Biology subjects

Wacker, S.

Publications and source records attributed to Wacker, S..

7 recordsLinked to original sources

bioRxiv2026

LAMPrEY: a Python-based automated quality control tool for large-scale proteomics datasets

Over the past years, proteomics has moved increasingly towards the analysis of large cohorts of biological specimens. This has been made possible by significant improvements in mass spectrometry technology, chromatographic separation methods, and improved data acquisition strategies. These technological advances now routinely enable experiments that yield vast datasets that substantially outstrip the capacity of existing proteomics data analysis approaches. Processing such large datasets requires purpose-built, quality control tools designed to organize and analyze the data while recording all processing parameters for reproducibility. To address this need, we developed an open-source, Python-based software platform, Large-scale Automated Multi-level Proteomics Evaluation by Python (LAMPrEY), a comprehensive quality-control pipeline for quantitative proteomics analyses of large cohorts of samples. LAMPrEY features GUI-based file submission, automated processing with MaxQuant and RawTools, an interactive analytics dashboard, and an application programming interface (API) for programmatic usage that collectively enable rapid, reproducible analysis and interpretation of proteomics data. We demonstrate the longitudinal monitoring and analytical capabilities of LAMPrEY using TMT11 quantitative proteomics data generated from 910 Enterococcus faecium isolates collected from bloodstream infection patients. LAMPrEY is an open-source software that can be accessed at www.lewisresearchgroup.org/software.

bioinformatics↗

bioRxiv2026

Female-biased sex ratios despite stable genetic sex determination across a climatic gradient in a marine fish

Adult sex ratio (ASR) is a fundamental parameter shaping population dynamics and evolutionary trajectories. In theory, ASR is governed by the sex determination (SD) system and sex-specific mortality. Yet, ASR is often hard to predict in natural populations because of ecological effects on its determinants. We address this ecological complexity by investigating the drivers of ASR across a steep climatic gradient in Scandinavian populations of the two-spotted goby Pomatoschistus flavescens. Demographic surveys accounting for over 25000 fish in 30 locations, spanning 10{degrees} of latitude, revealed a general female-bias of the ASR, ca. 75%. To assess the contribution of SD, we combined reduced representation sequencing of 180 adults with our novel long-read male genome assembly. We characterised the genetic architecture of an XX/XY SD system, and identified a male-specific duplicate from the TGF-{beta} signaling pathway, amhr2y, as a candidate sex-determining gene. Subsequent genotyping of eggs and juveniles showed consistently unbiased sex ratios across latitudes, implying that the female-biased arises at later life stages. Interpreted in the light of historical data, our findings allow us to reject environmental sex determination and sex-biased mortality as important drivers of ASR bias in this species. We propose instead that the female bias originates from sex-specific patterns of habitat distribution, which could result from ecological conditions interacting with the distinct reproductive strategies of females and males. Our results underscore the need to go beyond primary theoretical expectations to understand fundamental demographic parameters within their relevant ecological context.

evolutionary biology↗

bioRxiv2026

Local mating competition, but not climate, drives male reproductive success across a latitudinal gradient in a nest-brooding marine fish

Understanding ecological drivers of reproductive success is crucial to predict whether natural populations can cope with the pace of anthropogenically driven environmental change. In marine ecosystems, this knowledge is difficult to acquire due to the lack of tractable field systems. Here, we took advantage of the nest-brooding behavior of the two-spotted goby Pomatoschistus flavescens, an important planktivorous fish in Scandinavian coastal ecosystems, to study its reproduction across the steep climatic gradient of its natural range. We deployed 360 artificial nests in the field, covering six populations during the breeding season of 2022. We found that climate explained differences among populations in the phenotypes of nest-holding males, and in the impact of both marine growth and parental cannibalism on the broods. In addition, climate affected egg density and diameter. Despite these ecological effects, and although populations differed in average male reproductive success, reproductive success was not influenced by climate. Instead, it was largely determined by competition occurring at the local scale, in particular through the acquisition of high-quality nests, which was itself affected by the relative size of males within the local pool. We propose that the frequency-dependent nature of mating competition may buffer reproductive success against climatic influence in P. flavescens, and discuss the potential generality of such mechanisms and implications for population resilience.

evolutionary biology↗

bioRxiv2024

DigestR an open-source software tool for visualizing LC-MS proteomics data resulting from natural protein catabolism

Protein catabolism is an essential biological function supported by every living organism. Although liquid chromatography mass spectrometry proteomics has advanced considerably over the past decade, protein catabolism in natural systems is still difficult to study. One reason for this is the lack of software tools designed specifically for decoding the complex mixtures of peptides that result from in vivo protein digestion. To address this, we developed DigestR, an open-source software tool designed specifically for the analysis of LC-MS proteomics data. DigestR allows users to visualize naturally occurring peptides and align them to a reference proteome at display them at either a proteome-wide and protein-specific level. These visualization tools allow users to track the patters of peptides occurring in natural systems and map naturally-occurring proteolytic cut sites. To demonstrate these functions, we used DigestR to analyze a mixture of peptides resulting from the in vitro digestion of human hemoglobin and bovine albumin with a cocktail of well characterized proteases. As expected, DigestR correctly identified both the proteins involved and the proteolytic cut sites produced by our protease cocktail. We then used DigestR to analyze the complex semi-ordered hemoglobin digestion pathway used by the malaria parasite Plasmodium falciparum. We show that DigestR successfully identified the proteolytic cut sites linked to the Plasmepsins, a protease known to be involved in hemoglobin digestion by the parasite. Collectively, these findings show that DigestR can be used to help visualize and interpret the complex mixtures of peptides occurring through in vivo protein catabolism. DigestR can be downloaded from www.lewisresearchgroup.org/software.

bioinformatics↗

bioRxiv2024

Sexual display behavior follows consistent sex-specific reaction norms across latitude in response to operational sex-ratio.

Predicting the strength and direction of sexual selection is a challenging task for evolutionary theory, as the effects of ecological factors, social environment, and behavioural plasticity, all need to be taken into account. The Operational Sex Ratio (OSR) is a key variable, which has been shown to (i) affect the strength and direction of mating competition, as a social environment cue, and (ii) be affected itself by ecological conditions through sex-specific environmental effects. Yet, gaining a global view of (i) and (ii) in wild populations represents an arduous but necessary step to further our understanding of sexual selection dynamics in the wild. Here, we address this challenge by using reaction norms. We conducted an extensive field study on the two-spotted goby Pomatoschistus flavescens, monitoring six populations along a latitudinal gradient during an entire breeding season. Doing so, we compared across populations the temporal trajectories in social environment and sexual displays, which is unprecedented. We develop a reaction norm framework based on OSR theory to analyse the data. We show that what appears to be tremendous variation in sexual displays across populations and sampling times, follows consistent rules: sexual display behaviour follows behavioural reaction norms in response to the social environment that are consistent across populations, but social environment fluctuations are specific to each population. Recording behaviour not only over time, but also along a latitudinal gradient where ecological conditions change and in turn affect OSR, was necessary to gain insight into the relationship between social environment and sexual displays, which in turn contributes to sexual selection dynamics.

evolutionary biology↗

bioRxiv2023

SCALiR: a web application for automating absolute quantification of mass spectrometry-based metabolomics data

Metabolomics is an important approach for studying complex biological systems. Quantitative liquid chromatography-mass spectrometry (LC-MS)-based metabolomics is becoming a mainstream strategy but presents several technical challenges that limit its widespread use. Computing metabolite concentrations using standard curves generated from standard mixtures of known concentrations is a labor-intensive process which is often performed manually. Currently, there are few options for open-source software tools that can automatically calculate metabolite concentrations. Herein, we introduce SCALiR (Standard Curve Application for determining Linear Ranges), a new web-based software tool specifically built for this task, which allows users to automatically transform LC-MS signal data into absolute quantitative data (https://www.lewisresearchgroup.org/software). The algorithm used in SCALiR automatically finds the equation of the line of best fit for each standard curve and uses this equation to calculate compound concentrations from their LC-MS signal. Using a standard mix containing 77 metabolites, we found excellent correlation between the concentrations calculated by SCALiR and the expected concentrations of each compound (R2 = 0.99) and that SCALiR reproducibly calculated concentrations of mid-range standards across ten analytical batches (average coefficient of variation 0.091). SCALiR offers users several advantages, including that it (1) is open-source and vendor agnostic; (2) requires only 10 seconds of analysis time to compute concentrations of >75 compounds; (3) facilitates automation of quantitative workflows; and (4) performs deterministic evaluation of compound quantification limits. SCALiR provides the metabolomics community with a simple and rapid tool that enables rigorous and reproducible quantitative metabolomics studies.

biochemistry↗

bioRxiv2018

Two dispersers are better than one: a ‘bird-fig’ attracts bats via nocturnal scent

The plant genus Ficus is a keystone resource in tropical ecoystems. One of the unique features of figs is the diversity of fruit traits, which in many cases match their various dispersers, the so-called fruit syndromes. The classic example of this is the strong phenotypic differences found between figs with bat and bird dispersers (color, size, and presentation). The bird-fig Ficus colubrinae represents an exception to this trend since it attracts the small frugivorous bat species Ectophylla alba at night, but during the day attracts bird visitors. Here we investigate the mechanism by which this bird-fig attracts bats despite its fruit traits, which should appeal solely to birds. We performed feeding experiments with Ectophylla alba to assess the role of fruit scent in the detection of ripe fruits. Ectophylla alba was capable of finding ripe figs by scent alone under exclusion of other sensory cues. This suggests that scent is the main foraging cue for Ectophylla alba. Analyses of odor bouquets from the bat- and bird-dispersal phases (i.e. day and night) differed significantly in their composition of volatiles. The combination of these two findings raises the question whether E. alba and F. colubrinae resemble a co-adaptation that enables a phenotypically classic bird-fig to attract bat dispersers by an olfactory signal at night thus maximizing dispersal.

ecology↗