Biology subjects

Kish, A.

Publications and source records attributed to Kish, A..

6 recordsLinked to original sources

bioRxiv2026

ExocubeBio: an in-situ fluidic platform for microbial exposure on the International Space Station

Space-based platforms currently represent the most accurate means to experimentally assess the influence of the space environment on biological systems. However, performing such experiments remains technically challenging and requires highly specialized instrumentation. This study describes the current development and hardware qualification of ExocubeBio, a miniaturized experimental platform for in-situ biological space exposure. This experiment is scheduled for installation on the exterior of the International Space Station in 2027, as part of Exobio, the European Space Agencys new generation exobiology exposure facility. ExocubeBio will expose live microbial samples to the low Earth orbit environment, and combine autonomous in-situ optical density and fluorescence measurements, with the capacity to return preserved samples to Earth. Achieving these experimental goals requires a specialized, robust and reliable hardware system. The ExocubeBio hardware testing described here includes assessment of material biocompatibility and durability, functional validation of the miniaturized fluidic system, and optimization of the integrated optical subsystem for optical density and fluorescence measurements. These results demonstrate that the ExocubeBio experimental hardware components can each execute their core functional and operational requirements; subsystems allow for sample exposure, in-situ measurements of microbial cultures, and the chemical preservation of samples for post-flight analysis. As ExocubeBio transitions from hardware development to mission readiness, the results presented here validate the overall design and engineering approaches utilized. By combining the strengths of in-situ monitoring and sample return, ExocubeBio represents a significant advancement in space-based experimentation, and will provide new insights into microbial responses to the space environment.

microbiology↗

bioRxiv2026

Fluorescent probes as markers of cell envelope structure and function in halophilic archaea

Prokaryotes, particularly those in extreme environments, are capable of diverse metabolic states resulting in altered cell envelope structure and function. However, these changes are difficult to assess as standard fluorescent probes are often incompatible with extreme conditions and/or extremophile cell physiology. Halophilic archaea present the challenge of near-saturated intra-/extra-cellular salts, high membrane potential, and extended survival in altered metabolic states including entrapped within salt crystal fluid inclusions. We evaluated the compatibility of six fluorescent markers of cell envelope stability and activity with two model species, Halobacterium salinarum and Haloferax volcanii. Redox activity markers alamarBlue and pure resazurin solutions, membrane potential probes MitoTracker Orange-CMTMRos and Rhodamine 123, and SYTO 9 and propidium iodide (LIVE/DEAD kit) to assess cell membrane integrity were evaluated for use in bulk (microplate reader) and cell-specific (microscopy) applications. Limitations of each probe were identified, clarifying the utilization of each based on cell physiology, growth phase, medium composition, and probe exposure time including extended timescales needed to simulate the environmental conditions of haloarchaea. Of particular note, propidium iodide behavior was unreliable leading to double-labeling of cells and false interpretation of cells as dead. These data provide important insights into the study of prokaryotes in non-standard conditions.

microbiology↗

bioRxiv2022

Membrane lipid adaptation of soil Gram-negative bacteria isolates to temperature and pH

3-hydroxy fatty acids (3-OH FAs) are characteristic components of the Gram-negative bacterial membrane, recently proposed as promising temperature and pH (paleo) proxies in soil. Nevertheless, to date, the relationships between the 3-OH FA distribution and temperature/pH are only based on empirical studies, with no work at the microbial level. This work investigated the influence of growth temperature and pH on the lipid profile in three strains of soil Gram-negative bacteria belonging to the Bacteroidetes phylum. Even though the non-hydroxy FAs were more abundant than the 3-OH FAs in the investigated strains, we showed the important role of the 3-OH FAs in the membrane adaptation of Gram-negative bacteria to temperature. The strains shared a common adaptation mechanism to temperature, with a significant increase in the ratio of anteiso vs. iso or normal 3-OH FAs at lower temperature. In contrast with temperature, no common adaptation mechanism to pH was noticed, the variations in the FA lipid profiles differing from one strain to another. The models envisioning the reconstruction of environmental changes in soils should include the whole suite of 3-OH FAs present in the membrane of Gram-negative bacteria, as all of them can be influenced by temperature or pH at the microbial level.

microbiology↗

bioRxiv2022

Molecular Acclimation of Halobacterium salinarum to Halite Brine Inclusions

1Halophilic microorganisms have long been known to survive within the brine inclusions of salt crystals, as evidenced by the change in color for salt crystals containing pigmented halophiles. However, the molecular mechanisms allowing this survival has remained an open question for decades. While protocols for the surface sterilization of halite (NaCl) have enabled isolation of cells and DNA from within halite brine inclusions, "-omics" based approaches have faced two main technical challenges: (1) removal of all contaminating organic biomolecules (including proteins) from halite surfaces, and (2) performing selective biomolecule extractions directly from cells contained within halite brine inclusions with sufficient speed to avoid modifications in gene expression during extraction. In this study, we present methods to resolve these two technical challenges. In addition, we apply these methods to perform the first examination of the early acclimation of a model haloarchaeon (Halobacterium salinarum NRC-1) to halite brine inclusions. Examinations of the proteome of Halobacterium cells two months post-evaporation revealed a high degree of similarity with stationary phase liquid cultures, but with a sharp down-regulation of ribosomal proteins. Low quantities of RNA from halite brine inclusions corroborate the hypothesis of low transcriptional and translational activities. While proteins for central metabolism were part of the shared proteome between liquid cultures and halite brine inclusions, proteins involved in cell mobility (archaellum, gas vesicles) were either absent or less abundant in halite samples. Proteins unique to cells within brine inclusions included transporters, suggesting modified interactions between cells and the surrounding brine inclusion microenvironment. The methods and hypotheses presented here enable future studies of the survival of halophiles in both culture model and natural halite systems.

microbiology↗

bioRxiv2019

The Impact of Glyphosate-Based Herbicides and Their Components on Daphnia Magna

Recent studies suggest glyphosate-based herbicides (GBHs) are more harmful to animals than suggested by the EPA and industry-funded studies. Both glyphosate and the only known \"other\" ingredient in GBHs, polyethoxylated tallow amine (POEA), have been implicated as safety hazards. In this study, we investigated the effects of the commercial GBHs Roundup(R), Rodeo(R) and the two known GBH ingredients, POEA and glyphosate, on the survival and heart rates of Daphnia magna. D. magna were exposed to the retail herbicide mixture and the individual components dissolved in water to mimic possible environmental exposure. When exposed to Roundup(R) and Rodeo(R), D. magna survival and heart rates declined following a dose-response pattern. A commercial formulation of Roundup(R) containing 98% unlisted ingredients had the greatest effect on heart and survival rates, followed by two formulations of Rodeo with 4.62% unlisted ingredients and 1.72% unlisted ingredients, respectively. The Rodeo(R) formulation with 1.72% unlisted ingredients had an equal concentration of glyphosate as the Roundup(R) formulation, suggesting that the negative effects of GBHs are influenced by the unlisted ingredients. Although differences in survival rates were not observed between controls and glyphosate groups, groups exposed to glyphosate alone generally showed a significant (p<0.05) effect on D. magna heart rates. Heart rates following POEA exposure were consistently and, in most cases, significantly (p<0.05) lower than controls. POEA caused a decrease in survival rate for all concentrations, but followed a dose-response pattern only in the three highest concentrations. A Mock-GBH, made with POEA and glyphosate, significantly (p<0.05) lowered heart rates at some higher concentrations, with no dose-response pattern. The Mock-GBH negatively affected survival rates at approximately the same level as POEA alone. The heart rate data suggest that there are undisclosed ingredients in Roundup(R) and Rodeo(R) other than POEA and glyphosate that negatively affect D. magna since glyphosate and POEA combined yielded less pronounced negative responses than the full GBH products.

ecology↗

bioRxiv2018

Novel Mechanism for Surface Layer Shedding and Regenerating in Bacteria Exposed to Metal-Contaminated Conditions

Surface layers (S-layers) are self-assembling, ordered structures composed of repeating protein subunits found as components of the cell walls throughout the Bacteria and the Archaea. S-layers act as an interface between prokaryotic cells and their surrounding environment, and provide protection for microorganisms against diverse environmental stresses including heavy metal stress. We have previously characterized the process by which S-layers serve as a nucleation site for metal mineralization in the presence of high concentration of metals. Here, we test the hypothesis originally proposed in cyanobacteria that a \"shedding\" mechanism exists in prokaryotes for replacing S-layers that have become mineral-encrusted. We used a metallotolerant gram-positive bacterium bearing an S-layer, Lysinibacillus sp. TchIII 20n38, as a model organism. We characterize for the first time a mechanism for resistance to metals through S-layer shedding and regeneration. S-layers nucleate the formation of Fe-mineral on the cell surface, leading to the encrustation of the S-layer. Using a combination of scanning electron microscopy (SEM) and nanoSIMS, we show that mineral-encrusted S-layers are shed by the bacterial cells, and the emerging cells regenerate new S-layers as part of their cell wall structure. This novel mechanism for the survival of prokaryotes in metal-contaminated environments may also provide elements necessary for the development of renewable systems for metal bioremediation.

microbiology↗