Biology subjects

Klein, T.

Publications and source records attributed to Klein, T..

25 records · Page 2Linked to original sources

bioRxiv2021

Super-Resolution Imaging by Dual Iterative Structured Illumination Microscopy

Three-dimensional (3D) multicolor super-resolution imaging in the 50-100 nm range in fixed and living cells remains challenging. We extend the resolution of structured illumination microscopy (SIM) by an improved nonlinear iterative reconstruction algorithm that enables 3D multicolor imaging with improved spatiotemporal resolution at low illumination intensities. We demonstrate the performance of dual iterative SIM (diSIM) imaging cellular structures in fixed cells including synaptonemal complexes, clathrin coated pits and the actin cytoskeleton with lateral resolutions of 60-100 nm with standard fluorophores. Furthermore, we visualize dendritic spines in 70 {micro}m thick brain slices with an axial resolution < 200 nm. Finally, we image dynamics of the endoplasmatic reticulum and microtubules in living cells with up to 255 frames/s.

biophysics↗

bioRxiv2020

Half of the world's tree biodiversity is unprotected and is increasingly threatened by human activities

Although trees are key to ecosystem functioning, many forests and tree species across the globe face strong threats. Preserving areas of high biodiversity is a core priority for conservation; however, different dimensions of biodiversity and varied conservation targets make it difficult to respond effectively to this challenge. Here, we (i) identify priority areas for global tree conservation using comprehensive coverage of tree diversity based on taxonomy, phylogeny, and functional traits; and (ii) compare these findings to existing protected areas and global biodiversity conservation frameworks. We find that ca. 51% of the top-priority areas for tree biodiversity are located in current protected areas. The remaining half top-priority areas are subject to moderate to high human pressures, indicating conservation actions are needed to mitigate these human impacts. Our findings emphasize the effectiveness of using tree conservation priority areas for future global conservation planning.

ecology↗

bioRxiv2020

Cystoliths in Ficus leaves: increasing carbon fixation in saturating light by light scattering off a mineral substrate

The manner in which leaves adapt to different light intensities is key for enabling plants to survive in diverse environments and in constantly changing conditions. Many studies have addressed this subject, but little attention has been given to the effect that mineral deposits in leaves can have on photosynthesis. Here we study 6 species of Ficus and investigate how different cystolith configurations affect photosynthesis in both non-saturating and saturating light. We quantified the effect of light scattering by cystoliths on light absorption by measuring chlorophyll fluorescence intensity using microfluorimetry. We complement this by carbon assimilation measurements to directly estimate how light scattering by cystoliths affects the overall photosynthetic process. We show that light waste is reduced when irradiance is on a cystolith compared to cystolith free tissue. Moreover, light is channeled into the center of the leaf where photosynthesis occurs more efficiently than in the outer layers. This, in turn, leads to more efficient CO2 assimilation. We conclude that cystoliths contribute to photosynthesis optimization under saturating light. Cystoliths reduce the wasted portion of absorbed light under saturating irradiance by scattering light into the light-deprived leaf center. The increased efficiency may well provide important benefits to plants that form mineral scatterers.

plant biology↗

bioRxiv2020

A lipid atlas of human carotid atherosclerosis

Carotid atherosclerosis is one of the main causes of stroke, mortality and disability worldwide. The disease is characterized by plaques, heterogeneous depositions of lipids and necrotic debris in the vascular wall, which grow gradually and may remain asymptomatic for decades. However, at some point a plaque can evolve to a high-risk plaque phenotype, which may trigger a cerebrovascular event. Lipids play a key role in the development and progression of atherosclerosis. Using matrix-assisted laser desorption/ionization mass spectrometry imaging, we visualized the distribution of approximately 200 lipids in 106 tissue sections of 12 human carotid atherosclerotic plaques. We performed unsupervised classification of the mass spectrometry dataset, as well as a histology-driven multivariate analysis. These data allowed us to compare the spatial lipid patterns with morphological plaque features that have been associated with enhanced risk of symptoms. The abundances of sphingomyelin and oxidized cholesteryl ester species were elevated specifically in necrotic intima areas, while diacylglycerols and triacylglycerols were spatially correlated to areas containing the coagulation protein fibrin. This is the first study to systematically investigate spatial lipid patterns in atherosclerosis, analyze their relation to histological tissue type, and to demonstrate a clear co-localization between plaque features and specific lipid classes and individual lipid molecules in high-risk atherosclerotic plaques.

biochemistry↗

bioRxiv2019

Tracking down the molecular architecture of the synaptonemal complex by expansion microscopy

The synaptonemal complex (SC) is a meiosis-specific nuclear multiprotein complex that is essential for proper synapsis, recombination and segregation of homologous chromosomes. We combined structured illumination microscopy (SIM) with different ExM protocols including U-ExM, proExM, and magnified analysis of the proteome (MAP) to investigate the molecular organization of the SC. Comparison with structural data obtained by single-molecule localization microscopy of unexpanded SCs allowed us to investigate ultrastructure preservation of expanded SCs. For image analysis, we developed an automatic image processing software that enabled unbiased expansion factor determination. Here, MAP-SIM provided the best results and enabled reliable three-color super-resolution microscopy of the SCs of a whole set of chromosomes in a spermatocyte with 20-30 nm spatial resolution. Our data demonstrate that post-expansion labeling by MAP-SIM improves immunolabeling efficiency and allowed us thus to unravel previously hidden details of the molecular organization of SCs.

biophysics↗

bioRxiv2018

Standardized biogeographic grouping system for annotating populations in pharmacogenetic research

The varying frequencies of pharmacogenetic alleles between populations have important implications for the impact of these alleles in different populations. Current population grouping methods to communicate these patterns are insufficient as they are inconsistent and fail to reflect the global distribution of genetic variability. To facilitate and standardize the reporting of variability in pharmacogenetic allele frequencies, we present seven geographically-defined groups: American, Central/South Asian, East Asian, European, Near Eastern, Oceanian, and Sub-Saharan African, and two admixed groups: African American/Afro-Caribbean and Latino. These nine groups are defined by global autosomal genetic structure and based on data from large-scale sequencing initiatives. We recognize that broadly grouping global populations is an oversimplification of human diversity and does not capture complex social and cultural identity. However, these groups meet a key need in pharmacogenetics research by enabling consistent communication of the scale of variability in global allele frequencies and are now used by PharmGKB.

genetics↗

bioRxiv2018

Long term context dependent genetic adaptation of the viral genetic cloud

RNA viruses generate a cloud of genetic variants within each host. This cloud contains high frequency genotypes, and a very large number of rare variants. While the dynamics of frequent variants are affected by the fitness of each variant, the rare variants cloud is affected by more complex genetic factors, including context dependent mutations. It serves as a spearhead for the viral populations movement within the adaptive landscape. We here use an experimental evolution system to show that the genetic cloud surrounding the Coxsackie virus master sequence slowly, but steadily, evolves over hundreds of generations. The evolution of the rare variants cloud often precedes the appearance of high frequency variants. The rare variants clouds evolution is driven by a combination of a context-dependent mutation pattern and selection for and against specific nucleotide compositions.This combination affects the mutated dinucleotide distribution, and eventually leads to a non-uniform dinucleotide distribution in the main viral sequence. We then tested these conclusions on other RNA viruses with similar conclusions.

genetics↗