Biology subjects

Kaminsky, J.

Publications and source records attributed to Kaminsky, J..

5 recordsLinked to original sources

bioRxiv2025

Cryogenic 3D electron microscopy captures whole plant cell native ultrastructure

Volume electron microscopy (vEM) provides nanometer-scale, three-dimensional imaging of cells, but applying it to plant systems remains challenging. Cell walls, large vacuoles, and tissue thickness complicate sample preparation and cryogenic imaging. Here we report a cryogenic vEM (cryo-vEM) workflow for unstained plant protoplasts that achieves volumetric imaging of whole vitrified sorghum stem protoplasts without chemical fixation, dehydration, resin embedding, or heavy-metal staining. The method integrates optimized protoplast isolation, plunge-freezing vitrification for native-state preservation, automated cryogenic focus ion beam scanning electron microscopy (cryo-FIB-SEM) slice-and-view acquisition, contrast enhancement and stack alignment, and AI-assisted human-in-the-loop 3D segmentation. Using sorghum stem protoplasts as a demonstration, the workflow captured large-volume frozen-hydrated protoplast ultrastructure, allowing visualization of major organelles, including the nucleus, mitochondria, vacuoles, ER/Golgi-like membranes, lipid bodies, and subcellular features consistent with nuclear-envelope pores. We further quantified organelle volumes and surface areas from the segmented 3D data, highlighting the potential for quantitative cellular ultrastructure analysis. This cryo-vEM workflow provides a platform for near-native structural studies of isolated plant protoplasts.

plant biology↗

bioRxiv2023

Non-glycosylated IGF2 prohormones are more mitogenic than native IGF2

Insulin-like Growth Factor-2 (IGF2) is important for the regulation of human embryonic growth and development, and for adults physiology. Incorrect processing of the IGF2 precursor, pro-IGF2(156), leads to the formation of two IGF2 proforms, big-IGF2(87) and big-IGF2(104). Unprocessed and mainly non-glycosylated IGF2 proforms are found at abnormally high levels in certain diseases, but their mode of action is still unclear. Here, we found that pro-IGF2(156) has the lowest ability to form its inactivating complexes with IGF-Binding Proteins and has higher proliferative properties in cells than IGF2 and other IGF prohormones. We also showed that big-IGF2(104) has a seven-fold higher binding affinity for the IGF2 receptor than IGF2, and that pro-IGF2(87) binds and activates specific receptors and stimulates cell growth similarly to the mature IGF2. The properties of these pro-IGF2 forms, especially of pro-IGF2(156) and big-IGF2(104), indicate them as hormones that may be associated with human diseases related to the accumulation of IGF-2 proforms in the circulation.

biochemistry↗

bioRxiv2021

Use of Raman and Raman optical activity to extract atomistic details of saccharides in aqueous solution

Sugars are crucial components in biosystems and industrial applications. In aqueous environments, the natural state of short saccharides or charged glycosaminoglycans is floating and wiggling in solution. Therefore, tools to characterize their structure in a native aqueous environment are crucial but not always available. Here, we show that a combination of Raman/ROA and, on occasions, NMR experiments with Molecular Dynamics (MD) and Quantum Mechanics (QM) is a viable method to gain insights into structural features of sugars in solutions. Combining these methods provides information about accessible ring puckering conformers and their proportions. It also provides information about the conformation of the linkage between the sugar monomers, i.e., glycosidic bonds, allowing for identifying significantly accessible conformers and their relative abundance. For mixtures of sugar moieties, this method enables the deconvolution of the Raman/ROA spectra to find the actual amounts of its molecular constituents, serving as an effective analytical technique. For example, it allows calculating anomeric ratios for reducing sugars and analyzing more complex sugar mixtures to elucidate their real content. Altogether, we show that combining Raman/ROA spectroscopies with simulations is a versatile method applicable to saccharides. It allows for accessing many features with precision comparable to other methods routinely used for this task, making it a viable alternative. Furthermore, we prove that the proposed technique can scale up by studying the complicated Raffinose trisaccharide, and therefore, we expect its wide adoption to characterize sugar structural features in solution.

biophysics↗

bioRxiv2019

The impact of geographic targeting of oral cholera vaccination in sub-Saharan Africa: a modeling study

BackgroundIn May 2018, the World Health Assembly committed to reducing worldwide cholera deaths by 90% by 2030. Oral cholera vaccine (OCV) plays a key role in reducing the near-term risk of cholera, although global supplies are limited. Characterizing the potential impact and cost-effectiveness of mass OCV deployment strategies is critical for setting expectations and developing cholera control plans that maximize chances of success. Methods and FindingsWe compared the projected impacts of vaccination campaigns across sub-Saharan Africa from 2018 through 2030 when targeting geographically according to historical cholera burden and risk factors. We assessed the number of averted cases, deaths, disability-adjusted life-years, and cost-effectiveness with models that account for direct and indirect vaccine effects and population projections over time. Under current vaccine supply projections, an approach optimized to targeting by historical burden is projected to avert 828,971 (95% CI: 803,370-859,980) cases (equivalent to 34.0% of projected cases; 95% CI: 33.2-34.8). An approach that balances logistical feasibility with targeting historical burden is projected to avert 617,424 (95% CI: 599,150-643,891) cases. In contrast, approaches optimized for targeting locations with limited access to water and sanitation are projected to avert 273,939 (95% CI: 270,319-277,002) and 109,817 (95% CI: 103,735-114,110) cases, respectively. We find that the most logistically feasible targeting strategy costs $1,843 (95% CI: 1,328-14,312) per DALY averted during this period and that effective geographic targeting of OCV campaigns can have a greater impact on cost-effectiveness than improvements to vaccine efficacy and moderate increases in coverage. Although our modeling approach did not project annual changes in baseline cholera risk or incorporate immunity from natural cholera infection, our estimates of the relative performance of different vaccination strategies should be robust to these factors. ConclusionsOur study suggests that geographic targeting is critical to the cost-effectiveness and impact of oral cholera vaccination campaigns. Districts with the poorest access to improved water and sanitation are not the same as districts with the greatest historical cholera incidence. While OCV campaigns can improve cholera control in the near-term, without rapid progress in developing water and sanitation services, our results suggest that vaccine use alone are unlikely to allow us to achieve the 2030 goals.

epidemiology↗

bioRxiv2018

Perfect Counterfactuals for Epidemic Simulations

Simulation studies are often used to predict the expected impact of control measures in infectious disease outbreaks. Typically, two independent sets of simulations are conducted, one with the intervetnion, and one without, and epidemic sizes (or some related metric) are compared to estimate the effect of the intervention. Since it is possible that controlled epidemics are larger than uncontrolled ones if there is substantial stochastic variation between epidemics, uncertainty intervals from this approach can include a negative effect even for an effective intervention. To more precisely estimate the number of cases an intervention will prevent within a single epidemic, here we develop a single world approach to matching simulations of controlled epidemics to their exact uncontrolled counterfac-tual. Our method borrows concepts from percolation approaches prune out possible epidemic histories and create potential epidemic graph that can be realized to create perfectly matched controlled and uncontrolled epidemics. We present an implementation of this method for a common class of compartmental models, and its application in a simple SIR model. Results illustrate how, at the cost of some computation time, this method substantially narrows confidence intervals and avoids non-sensical inferences.

epidemiology↗