Artem Pliss

Ribosomal genes in focus: new transcripts label the dense fibrillar components and form clusters indicative of “Christmas trees” in situ

T he organization of transcriptionally active ribosomal genes in animal cell nucleoli is investigated in this study in order to address the long-standing controversy with regard to the intranucleolar localization of these genes. Detailed analyses of HeLa cell nucleoli include direct localization of ribosomal genes by in situ hybridization and their indirect localization via nascent ribosomal transcript mappings. On the light microscopy (LM) level, ribosomal genes map in 10–40 fluorescence foci per nucleus, and transcription activity is associated with most foci. We demonstrate that each nucleolar focus observed by LM corresponds, on the EM level, to an individual fibrillar center (FC) and surrounding dense fibrillar components (DFCs). The EM data identify the DFC as the nucleolar subcompartment in which rRNA synthesis takes place, consistent with detection of rDNA within the DFC. The highly sensitive method for mapping nascent transcripts in permeabilized cells on ultrastructural level provides intense and unambiguous clustered immunogold signal over the DFC, whereas very little to no label is detected over the FC. This signal is strongly indicative of nascent “Christmas trees” of rRNA associated with individual rDNA genes, sampled on the surface of thin sections. Stereological analysis of the clustered transcription signal further suggests that these Christmas trees may be contorted in space and exhibit a DNA compaction ratio on the order of 4–5.5.

Nonlinear Optical Imaging and Raman Microspectrometry of the Cell Nucleus throughout the Cell Cycle

Fundamental understanding of cellular processes at molecular level is of considerable importance in cell biology as well as in biomedical disciplines for early diagnosis of infection and cancer diseases, and for developing new molecular medicine-based therapies. Modern biophotonics offers exclusive capabilities to obtain information on molecular composition, organization, and dynamics in a cell by utilizing a combination of optical spectroscopy and optical imaging. We introduce here a combination of Raman microspectrometry, together with coherent anti-Stokes Raman scattering (CARS) and two-photon excited fluorescence (TPEF) nonlinear optical microscopy, to study macromolecular organization of the nucleus throughout the cell cycle. Site-specific concentrations of proteins, DNA, RNA, and lipids were determined in nucleoli, nucleoplasmic transcription sites, nuclear speckles, constitutive heterochromatin domains, mitotic chromosomes, and extrachromosomal regions of mitotic cells by quantitative confocal Raman microspectrometry. A surprising finding, obtained in our study, is that the local concentration of proteins does not increase during DNA compaction. We also demonstrate that postmitotic DNA decondensation is a gradual process, continuing for several hours. The quantitative Raman spectroscopic analysis was corroborated with CARS/TPEF multimodal imaging to visualize the distribution of protein, DNA, RNA, and lipid macromolecules throughout the cell cycle.

Tunable Narrow Band Emissions from Dye-Sensitized Core/Shell/Shell Nanocrystals in the Second Near-Infrared Biological Window

We introduce a hybrid organic-inorganic system consisting of epitaxial NaYF4:Yb3+/X3+@NaYbF4@NaYF4:Nd3+ (X = null, Er, Ho, Tm, or Pr) core/shell/shell (CSS) nanocrystal with organic dye, indocyanine green (ICG) on the nanocrystal surface. This system is able to produce a set of narrow band emissions with a large Stokes-shift (>200 nm) in the second biological window of optical transparency (NIR-II, 1000-1700 nm), by directional energy transfer from light-harvesting surface ICG, via lanthanide ions in the shells, to the emitter X3+ in the core. Surface ICG not only increases the NIR-II emission intensity of inorganic CSS nanocrystals by ∼4-fold but also provides a broadly excitable spectral range (700-860 nm) that facilitates their use in bioapplications. We show that the NIR-II emission from ICG-sensitized Er3+-doped CSS nanocrystals allows clear observation of a sharp image through 9 mm thick chicken breast tissue, and emission signal detection through 22 mm thick tissue yielding a better imaging profile than from typically used Yb/Tm-codoped upconverting nanocrystals imaged in the NIR-I region (700-950 nm). Our result on in vivo imaging suggests that these ICG-sensitized CSS nanocrystals are suitable for deep optical imaging in the NIR-II region.

Electron microscopy of DNA replication in 3-D: Evidence for similar-sized replication foci throughout S-phase†

DNA replication sites (RS) in synchronized HeLa cells have been studied at the electron microscopic level. Using an improved method for detection following the in vivo incorporation of biotin‐16‐deoxyuridine triphosphate, discrete RS, or foci are observed throughout the S‐phase. In particular, the much larger RS or foci typically observed by fluorescence microscopic approaches in mid‐ and late‐S‐phase, are found to be composed of smaller discrete foci that are virtually identical in size to the RS observed in early‐S‐phase. Pulse‐chase experiments demonstrate that the RS of early‐S‐phase are maintained when chased through S‐phase and into the next cell generation. Stereologic analysis demonstrates that the relative number of smaller sized foci present at a given time remains constant from early through mid‐S‐phase with only a slight decrease in late‐S‐phase. 3‐D reconstruction of serial sections reveals a network‐like organization of the RS in early‐S‐phase and confirms that numerous smaller‐sized replication foci comprise the larger RS characteristic of late‐S‐phase.

Biophotonic probing of macromolecular transformations during apoptosis

We introduce here multiplex nonlinear optical imaging as a powerful tool for studying the molecular organization and its transformation in cellular processes, with the specific example of apoptosis. Apoptosis is a process of self-initiated cell death, critically important for physiological regulation and elimination of genetic disorders. Nonlinear optical microscopy, combining the coherent anti-Stokes Raman scattering (CARS) microscopy and two-photon excited fluorescence (TPEF), has been used for analysis of spatial distribution of major types of biomolecules: proteins, lipids, and nucleic acids in the cells while monitoring their changes during apoptosis. CARS imaging revealed that in the nuclei of proliferating cells, the proteins are distributed nearly uniformly, with local accumulations in several nuclear structures. We have found that this distribution is abruptly disrupted at the onset of apoptosis and is transformed to a progressively irregular pattern. Fluorescence recovery after photobleaching (FRAP) studies indicate that pronounced aggregation of proteins in the nucleoplasm of apoptotic cells coincides with a gradual reduction in their mobility.

Spatio‐temporal dynamics at rDNA foci: Global switching between DNA replication and transcription

We have investigated the in situ organization of ribosomal gene (rDNA) transcription and replication in HeLa cells. Fluorescence in situ hybridization (FISH) revealed numerous rDNA foci in the nucleolus. Each rDNA focus corresponds to a higher order chromatin domain containing multiple ribosomal genes. Multi‐channel labeling experiments indicated that, in the majority of cells, all the rDNA foci were active in transcription as demonstrated by co‐localization with signals to transcription and fibrillarin, a protein involved in ribosomal RNA processing. In some cells, however, a small portion of the rDNA foci did not overlap with signals to transcription and fibrillarin. Labeling for DNA replication revealed that those rDNA foci inactive in transcription were restricted to the S‐phase of the cell cycle and were replicated predominantly from mid to late S‐phase. Electron microscopic analysis localized the nucleolar transcription, replication, and fibrillarin signals to the dense fibrillar components of the nucleolus and at the borders of the fibrillar centers. We propose that the rDNA foci are the functional units for coordinating replication and transcription of the rRNA genes in space and time. This involves a global switching mechanism, active from mid to late S‐phase, for turning off transcription and turning on replication at individual rDNA foci. Once all the rRNA genes at individual foci are replicated, these higher order chromatin domains are reprogrammed for transcription.

Fluorescence lifetime of fluorescent proteins as an intracellular environment probe sensing the cell cycle progression.

The fluorescence lifetime of fluorescent proteins is affected by the concentration of solutes in a medium, in inverse correlation with local refractive index. In this paper, we introduce the concept of using this dependence to probe cellular molecular environment and its transformation during cellular processes. We employ the fluorescence lifetime of Green Fluorescent Protein and tdTomato Fluorescent Protein expressed in cultured cells and probe the changes in the local molecular environment during the cell cycle progression. We report that the longest fluorescence lifetimes occurred during mitosis. Following the cell division, the fluorescence lifetimes of these proteins were rapidly shortened. Furthermore the fluorescence lifetime of tdTomato in the nucleoplasm gradually increased throughout the span of S-phase and remained constantly long until the end of interphase. We interpret the observed fluorescence lifetime changes to be derived from changes in concentration of macromolecular solutes in the cell interior throughout cell cycle progression.

Chromatin dynamics in living cells: Identification of oscillatory motion

Genomic DNA in mammalian cells is organized into ∼1 Mbp chromatin domains (ChrD) which represent the basic structural units for DNA compaction, replication, and transcription. Remarkably, ChrD are highly dynamic and undergo both translational movement and configurational changes. In this study, we introduce an automated motion tracking analysis to measure, both in 2D and 3D, the linear displacement of early, mid and late S‐phase replicated ChrD over short time periods (<1 sec). We conclude that previously identified large‐scale transitions in the spatial position and configuration of chromatin, originate from asymmetric oscillations of the ChrD detectable in fractions of a second. The rapid oscillatory motion correlates with the replication timing of the ChrD with early S replicated ChrD showing the highest levels of motion and late S‐phase chromatin the lowest. Virtually identical levels of oscillatory motion were detected when ChrD were measured during active DNA replication or during inhibition of transcription with DRB or α‐amanitin. While this motion is energy independent, the oscillations of early S and mid S, but not late S replicated chromatin, are reduced by cell permeabilization. This suggests involvement of soluble factors in the regulation of chromatin dynamics. The DNA intercalating agent actinomycin D also significantly inhibits early S‐labeled chromatin oscillation. We propose that rapid asymmetric oscillations of <1 sec are the basis for translational movements and configurational changes in ChrD previously detected over time spans of minutes–hours, and are the result of both the stochastic collisions of macromolecules and specific molecular interactions. J. Cell. Physiol. 228: 609–616, 2013.

Spatio-temporal dynamics at rDNA foci: Global switching between DNA replication and transcription

We have investigated the in situ organization of ribosomal gene (rDNA) transcription and replication in HeLa cells. Fluorescence in situ hybridization (FISH) revealed numerous rDNA foci in the nucleolus. Each rDNA focus corresponds to a higher order chromatin domain containing multiple ribosomal genes. Multi‐channel labeling experiments indicated that, in the majority of cells, all the rDNA foci were active in transcription as demonstrated by co‐localization with signals to transcription and fibrillarin, a protein involved in ribosomal RNA processing. In some cells, however, a small portion of the rDNA foci did not overlap with signals to transcription and fibrillarin. Labeling for DNA replication revealed that those rDNA foci inactive in transcription were restricted to the S‐phase of the cell cycle and were replicated predominantly from mid to late S‐phase. Electron microscopic analysis localized the nucleolar transcription, replication, and fibrillarin signals to the dense fibrillar components of the nucleolus and at the borders of the fibrillar centers. We propose that the rDNA foci are the functional units for coordinating replication and transcription of the rRNA genes in space and time. This involves a global switching mechanism, active from mid to late S‐phase, for turning off transcription and turning on replication at individual rDNA foci. Once all the rRNA genes at individual foci are replicated, these higher order chromatin domains are reprogrammed for transcription.

Organelle specific imaging in live cells and immuno-labeling using resonance Raman probe

Raman microspectroscopy is one of the most powerful tools in molecular sensing, offering a non-invasive and comprehensive characterization of the intracellular environment. To analyze and monitor molecular content in specific cellular compartments, different parts of cellular architecture must be unambiguously identified to guide Raman image/spectra acquisition. In this regards, the development of Raman molecular probes, producing spectrally distinct and intense signal is of outmost practical importance. Here we report on a new generation of Raman molecular probes, designed for application in live cells and immuno-labeling, capable of providing unprecedentedly high detection sensitivity through Resonance Raman (RR) enhancement. In contrast to existing Raman markers, the proposed RR reporter is designed to produce RR enhancement under excitation in the visible spectral range, far away from absorption of cellular biomolecules. We show that this concept allows for facile identification of labeled cellular domains, simultaneously with mapping of the macromolecules using spontaneous Raman technique. We demonstrate the breakthrough potential of these RR probes for selective labeling and rapid Raman imaging of membranes as well as mitochondria in live cells. We also show that these resonant Raman probes open the way for Raman-based intracellular immuno-labeling.