scholarly journals Learning the distribution of single-cell chromosome conformations in bacteria reveals emergent order across genomic scales

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Joris J. B. Messelink ◽  
Muriel C. F. van Teeseling ◽  
Jacqueline Janssen ◽  
Martin Thanbichler ◽  
Chase P. Broedersz
Keyword(s):  
Single Cell ◽  
Caulobacter Crescentus ◽  
Model Organism ◽  
Super Resolution ◽  
Chromosome Organization ◽  
General Strategy ◽  
Cell Axis ◽  
Cellular Processes ◽  
Emergent Order ◽  
Genomic Clusters

AbstractThe order and variability of bacterial chromosome organization, contained within the distribution of chromosome conformations, are unclear. Here, we develop a fully data-driven maximum entropy approach to extract single-cell 3D chromosome conformations from Hi–C experiments on the model organism Caulobacter crescentus. The predictive power of our model is validated by independent experiments. We find that on large genomic scales, organizational features are predominantly present along the long cell axis: chromosomal loci exhibit striking long-ranged two-point axial correlations, indicating emergent order. This organization is associated with large genomic clusters we term Super Domains (SuDs), whose existence we support with super-resolution microscopy. On smaller genomic scales, our model reveals chromosome extensions that correlate with transcriptional and loop extrusion activity. Finally, we quantify the information contained in chromosome organization that may guide cellular processes. Our approach can be extended to other species, providing a general strategy to resolve variability in single-cell chromosomal organization.

scholarly journals A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Jasper H. M. van der Velde ◽  
Jens Oelerich ◽  
Jingyi Huang ◽  
Jochem H. Smit ◽  
Atieh Aminian Jazi ◽  
...  
Keyword(s):  
Single Molecule ◽  
Unnatural Amino Acids ◽  
Photophysical Properties ◽  
Super Resolution ◽  
Single Step ◽  
General Strategy ◽  
Self Healing ◽  
Chemical Transformations ◽  
Scaffolding Strategy ◽  
Organic Fluorophore

Abstract Intramolecular photostabilization via triple-state quenching was recently revived as a tool to impart synthetic organic fluorophores with ‘self-healing’ properties. To date, utilization of such fluorophore derivatives is rare due to their elaborate multi-step synthesis. Here we present a general strategy to covalently link a synthetic organic fluorophore simultaneously to a photostabilizer and biomolecular target via unnatural amino acids. The modular approach uses commercially available starting materials and simple chemical transformations. The resulting photostabilizer–dye conjugates are based on rhodamines, carbopyronines and cyanines with excellent photophysical properties, that is, high photostability and minimal signal fluctuations. Their versatile use is demonstrated by single-step labelling of DNA, antibodies and proteins, as well as applications in single-molecule and super-resolution fluorescence microscopy. We are convinced that the presented scaffolding strategy and the improved characteristics of the conjugates in applications will trigger the broader use of intramolecular photostabilization and help to emerge this approach as a new gold standard.

scholarly journals Supramolecular Structures of the Dictyostelium Lamin NE81

Cells ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 162
Author(s):  
Marianne Grafe ◽  
Petros Batsios ◽  
Irene Meyer ◽  
Daria Lisin ◽  
Otto Baumann ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Nuclear Envelope ◽  
Model Organism ◽  
Super Resolution ◽  
Nuclear Lamina ◽  
Stimulated Emission ◽  
Structural Level ◽  
Animal Cells ◽  
Nuclear Lamins

Nuclear lamins are nucleus-specific intermediate filaments (IF) found at the inner nuclear membrane (INM) of the nuclear envelope (NE). Together with nuclear envelope transmembrane proteins, they form the nuclear lamina and are crucial for gene regulation and mechanical robustness of the nucleus and the whole cell. Recently, we characterized Dictyostelium NE81 as an evolutionarily conserved lamin-like protein, both on the sequence and functional level. Here, we show on the structural level that the Dictyostelium NE81 is also capable of assembling into filaments, just as metazoan lamin filament assemblies. Using field-emission scanning electron microscopy, we show that NE81 expressed in Xenopous oocytes forms filamentous structures with an overall appearance highly reminiscent of Xenopus lamin B2. The in vitro assembly properties of recombinant His-tagged NE81 purified from Dictyostelium extracts are very similar to those of metazoan lamins. Super-resolution stimulated emission depletion (STED) and expansion microscopy (ExM), as well as transmission electron microscopy of negatively stained purified NE81, demonstrated its capability of forming filamentous structures under low-ionic-strength conditions. These results recommend Dictyostelium as a non-mammalian model organism with a well-characterized nuclear envelope involving all relevant protein components known in animal cells.

scholarly journals Unsupervised integration of single-cell multi-omics datasets with disparities in cell-type representation

2021 ◽  
Author(s):  
Pinar Demetci ◽  
Rebecca Santorella ◽  
Bjorn Sandstede ◽  
Ritambhara Singh
Keyword(s):  
Single Cell ◽  
Optimal Transport ◽  
Integrated Analysis ◽  
Omics Data ◽  
Cell Alignment ◽  
Cell Type ◽  
Type Representation ◽  
Cellular Processes ◽  
Self Tuning ◽  
Unsupervised Algorithms

Integrated analysis of multi-omics data allows the study of how different molecular views in the genome interact to regulate cellular processes; however, with a few exceptions, applying multiple sequencing assays on the same single cell is not possible. While recent unsupervised algorithms align single-cell multi-omic datasets, these methods have been primarily benchmarked on co-assay experiments rather than the more common single-cell experiments taken from separately sampled cell populations. Therefore, most existing methods perform subpar alignments on such datasets. Here, we improve our previous work Single Cell alignment using Optimal Transport (SCOT) by using unbalanced optimal transport to handle disproportionate cell-type representation and differing sample sizes across single-cell measurements. We show that our proposed method, SCOTv2, consistently yields quality alignments on five real-world single-cell datasets with varying cell-type proportions and is computationally tractable. Additionally, we extend SCOTv2 to integrate multiple ($M\geq2$) single-cell measurements and present a self-tuning heuristic process to select hyperparameters in the absence of any orthogonal correspondence information.

scholarly journals Functional analysis of the methyltransferase SMYD in the single-cell model organism Tetrahymena thermophila

2020 ◽  
Vol 2 (2) ◽  
pp. 109-122
Author(s):  
Xiaolu Zhao ◽  
Yuan Li ◽  
Lili Duan ◽  
Xiao Chen ◽  
Fengbiao Mao ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Single Cell ◽  
Tetrahymena Thermophila ◽  
Cell Model ◽  
Model Organism ◽  
Single Cell Model

The Small GTPase Superfamily in Plants: A Conserved Regulatory Module with Novel Functions

2020 ◽  
Vol 71 (1) ◽  
pp. 247-272
Author(s):  
Erik Nielsen
Keyword(s):  
Membrane Trafficking ◽  
Binding Proteins ◽  
Model Organism ◽  
Nucleocytoplasmic Transport ◽  
Small Gtpase ◽  
Gtp Binding Proteins ◽  
Cellular Processes ◽  
Gtp Binding ◽  
Regulatory Module ◽  
Transport Vesicle

Small GTP-binding proteins represent a highly conserved signaling module in eukaryotes that regulates diverse cellular processes such as signal transduction, cytoskeletal organization and cell polarity, cell proliferation and differentiation, intracellular membrane trafficking and transport vesicle formation, and nucleocytoplasmic transport. These proteins function as molecular switches that cycle between active and inactive states, and this cycle is linked to GTP binding and hydrolysis. In this review, the roles of the plant complement of small GTP-binding proteins in these cellular processes are described, as well as accessory proteins that control their activity, and current understanding of the functions of individual members of these families in plants—with a focus on the model organism Arabidopsis—is presented. Some potential novel roles of these GTPases in plants, relative to their established roles in yeast and/or animal systems, are also discussed.

scholarly journals Super-Resolution Microscopy of Chromatin

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 493 ◽  
Author(s):  
Birk
Keyword(s):  
Gene Regulation ◽  
Data Analysis ◽  
Super Resolution ◽  
Fluorescence Labeling ◽  
Cellular Processes ◽  
Direct Assessment ◽  
Chromatin Interactions ◽  
Resolution Imaging ◽  
Super Resolution Microscopy ◽  
Insight Into

Since the advent of super-resolution microscopy, countless approaches and studies have been published contributing significantly to our understanding of cellular processes. With the aid of chromatin-specific fluorescence labeling techniques, we are gaining increasing insight into gene regulation and chromatin organization. Combined with super-resolution imaging and data analysis, these labeling techniques enable direct assessment not only of chromatin interactions but also of the function of specific chromatin conformational states.

Seventy Years on from the Luria and Delbrûck Fluctuation Analysis: A Comparison of three Methods for Estimating Mutation Rate

2015 ◽  
Vol 6 ◽  
pp. 50-58
Author(s):  
I W Nyinoh
Keyword(s):  
Mutation Rate ◽  
Resistance Mutation ◽  
Model Organism ◽  
Relative Fitness ◽  
Mutation Rates ◽  
Fluctuation Analysis ◽  
Cellular Processes ◽  
Scientific Disciplines ◽  
Rate Fluctuation ◽  
Contemporary Interpretation

Seventy years ago, Luria and Delbrûck discovered fluctuation assay for estimating mutation rates. While this method is slightly dated, it is one of the few methods for estimating mutation rates in batch culture. Mutation rates when determined expose information on cellular processes and fundamental mutagenic mechanisms. Formerly, inferences drawn from fluctuation assay were sufficient to answer a specific question inbacterial genetics. However, contemporary interpretation of results goes far beyond the motive originally intended. As the fluctuation assay has gained popularity in various scientific disciplines, analyses of results obtained are not same. This study aims to compare the estimation of mutation rates using the Poison distribution (Po) method with, the Ma-Sarka Sandri maximum likelihood estimator and the Lea-Coulson median estimator. Mycobacterium smegmatismc 2 155was used as a model organism for Mycobacterium tuberculosis, and spontaneous mutations that arose in stationary phase cells exposed to antibiotic stress were investigated. Ten to twenty-four parallel cultures were tested with various anti-tuberculosis drugs; isoniazid, kanamycin, rifampicin and streptomycin. Minimum Inhibitory Concentration (MIC) of the drugs were also determinedto be; 8 ìg/mL, 0.24 ìg/mL, 16 ìg/mL and 0.5 ìg/mL for isoniazid, kanamycin, rifampicin and streptomycin respectively. The mutation rates obtained with the methods were very similar. To improve the power of deductions drawn from fluctuation assay, efforts should be made to experimentally determine the relative fitness of wild-type to mutant bacteria.This comparison is only a guide providing evidence regarding the authenticity of some of the methods currently available to researchers interested in estimating bacterial mutation rates.Keywords: antibiotic resistance, mutation rate, fluctuation assay, fluctuation analysis calculator.

scholarly journals The FlatwormMacrostomum lignanoIs a Powerful Model Organism for Ion Channel and Stem Cell Research

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Daniil Simanov ◽  
Imre Mellaart-Straver ◽  
Irina Sormacheva ◽  
Eugene Berezikov
Keyword(s):  
Stem Cell ◽  
Membrane Potential ◽  
Ion Channels ◽  
Cell Activity ◽  
Model Organism ◽  
Membrane Potentials ◽  
Stem Cell Maintenance ◽  
Cellular Processes ◽  
Proliferation And Differentiation ◽  
Voltage Gradients

Bioelectrical signals generated by ion channels play crucial roles in many cellular processes in both excitable and nonexcitable cells. Some ion channels are directly implemented in chemical signaling pathways, the others are involved in regulation of cytoplasmic or vesicular ion concentrations, pH, cell volume, and membrane potentials. Together with ion transporters and gap junction complexes, ion channels form steady-state voltage gradients across the cell membranes in nonexcitable cells. These membrane potentials are involved in regulation of such processes as migration guidance, cell proliferation, and body axis patterning during development and regeneration. While the importance of membrane potential in stem cell maintenance, proliferation, and differentiation is evident, the mechanisms of this bioelectric control of stem cell activity are still not well understood, and the role of specific ion channels in these processes remains unclear. Here we introduce the flatwormMacrostomum lignanoas a versatile model organism for addressing these topics. We discuss biological and experimental properties ofM. lignano, provide an overview of the recently developed experimental tools for this animal model, and demonstrate how manipulation of membrane potential influences regeneration inM. lignano.

scholarly journals Polyhedra Self-Assembled from DNA Tripods and Characterized with 3D DNA-PAINT

Science ◽  
2014 ◽  
Vol 344 (6179) ◽  
pp. 65-69 ◽  
Author(s):  
Ryosuke Iinuma ◽  
Yonggang Ke ◽  
Ralf Jungmann ◽  
Thomas Schlichthaerle ◽  
Johannes B. Woehrstein ◽  
...  
Keyword(s):  
Self Assembly ◽  
Fluorescent Microscopy ◽  
Three Dimensional ◽  
Super Resolution ◽  
Triangular Prism ◽  
Hexagonal Prism ◽  
General Strategy ◽  
Transmission Electron ◽  
Pentagonal Prism ◽  
Means Of Transmission

DNA self-assembly has produced diverse synthetic three-dimensional polyhedra. These structures typically have a molecular weight no greater than 5 megadaltons. We report a simple, general strategy for one-step self-assembly of wireframe DNA polyhedra that are more massive than most previous structures. A stiff three-arm-junction DNA origami tile motif with precisely controlled angles and arm lengths was used for hierarchical assembly of polyhedra. We experimentally constructed a tetrahedron (20 megadaltons), a triangular prism (30 megadaltons), a cube (40 megadaltons), a pentagonal prism (50 megadaltons), and a hexagonal prism (60 megadaltons) with edge widths of 100 nanometers. The structures were visualized by means of transmission electron microscopy and three-dimensional DNA-PAINT super-resolution fluorescent microscopy of single molecules in solution.

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