Biology subjects

Litvinov, D.

Publications and source records attributed to Litvinov, D..

2 recordsLinked to original sources

bioRxiv2024

Surforama: interactive exploration of volumetric data by leveraging 3D surfaces

MotivationVisualization and annotation of segmented surfaces is of paramount importance for studying membrane proteins in their native cellular environment by cryogenic electron tomography (cryo-ET). Yet, analyzing membrane proteins and their organization is challenging due to their small sizes and the need to consider local context constrained to the membrane surface. ResultsTo interactively visualize, annotate, and analyze proteins in cellular context from cryo-ET data, we have developed Surforama, a Python package and napari plugin. For interactive visualization of membrane proteins in tomograms, Surforama renders the local densities projected on the surface of the segmentations. Suforama additionally provides tools to annotate and analyze particles on the membrane surfaces. Finally, for compatibility with other tools in the cryo-ET analysis ecosystem, results can be exported as RELION-formatted STAR files. As a demonstration, we performed subtomogram averaging and neighborhood analysis of photosystem II proteins in thylakoid membranes from the green alga Chlamydomonas reinhardtii. Availability and implementationPython package, code and examples are available at: https://github.com/cellcanvas/surforama

bioinformatics↗

bioRxiv2023

Melanin found in wheat spike husks

Melanin is the dark polymer pigment found in all kingdoms of life. Plant melanin, formed through the oxidation and polymerization of phenolic compounds, does not contain nitrogen, however it possesses similar properties with melanin of animal, fungal or bacterial origin. Melanin in plants is usually found in seed coats or fruit pericarp and is ascribed mechanical barrier or some other protective functions. Wild and formerly locally cultivated wheat species, like Persian wheat (Triticum carthlicum Nevski) frequently exhibit black color of spike husks and awns. The pigment causing it and the biological purpose of this coloration was not clarified before. In this paper using standard chemical extraction procedures for anthocyanins and melanin, ultraviolet-visible-near-infrared spectroscopy and hyperspectral imaging, we prove that the black color of Persian wheat spikes is caused by melanin but not anthocyanins. Also, we show that the dark pigment in husks and awns is located in epiderma and subepidermal sclerenchyma cells, that implies melanin potentially to have mechanical-enhancing and protection function. Other possible functions of melanin in cereals are discussed.

plant biology↗