Biology subjects

Salek, M.

Publications and source records attributed to Salek, M..

9 recordsLinked to original sources

bioRxiv2026

Population collapse of the Egyptian fruit bat on Cyprus (2005-2022) was likely driven by roost disturbance and declining food availability linked to climate change

Peripheral island populations are often especially vulnerable to environmental change, yet they may also represent unique components of biodiversity. We assessed long-term population change in the Egyptian fruit bat (Rousettus aegyptiacus) on Cyprus, the only insular and geographically isolated population of this pteropodid in Europe, and evaluated two non-exclusive explanations for its decline: roost disturbance and reduced food availability. We analysed roost counts from 21 underground sites monitored between 2005 and 2022 and modelled temporal trends in commercially produced fruits used by the species. The monitored population declined from c. 7200 to c. 1050 individuals, corresponding to an estimated decrease of 85.4%. The decline was steepest during 2005-2011, slowed during 2012-2017, and was followed by partial recovery in 2018-2022. Colonies in easily accessible roosts declined significantly faster than those in less accessible roosts, consistent with an important role of human disturbance. Fruit production showed strong long-term declines and multiple structural breaks clustered in the mid-2000s, coinciding with the most severe phase of population decline and a major drought period on Cyprus. The fate of the missing portion of the population remains uncertain. Although large-scale mortality cannot be excluded, there was no clear evidence of widespread starvation-related mortality, and emigration to nearby mainland areas remains a plausible but untested explanation. Overall, our results indicate that the collapse of this peripheral island population was most likely driven by a combination of roost disturbance and reduced food availability associated with climate-related environmental change, highlighting the urgent need for strict roost protection and measures to secure food and water resources.

ecology↗

bioRxiv2026

Investigation of sterile hydrogels as topical vehicles for APOSEC™, a stressed peripheral blood mononuclear cell secretome for the treatment of poorly healing wounds

APOSECTM, a complex mixture of secreted proteins, lipids, and extracellular vesicles from stressed peripheral blood monocytes, is currently in clinical trials for the treatment of chronic, poorly healing wounds. When applied to open wounds, 1 mL reconstituted APOSECTM lyophilisate is syringe-mixed with 3 g sterile hydrogel prior to administration. This study investigates the pharmaceutical performance of this novel administration system. A gel formulation (APOgel) was developed for terminal sterilisation in pre-filled syringes with post-sterilisation viscosity ([~]325-350{square}Pa*s at 1{square}s-1) comparable to a commercial benchmark gel. Syringe mixing of APOgel with a liquid APOSECTM surrogate (3:1) reduced viscosity by [~]67% but was highly reproducible across different operators (CV < 6%). Administration of three sequential dose units of the mixture from the syringe revealed an [~]20% higher content of active ingredients in the first and final dispensed compared to the middle unit, indicating non-uniform mixing in the closed syringe system. In vitro release studies over 72{square}h showed a 32% and 48% higher release of a small molecule marker and total proteins from the sterile APOgel compared to the benchmark gel as well as more pronounced gel swelling. However, efficacy studies in a murine wound healing model showed no significant difference between APOgel and the benchmark. These findings indicate that terminal sterilisation of gels for topical applications may provide benefits for more rapid release of active agents but syringe mixing of gels and a liquid requires optimisation to ensure uniform drug distribution. HighlightsO_LIAn autoclavable hydrogel for APOSECTM delivery was developed C_LIO_LIA novel syringe-mixing system for combining a gel with a liquid with subsequent dispensing of different volume units showed non-homogenous active ingredient distribution C_LIO_LIFinal optimised APOSECTM-APOgel formulation maintains functional wound-healing efficacy C_LI

pharmacology and toxicology↗

bioRxiv2025

Social environment affects vocal individuality in a non-learning species

Individual recognition is fundamental to the social behaviour of many animals. In high-density populations, animals encounter and compete with conspecific rivals more frequently, which should enhance the individuality of their signals to facilitate recognition among neighbours. We investigated vocal individuality in male territorial calls of two populations of little owls (Athene noctua) with different densities. Further, to explore the potential influence of local population distribution on individuality, we also examined isolated males without neighbours and clumped males with neighbours. Our findings indicate higher individuality at higher densities across both scenarios, measured using two individuality metrics: Beechers information statistic and Discrimination score. Additionally, clumped males exhibited significantly lower acoustic niche overlaps compared to isolated males, suggesting that the immediate social environment might be more influential than larger-scale population density patterns. This study is the first to demonstrate that vocal individuality in a territorial species is influenced by conspecific density, similar to findings in group-living and colonial species.

animal behavior and cognition↗

bioRxiv2023

Single nucleus RNA sequencing reveals glial cell type-specific responses to ischemic stroke

Reactive neuroglia critically shape the brains response to ischemic stroke. However, their phenotypic heterogeneity impedes a holistic understanding of the cellular composition and microenvironment of the early ischemic lesion. Here we generated a single cell resolution transcriptomics dataset of the injured brain during the acute recovery from permanent middle cerebral artery occlusion. This approach unveiled infarction and subtype specific molecular signatures in oligodendrocyte lineage cells and astrocytes, which ranged among the most transcriptionally perturbed cell types in our dataset. Specifically, we characterized and compared infarction restricted proliferating oligodendrocyte precursor cells (OPCs), mature oligodendrocytes and heterogeneous reactive astrocyte populations. Our analyses unveiled unexpected commonalities in the transcriptional response of oligodendrocyte lineage cells and astrocytes to ischemic injury. Moreover, OPCs and reactive astrocytes were involved in a shared immuno-glial cross talk with stroke specific myeloid cells. In situ, osteopontin positive myeloid cells accumulated in close proximity to proliferating OPCs and reactive astrocytes, which expressed the osteopontin receptor CD44, within the perilesional zone specifically. In vitro, osteopontin increased the migratory capacity of OPCs. Collectively, our study highlights molecular cross talk events which might govern the cellular composition and microenvironment of infarcted brain tissue in the early stages of recovery.

neuroscience↗

bioRxiv2023

optiPRM: A targeted immunopeptidomics LC-MS workflow with ultra-high sensitivity for the detection of mutation-derived tumor neoepitopes from limited input material

Personalized cancer immunotherapies such as vaccines and T cell receptor (TCR)-transgenic T cells rely on the presentation of tumor-specific peptides by human leukocyte antigen (HLA) class I molecules to cytotoxic T cells. Such neoepitopes can for example arise from somatic mutations and their identification is crucial for the rational design of new therapeutic interventions. For their detection by liquid chromatography mass spectrometry (LC-MS), we have developed a parameter optimization workflow to tune targeted assays for maximum detection sensitivity on a per peptide basis, termed optiPRM. Optimization of collision energy using optiPRM allows for improved detection of low abundant peptides that are very hard to detect using standard parameters. Applying this to immunopeptidomics, we detected a neoepitope in a patient-derived xenograft (PDX) from as little as 2.5x106 cells input. Application of the workflow on small patient tumor samples allowed for the detection of five mutation-derived neoepitopes in three patients. One neoepitope was confirmed to be recognized by patient T cells. In conclusion, we here present optiPRM, a targeted MS workflow reaching ultra-high sensitivity by per peptide parameter optimization, which allowed for the identification of actionable neoepitopes from sample sizes usually available in the clinic.

immunology↗

bioRxiv2022

Realtime morphological characterization and sorting of unlabeled viable cells using deep learning

Phenotyping of single cells has dramatically lagged advances in molecular characterization and remains a manual, subjective, and destructive process. We introduce COSMOS, a platform for phenotyping and enrichment of cells based on deep learning interpretation of high-content morphology data in realtime. By training models on an atlas of >1.5 billion images, we demonstrate enrichment of unlabeled cells up to 33,000 fold. We apply COSMOS to multicellular tissue biopsy samples demonstrating that it can identify malignant cells with similar accuracy to molecular approaches while enriching viable cells for functional evaluation. We show high-dimensional embedding vectors of morphology generated by COSMOS without any need for complex sample pre-processing, gating, or bioinformatics capabilities, which enables discovery of cellular phenotypes, and integration of morphology into multi-dimensional analyses. One sentence summaryA novel platform capable of high-throughput imaging and gently sorting cells using deep morphological assessment.

cell biology↗

bioRxiv2021

Light contamination in stable isotope-labelled internal peptide standards is frequent and a potential source of false discovery and quantitation error in proteomics

In mass spectrometry-based proteomics, heavy internal standards are used to validate target peptide detections and to calibrate peptide quantification. Here we report light contamination present in heavy labelled synthetic peptides of high isotopic enrichment. Application of such peptides as assay-internal standards potentially compromises the detection and quantification especially of low abundant cellular peptides. Therefore, it is important to adopt guidelines to prevent false-positive identifications of endogenous light peptides as well as errors in their quantification from biological samples.

biochemistry↗

bioRxiv2019

Measuring individual identity information in animal signals: Overview and performance of available identity metrics

O_LIIdentity signals have been studied for over 50 years but there is no consensus as to how to quantify individuality. While there are a variety of different metrics to quantify individual identity, or individuality, these methods remain un-validated and the relationships between them unclear. C_LIO_LIWe contrasted three univariate and four multivariate metrics (and their different computational variants) and evaluated their performance on simulated and empirical datasets. C_LIO_LIOf the metrics examined, Beechers information statistic (HS) was the best one and could easily and reliably be converted into the commonly used discrimination score (and vice versa) after accounting for the number of individuals and calls per individual in a given dataset. Although Beechers information statistic is not entirely independent of sampling parameters, this problem can be removed by reducing the number of parameters or by increasing the number of individuals. C_LIO_LIBecause it is easily calculated, has superior performance, can be used to describe single variables or signal as a whole, and because it tells us the maximum number of individuals that can be discriminated given a set of measurements, we recommend that individuality should be quantified using Beechers information statistic. C_LI

ecology↗

bioRxiv2018

Diverse incubation rhythms in a facultatively uniparental shorebird -- the Northern Lapwing

Incubation by both parents is the most common form of care for eggs. Although the involvement of the two parents may vary dramatically between and within pairs, as well as over the day and breeding season, detailed description of this variation (especially in species with variable male contribution to incubation) is rare. Here, we continuously video-monitored 113 nests of Northern Lapwing Vanellus vanellus over the breeding season to reveal the diversity of incubation rhythms and parental involvement. We found great between-nest variation in the overall nest attendance (68 -94%; median = 87%) and in how much males incubated (0 - 37%; median = 13%). Notably, the less the males incubated, the lower was the overall nest attendance, even though females partially compensated for the males decrease. Overall, incubation rhythms changed little over the season and incubation period. However, as nights shorten with the progressing breeding season, the female longest night incubation bout shortened too. Essentially, nest attendance was highest, incubation bouts longest, exchange gaps shortest and male involvement lowest during the night. Also, males tended to incubate the most after sunrise and before sunset. To conclude, we revealed strong circadian rhythms and remarkable between nest differences in Northern Lapwing incubation (especially in male involvement), yet despite seasonal environmental trends (e.g. increasing temperature) Lapwing incubation rhythms remained relatively stable over the season and incubation period.

animal behavior and cognition↗