaceae and Apiaceae were the most visited and more than 90% of the visited taxa turned out to be wild flowers. We also analysed the potential effect of environmental variables and wild bee species traits in governing their choice of pollinated plants. The community composition of pollinated plants varied depending on the flowering stages of the sunflower and the farming system. Our results also show that pollination niche breadth (alpha diversity) varied depending on the flowering stages of the sunflower but was not different between organic and conventional farming systems. Regarding wild bee species traits, the community composition of pollinated plants varied in relation to wild bees body sizes and, sociality levels. Our results are consistent with previous studies, suggesting that solitary bees are more specialists when it comes to flower selection than social bees, which are more generalist. The metabarcoding of pollen loads enabled us to draw a global picture of plant-wild bee interactions in an intensive agroecosystem. Our findings support the hypothesis that a higher diversity of weeds may increase wild bee diversity in intensive agroecosystems.

ecology↗

bioRxiv2021

A dynamic clamp protocol to artificially modify cell capacitance

AO_SCPLOWBSTRACTC_SCPLOWDynamics of excitable cells and networks depend on the membrane time constant, set by membrane resistance and capacitance. Whereas pharmacological and genetic manipulations of ionic conductances are routine in electrophysiology, experimental control over capacitance remains a challenge. Here, we present capacitance clamp, an approach that allows to mimic a modified capacitance in biological neurons via an unconventional application of the dynamic clamp technique. We first demonstrate the feasibility to quantitatively modulate capacitance in a mathematical neuron model and then confirm the functionality of capacitance clamp in in vitro experiments in granule cells of rodent dentate gyrus with up to threefold virtual capacitance changes. Clamping of capacitance thus constitutes a novel technique to probe and decipher mechanisms of neuronal signaling in ways that were so far inaccessible to experimental electrophysiology.

neuroscience↗

bioRxiv2021

Exosome TDP-43 profile in canine model of ALS: A preliminary study in developing surrogate biomarker

ObjectiveBlood-based biomarkers provide a crucial information in progress of neurodegenerative diseases with minimally invasive sampling method. Validated blood-based biomarker application in people with amyotrophic lateral sclerosis would derive numerous benefits. Canine degenerative myelopathy is a naturally occurring animal disease model to study the biology of human amyotrophic lateral sclerosis. Serum derived exosomes are potential carriers for cell-specific cargoes making them ideal venue to study biomarkers for a variety of diseases and biological processes. This study assessed the exosomal proteins that may be assigned as surrogate biomarker that may reflect biochemical changes in central nervous system. MethodsExosomes were isolated from canine serum using commercial exosome isolation reagents. Exosomes target proteins contents were analysed by Western blotting method. ResultsThe profiles of potential biomarker candidates in spinal cord homogenate and that of serum-derived exosomes were found elevated in dogs with degenerative myelopathy as compare to control subjects. ConclusionsSerum-derived exosomal biomolecules can serve as surrogate biomarkers in neuro degenerative diseases. Key MessagesO_LIA canine with degenerative myelopathy can serve as a model animal to study human amyotrophic lateral sclerosis. C_LIO_LISerum-derived exosomes contains Transactive Response DNA Binding Protein 43 (TDP-43), potential biomarker candidate. C_LIO_LIThe levels of spinal cord TDP-43 proteins and that of serum-derived exosomes exhibited a similar profiling. Therefore, serum derived exosomes may be used as a venue for establishing blood-based biomarkers for neurodegenerative diseases. C_LI

neuroscience↗