Biology subjects

Stankovic, D.

Publications and source records attributed to Stankovic, D..

5 recordsLinked to original sources

bioRxiv2026

Atf3 Integrates Lipid and Cytoskeletal Remodeling to Drive Macrophage Fusion

Macrophages are highly plastic innate immune cells that can form multinucleated giant cells (MGCs) under physiological and pathological conditions, such as osteoclasts and foreign body giant cells. The mechanisms governing macrophage multinucleation remain incompletely understood. Here, we identify activating transcription factor 3 (Atf3) as an essential regulator of MGC formation via cell-cell fusion in response to persistent Interleukin 4 (IL-4) and STAT6 signaling, characteristic of the foreign body reaction. Atf3-deficient macrophages activate STAT6-dependent transcriptional programs in response to IL-4, including fusion-associated genes, yet fail to undergo multinucleation. This defect is associated with impaired actin cytoskeleton remodeling, abnormal nuclear morphology, reduced lamin A/C expression, and genome instability. Mechanistically, loss of Atf3 derepresses the Cholesterol-25-hydroxylase (Ch25h), elevating 25-hydroxycholesterol (25-HC), suppressing the mevalonate pathway, and reducing cholesterol and isoprenoid biosynthesis essential for cytoskeletal dynamics. Deletion of Ch25h in Atf3-deficient macrophages restores cholesterol levels and actin turnover, but not lamin A/C or fusion. These findings establish Atf3 as a central transcriptional node integrating lipid metabolism with cytoskeletal and nucleoskeletal remodeling to control IL-4-driven macrophage multinucleation.

cell biology↗

bioRxiv2025

The Freshwater Sounds Archive

Freshwater ecosystems are full of underwater sounds produced by amphibians, aquatic arthropods, reptiles, plants, fishes, and methane bubbles escaping from the sediment. Although much headway has been made in recent years investigating the overall soundscapes of various freshwater ecosystems around the world, there remains a significant knowledge gap in our collective inability to accurately and reliably link recorded sounds with the species that produced them. Here, we present The Freshwater Sounds Archive, a new global initiative, which seeks to address this knowledge gap by collating species-specific freshwater sound recordings into a publicly available database. By means of metadata collection, we also present a snapshot of the species studied, the recording equipment, and recording parameters used by freshwater ecoacousticians globally. In total, 61 entries were submitted to the archive between the 4th of March 2023 and the 30th of April 2025, representing 16 countries and 6 continents. The most numerous taxonomic group was arthropods (29 entries), followed by fishes (14 entries), amphibians (10 entries), macrophytes (7 entries), and a freshwater mollusk (1 entry). The majority of the submissions were from European countries (27 entries), of which the United Kingdom was the most represented with 14 entries. The next most represented region was North America (11 entries), followed by South America (8 entries), Oceania and Asia (5 entries each), Africa (3 entries), and the Middle East and Central America with 1 entry each. The global south, polar regions, and areas with an elevation >500 m (asl) were underrepresented. The field of freshwater ecoacoustics to date has largely focused on the analysis of sound types due to a current lack of knowledge of species-specific sounds. The Freshwater Sounds Archive presents an opportunity to move beyond the sound type approach, and towards an approach with higher taxonomic resolution, ultimately resulting in species-specific descriptions. Furthermore, The Freshwater Sounds Archive will provide freshwater ecoacousticians with one of the main tools required to start creating annotated training datasets for machine learning models from soundscape recordings by referring to known species sounds present in the archive. In the long-term, this will result in the automatic detection and classification of species-specific freshwater sounds from soundscape recordings, such as indicator, invasive, and endangered species.

ecology↗

bioRxiv2023

Electrochemical biosensor based on NAD(P)H-dependent Quinone Reductase for rapid and efficient detection of vitamin K3

Vitamin K refers to a group of vitamins that play an important role in blood coagulation and regulation of bone and vascular metabolism. However, vitamin K3 may give severe side effects in animal and humans when improperly added to food and feed due to its toxicity. Here, an electrochemical biosensor, based on the YaiB NADPH-dependent quinone reductase from Lactococcus lactis (YaiB), was developed to achieve rapid and redox probe-free detection of vitamin K3. First, we demonstrated the ability of the carbon electrode to distinguish between 1,4-benzoquinone and hydroquinone. Then, we engineered YaiB to work as a bioreceptor immobilized at the electrode and we demonstrated its sensitivity and specificity to reduce vitamin K3. Finally, to demonstrate the practical potential of the biosensor, we tested it directly in spiked milk samples, achieving 15-minute quantification of the vitamin K3. The limit of detection was 0.18M and 0.86 M in buffer and milk, respectively.

biophysics↗

bioRxiv2023

Xrp1 governs the stress response program to spliceosome dysfunction

Co-transcriptional processing of nascent pre-mRNAs by the spliceosome is vital to regulating gene expression and maintaining genome integrity. Here, we show that the deficiency of functional U5 snRNPs in Drosophila imaginal cells causes extensive transcriptome remodeling and accumulation of highly mutagenic R-loops, triggering a robust stress response and cell cycle arrest. Despite compromised proliferative capacity, the U5 snRNP deficient cells increased protein translation and cell size, causing intra-organ growth disbalance before being gradually eliminated via apoptosis. We identify the Xrp1-Irbp18 heterodimer as the primary driver of transcriptional and cellular stress program downstream of U5 snRNP malfunction. Knockdown of Xrp1 or Irbp18 in U5 snRNP deficient cells attenuated JNK and p53 activity, restored normal cell cycle progression and growth, and inhibited cell death. Reducing Xrp1-Irbp18, however, did not rescue the splicing defects and the organismal lethality, highlighting the requirement of accurate splicing for cellular and tissue homeostasis. Our work provides novel insights into the crosstalk between splicing and the DNA damage response and defines the Xrp1-Irbp18 heterodimer as a critical sensor of spliceosome malfunction.

cell biology↗

bioRxiv2022

Drosophila pVALIUM10 TRiP RNAi lines cause undesired silencing of Gateway-based transgenes

Post-transcriptional gene silencing using double-stranded RNA has revolutionized the field of functional genetics, allowing fast and easy disruption of gene function in various organisms. In Drosophila, many transgenic RNAi lines have been generated in large-scale efforts, including the Drosophila Transgenic RNAi Project (TRiP), to facilitate in vivo knockdown of virtually any Drosophila gene with spatial and temporal resolution. The available transgenic RNAi lines represent a fundamental resource for the fly community, providing an unprecedented opportunity to address a vast range of biological questions relevant to basic and biomedical research fields. However, caution should be applied regarding the efficiency and specificity of the RNAi approach. Here, we demonstrate that pVALIUM10-based RNAi lines, representing ~13% of the total TRiP collection (1,808 out of 13,410 TRiP pVALIUM-based RNAi lines), cause unintended off-target silencing of transgenes expressed from Gateway destination vectors generated via site-specific recombination. The silencing is mediated by targeting attB1 and attB2 sequences generated in the recombination reaction and included in the transcribed mRNA. Deleting these attB sites from the Gateway expression vector prevents silencing and restores expected transgene expression.

genetics↗