Biology subjects

Kostal, V.

Publications and source records attributed to Kostal, V..

5 recordsLinked to original sources

bioRxiv2025

Endogenous circannual cycles drive seasonal cold hardening in temperate ants

The ability to acquire cold tolerance and cope with seasonality underlies the broad geographical distribution of ectotherms. Among insects, cold-adapted ants, which are successful terrestrial insects in temperate and boreal ecosystems, rely on complex circannual life cycles to survive multiple consecutive winters. Following winter reactivation, colonies enter a fixed developmental phase whose duration is controlled by "Kipyatkovs sand-glass device", an endogenous programmed timer that ultimately enforces a new dormancy period for colonies after a set period, even under permissive light or temperature cues. Here, using five temperate ant species, we leveraged this system to tease apart the contribution of intrinsic seasonal programming and extrinsic thermal cues on worker cold tolerance, metabolic rates, and metabolomic profiles. We show that obligate colony-level dormancy alone is sufficient to modulate both the critical thermal minimum (CTmin) and the temperature causing 50% mortality during acute cold exposure (LTe50), and further interacts with cold acclimation to shape worker phenotypic cold tolerance. While colony-level dormancy was only associated with limited metabolomic reorganization, cold acclimation triggered the accumulation of metabolites potentially involved in osmotic balance and membrane reorganization. Our results highlight a circannual cycle of endogenous cold hardening that operates independently of environmental exposure in temperate ants, providing new insight into the physiological adaptations underpinning the evolutionary success of this insect family in highly seasonal climates.

evolutionary biology↗

bioRxiv2024

Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters for Glycosaminoglycans via Ab Initio Molecular Dynamics Simulations

Glycosaminoglycans (GAGs) are negatively charged polysaccharides found on cell surfaces, where they regulate transport pathways of foreign molecules toward the cell. The structural and functional diversity of GAGs is largely attributed to varied sulfa-tion patterns along the polymer chains, which makes understanding their molecular recognition mechanisms crucial. Molecular dynamics (MD) simulations, with their un-matched microscopic perspective, have the potential to be a reference tool for exploring the patterns responsible for biologically relevant interactions. However, the capability of molecular dynamics models (i.e., force fields) used in biosimulations to accurately capture sulfation-specific interactions is not well established. In this work, we evalu-ate the performance of molecular dynamics force fields for sulfated GAGs by studying ion pairing of Ca2+ to sulfated moieties -- N-methylsulfamate and methylsulfate -- that resemble N- and O-sulfation found in GAGs, respectively. We tested nonpolariz-able (CHARMM36 and GLYCAM06), explicitly polarizable (Drude and AMOEBA), and implicitly polarizable through charge scaling (prosECCo75 and GLYCAM-ECC75) force fields. The Ca-sulfamate/sulfate interaction free energy profiles obtained with the tested force fields were compared against reference ab initio molecular dynamics (AIMD) simulations. AIMD reveals that the preferential Ca2+ binding mode to sul-fated GAG groups is solvent-shared pairing, and only the charge-scaled models agree satisfactorily with the AIMD data. All other force fields exhibit poorer performance, sometimes even qualitatively. Surprisingly, even explicitly polarizable force fields dis-play a notable shortfall in their performance, attributed to difficulties in their optimiza-tion and possible inherent limitations in depicting high-charge-density ion interactions accurately. Finally, the underperforming force fields lead to unrealistic aggregation of sulfated saccharides, qualitatively distorting our understanding of the soft glycocalyx environment. Our results highlight the importance of accurately treating electronic polarization in MD simulations of sulfated GAGs and caution against over-reliance on currently available models without thorough validation and optimization.

biophysics↗

bioRxiv2022

Insect cell plasma membranes do, while soluble enzymes do not, need stabilization by accumulated cryoprotectant molecules during freezing stress.

Ability to survive freezing of extracellular body fluids evolved in several species of vertebrate ectotherms, many plants, and occurs relatively often in freeze-tolerant insects. Most of the multicellular organisms, however, are freeze-sensitive. Here we test coupled hypotheses postulating that: (i) irreversible denaturation of proteins and loss of integrity of biological membranes are two ultimate molecular mechanisms of freezing injury in freeze-sensitive insects; and (ii) seasonally accumulated small cryoprotective molecules (CPs) protect the proteins and membranes against the injury in freeze-tolerant insects. We show that seven different enzymes exhibit no or only partial loss of activity upon lethal freezing stress applied in vivo to whole freeze-sensitive larva of drosophilid fly, Chymomyza costata. In contrast, the enzymes lost activity when extracted and frozen in vitro in a diluted buffer solution. This loss of activity was fully prevented by adding to buffer relatively low concentrations of a wide array of different compounds including C. costata native CPs, other metabolites, bovine serum albumin (BSA), and even biologically inert artificial compounds Histodenz and Ficoll. Next, we show that the plasma membranes of fat body cells lose integrity when frozen in vivo in freeze-sensitive but not in freeze-tolerant larvae. Freezing fat body cells in vitro, however, resulted in loss of membrane integrity in both freeze-sensitive and freeze-tolerant larvae. Different additives showed widely different capacities (from none to high) to protect membrane integrity when added to in vitro freezing medium. A complete rescue of membrane integrity was observed for a mixture of proline, trehalose and BSA. Significance statementHere we suggest that insect soluble enzymes are not primary targets of freezing injury. They are not inactivated in freeze-sensitive insects exposed to lethal freezing stress as they are sufficiently protected from loss of activity by complex composition of native biological solutions. Next we show that cell plasma membranes are likely targets of freezing injury. The membranes lose integrity in freeze-sensitive insects exposed to freezing stress, while their integrity is protected by accumulated small cryoprotective molecules, and also by proteins, in freeze-tolerant insects.

physiology↗

bioRxiv2021

A mixture of innate cryoprotectants is key for cryopreservation of a drosophilid fly larva.

Insects that naturally tolerate internal freezing produce complex mixtures of multiple cryoprotectants (CPs). Better knowledge on composition of these mixtures, and on mechanisms of how the individual CPs interact, could inspire development of laboratory CP formulations optimized for cryopreservation of cells and other biological material. Here we identify and quantify (using high resolution mass spectrometry) a range of putative CPs in larval tissues of a subarctic fly, Chymomyza costata that survives long-term cryopreservation in liquid nitrogen. The CPs (proline, trehalose, glutamine, asparagine, glycine betaine, glycerophosphoethanolamine, glycerophosphocholine, and sarcosine) accumulate in hemolymph in a ratio of 313:108:55:26:6:4:3:0.5 mmol.L-1. Using calorimetry, we show that the artificial mixtures, mimicking the concentrations of major CPs in hemolymph of freeze-tolerant larvae, suppress the melting point of water and significantly reduce the ice fraction. We demonstrate in a bioassay that mixtures of CPs administered through the diet act synergistically rather than additively to enable cryopreservation of otherwise freeze-sensitive larvae. Using MALDI-MSI, we show that during slow extracellular freezing trehalose becomes concentrated in partially dehydrated hemolymph where it stimulates transition to the amorphous glass phase. In contrast, proline moves to the boundary between extracellular ice and dehydrated hemolymph and tissues where it likely forms a layer of dense viscoelastic liquid. We propose that amorphous glass and viscoelastic liquids may protect macromolecules and cells from thermomechanical shocks associated with freezing and transfer into and out of liquid nitrogen. Summary statementThe composition of natural cryoprotectant mixture of the extremely freeze-tolerant insect is revealed. Components of the mixture work in synergy and behave differently during organismal freezing and cryopreservation.

physiology↗

bioRxiv2020

Highly contiguous assemblies of 101 drosophilid genomes

Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long read sequencing allow high quality genome assemblies for tens or even hundreds of species to be generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of high-quality assemblies for 101 lines of 95 drosophilid species encompassing 14 species groups and 35 sub-groups with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. These assemblies, along with detailed wet lab protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution within this key group.

evolutionary biology↗