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Communications Biology Jun 2024Chromatin organization and dynamics play important roles in governing the regulation of nuclear processes of biological cells. However, due to the constant diffusive...
Chromatin organization and dynamics play important roles in governing the regulation of nuclear processes of biological cells. However, due to the constant diffusive motion of chromatin, examining chromatin nanostructures in living cells has been challenging. In this study, we introduce interferometric scattering correlation spectroscopy (iSCORS) to spatially map nanoscopic chromatin configurations within unlabeled live cell nuclei. This label-free technique captures time-varying linear scattering signals generated by the motion of native chromatin on a millisecond timescale, allowing us to deduce chromatin condensation states. Using iSCORS imaging, we quantitatively examine chromatin dynamics over extended periods, revealing spontaneous fluctuations in chromatin condensation and heterogeneous compaction levels in interphase cells, independent of cell phases. Moreover, we observe changes in iSCORS signals of chromatin upon transcription inhibition, indicating that iSCORS can probe nanoscopic chromatin structures and dynamics associated with transcriptional activities. Our scattering-based optical microscopy, which does not require labeling, serves as a powerful tool for visualizing dynamic chromatin nano-arrangements in live cells. This advancement holds promise for studying chromatin remodeling in various crucial cellular processes, such as stem cell differentiation, mechanotransduction, and DNA repair.
Topics: Chromatin; Humans; Spectrum Analysis; Interferometry; Chromatin Assembly and Disassembly; Cell Nucleus
PubMed: 38914653
DOI: 10.1038/s42003-024-06457-2 -
PeerJ 2024Breast carcinoma (BRCA) is a life-threatening malignancy in women and shows a poor prognosis. Cuproptosis is a novel mode of cell death but its relationship with BRCA is...
BACKGROUND
Breast carcinoma (BRCA) is a life-threatening malignancy in women and shows a poor prognosis. Cuproptosis is a novel mode of cell death but its relationship with BRCA is unclear. This study attempted to develop a cuproptosis-relevant prognostic gene signature for BRCA.
METHODS
Cuproptosis-relevant subtypes of BRCA were obtained by consensus clustering. Differential expression analysis was implemented using the 'limma' package. Univariate Cox and multivariate Cox analyses were performed to determine a cuproptosis-relevant prognostic gene signature. The signature was constructed and validated in distinct datasets. Gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA) were also conducted using the prognostic signature to uncover the underlying molecular mechanisms. ESTIMATE and CIBERSORT algorithms were applied to probe the linkage between the gene signature and tumor microenvironment (TME). Immunotherapy responsiveness was assessed using the Tumor Immune Dysfunction and Exclusion (TIDE) web tool. Real-time quantitative PCR (RT-qPCR) was performed to detect the expressions of cuproptosis-relevant prognostic genes in breast cancer cell lines.
RESULTS
Thirty-eight cuproptosis-associated differentially expressed genes (DEGs) in BRCA were mined by consensus clustering and differential expression analysis. Based on univariate Cox and multivariate Cox analyses, six cuproptosis-relevant prognostic genes, namely SAA1, KRT17, VAV3, IGHG1, TFF1, and CLEC3A, were mined to establish a corresponding signature. The signature was validated using external validation sets. GSVA and GSEA showed that multiple cell cycle-linked and immune-related pathways along with biological processes were associated with the signature. The results ESTIMATE and CIBERSORT analyses revealed significantly different TMEs between the two Cusig score subgroups. Finally, RT-qPCR analysis of cell lines further confirmed the expressional trends of SAA1, KRT17, IGHG1, and CLEC3A.
CONCLUSION
Taken together, we constructed a signature for projecting the overall survival of BRCA patients and our findings authenticated the cuproptosis-relevant prognostic genes, which are expected to provide a basis for developing prognostic molecular biomarkers and an in-depth understanding of the relationship between cuproptosis and BRCA.
Topics: Humans; Breast Neoplasms; Female; Prognosis; Computational Biology; Biomarkers, Tumor; Gene Expression Regulation, Neoplastic; Gene Expression Profiling; Tumor Microenvironment; Cell Line, Tumor
PubMed: 38912044
DOI: 10.7717/peerj.17419 -
ACS Bio & Med Chem Au Jun 2024Synthetic modification of oligodeoxynucleotides (ODNs) via conjugation to nucleic acid binding small molecules can improve hybridization and pharmacokinetic properties....
Synthetic modification of oligodeoxynucleotides (ODNs) via conjugation to nucleic acid binding small molecules can improve hybridization and pharmacokinetic properties. In the present study, five Hoechst 33258 derived benzimidazoles were conjugated to T rich ODNs and their hybridization effectiveness was tested. Thermal denaturation studies revealed significant stabilization of complementary duplexes by ODN-benzimidazole conjugates, with the extent of stabilization being highly dependent on the length of the linker between DNA and benzimidazole. The increases in thermal stability were determined to be due to the binding of the benzimidazole moiety to the duplex. Circular dichroism and molecular modeling studies provided insights toward the influence of conjugation on duplex structure and how linker length impacts placement of the benzimidazole moiety in the minor groove. Furthermore, thermal denaturation studies with the complementary strand containing a single base mismatch or being RNA revealed that covalent conjugation of benzimidazoles to an ODN also enhances the sequence specificity. The fundamental studies reported herein provide a strategy to improve the stability and specificity properties of the ODN probes, which can be of use for targeting and diagnostics applications.
PubMed: 38911908
DOI: 10.1021/acsbiomedchemau.3c00074 -
ACS Photonics Jun 2024Electrically connected and plasmonically enhanced molecular junctions combine the optical functionalities of high field confinement and enhancement (cavity function),...
Electrically connected and plasmonically enhanced molecular junctions combine the optical functionalities of high field confinement and enhancement (cavity function), and of high radiative efficiency (antenna function) with the electrical functionalities of molecular transport. Such combined optical and electrical probes have proven useful for the fundamental understanding of metal-molecule contacts and contribute to the development of nanoscale optoelectronic devices including ultrafast electronics and nanosensors. Here, we employ a self-assembled metal-molecule-metal junction with a nanoparticle bridge to investigate correlated fluctuations in conductance and tunneling-induced light emission at room temperature. Despite the presence of hundreds of molecules in the junction, the electrical conductance and light emission are both highly sensitive to atomic-scale fluctuations-a phenomenology reminiscent of picocavities observed in Raman scattering and of luminescence blinking from photoexcited plasmonic junctions. Discrete steps in conductance associated with fluctuating emission intensities through the multiple plasmonic modes of the junction are consistent with a finite number of randomly localized, point-like sources dominating the optoelectronic response. Contrasting with these microscopic fluctuations, the overall plasmonic and electronic functionalities of our devices feature long-term survival at room temperature and under an electrical bias of a few volts, allowing for measurements over several months.
PubMed: 38911841
DOI: 10.1021/acsphotonics.4c00291 -
ACS Energy Letters Jun 2024Understanding photophysical processes in lead halide perovskites is an important aspect of optimizing the performance of optoelectronic devices. The determination of... (Review)
Review
Understanding photophysical processes in lead halide perovskites is an important aspect of optimizing the performance of optoelectronic devices. The determination of exact charge carrier extraction rate constants remains elusive, as there is a large and persistent discrepancy in the reported absolute values. In this review, we concentrate on experimental procedures adopted in the literature to obtain kinetic estimates of charge transfer processes and limitations imposed by the spectroscopy technique employed. Time-resolved techniques (e.g., transient absorption-reflection and time-resolved photoluminescence spectroscopy) are commonly employed to probe charge transfer at perovskite/transport layer interfaces. The variation in sample preparation and measurement conditions can produce a wide dispersion of the measured kinetic parameters. The selected time window and the kinetic fitting model employed introduce additional uncertainty. We discuss here evaluation strategies that rely on multiexponential fitting protocols (regular or stretched) and show how the dispersion in the reported values for carrier transfer rate constants can be resolved.
PubMed: 38911533
DOI: 10.1021/acsenergylett.4c00736 -
Talanta Jun 2024The certification of cosmetic products has always been a prominent concern. Here, we have developed a pH sensor and applied it in the field of cosmetic safety....
The certification of cosmetic products has always been a prominent concern. Here, we have developed a pH sensor and applied it in the field of cosmetic safety. Initially, we designed two probes, CH with aggregation-induced emission (AIE) effect and the near-infrared fluorophore derivative CYTYR. By encapsulating them with DSPE-PEG2000-NH, we obtained the CHCY-lipo nano-micelles with fluorescence resonance energy transfer (FRET) response. By combining them into a sensor array called pC, we achieved sensitive detection of a wide pH range, ranging from 4.69 to 9.25. To validate the performance of the pC sensor array, we employed a multi-channel mode and applied it to differentiate commercial anti-aging creams. Through linear discriminant analysis and 3D fingerprint analysis, the pC sensor array successfully distinguished anti-aging creams from different countries, providing a rapid and accurate method for cosmetic safety identification. The results of this study demonstrate the potential of the pC sensor array for quick authentication of cosmetic products, offering significant support and application prospects in safeguarding consumer health.
PubMed: 38909596
DOI: 10.1016/j.talanta.2024.126447 -
Time-resolved fluorescence of tryptophan characterizes membrane perturbation by cyclic lipopeptides.Biophysical Journal Jun 2024Viscosin is a membrane-permeabilizing, cyclic lipopeptide (CLiP) produced by Pseudomonas species. Here, we have studied four synthetic analogs (L1W, V4W, L5W, L7W), each...
Viscosin is a membrane-permeabilizing, cyclic lipopeptide (CLiP) produced by Pseudomonas species. Here, we have studied four synthetic analogs (L1W, V4W, L5W, L7W), each with one leucine (Leu; L) or valine residue exchanged for tryptophan (Trp; W) by means of time-resolved fluorescence spectroscopy of Trp. To this end, we recorded the average fluorescence lifetime, rotational correlation time and limiting anisotropy, dipolar relaxation time and limiting extent of relaxation, rate constant of acrylamide quenching, effect of HO-DO exchange, and time-resolved halfwidth of the spectrum in the absence and presence of POPC liposomes. Structure, localization, and hydration of the peptides were described by molecular dynamics simulations. The combination of the parameters provides a good description of the molecular environments of the Trp positions and the behavior of viscosin as a whole. Of particular value for characterizing the impact of viscosin on the membrane is the dipolar relaxation of Trp4 in V4W, which is deeply embedded in the hydrophobic core. The limiting relaxation level represents the membrane perturbation - unlike typical membrane probes - at the site of the perturbant. Fractions of Trp4 relax at different rates; the one not in contact with water upon excitation relaxes via recruitment of a water molecule on the 10 ns time scale. This rate is sensitive to the concerted membrane perturbation by more than one lipopeptide, which appears at high lipopeptide concentration and is assumed a prerequisite for the final formation of a membrane-permeabilizing defect. Trp7 relaxes primarily with respect to neighboring Ser residues. Trp5 flips between a membrane-inserted and surface-exposed orientation.
PubMed: 38909278
DOI: 10.1016/j.bpj.2024.06.022 -
Science Advances Jun 2024Single-cell technology has allowed researchers to probe tissue complexity and dynamics at unprecedented depth in health and disease. However, the generation of...
Single-cell technology has allowed researchers to probe tissue complexity and dynamics at unprecedented depth in health and disease. However, the generation of high-dimensionality single-cell atlases and virtual three-dimensional tissues requires integrated reference maps that harmonize disparate experimental designs, analytical pipelines, and taxonomies. Here, we present a comprehensive single-cell transcriptome integration map of cardiac fibrosis, which underpins pathophysiology in most cardiovascular diseases. Our findings reveal similarity between cardiac fibroblast (CF) identities and dynamics in ischemic versus pressure overload models of cardiomyopathy. We also describe timelines for commitment of activated CFs to proliferation and myofibrogenesis, profibrotic and antifibrotic polarization of myofibroblasts and matrifibrocytes, and CF conservation across mouse and human healthy and diseased hearts. These insights have the potential to inform knowledge-based therapies.
Topics: Animals; Fibrosis; Single-Cell Analysis; Humans; Fibroblasts; Transcriptome; Mice; Myocardium; Myofibroblasts; Gene Expression Profiling
PubMed: 38905342
DOI: 10.1126/sciadv.adk8501 -
ArXiv May 2024A recent experimental study reports on measuring the temporal duration and the spatial extent of failed attempts to cross an activation barrier (i.e., "loops") for a...
A recent experimental study reports on measuring the temporal duration and the spatial extent of failed attempts to cross an activation barrier (i.e., "loops") for a folding transition in a single molecule and for a Brownian particle trapped within a bistable potential. Within the model of diffusive dynamics, however, both of these quantities are, on the average, exactly zero because of the recrossings of the barrier region boundary. That is, an observer endowed with infinite spatial and temporal resolution would find that finite loops do not exist (or, more precisely, form a set of measure zero). Here we develop a description of the experiment that takes finite experimental resolution into account and show how the experimental uncertainty of localizing the point, in time and space, where the barrier is crossed leads to observable distributions of loop times and sizes. Although these distributions generally depend on the experimental resolution, this dependence, in certain cases, may amount to a simple resolution-dependent factor and thus the experiments do probe inherent properties of barrier crossing dynamics.
PubMed: 38903733
DOI: No ID Found -
Frontiers in Oncology 2024Fluorescence hybridization (FISH) is an essential ancillary study used to identify clinically aggressive subsets of large B-cell lymphomas that have , or...
INTRODUCTION
Fluorescence hybridization (FISH) is an essential ancillary study used to identify clinically aggressive subsets of large B-cell lymphomas that have , or rearrangements. Small-volume biopsies such as fine needle aspiration biopsy (FNAB) and core needle biopsy (CNB) are increasingly used to diagnose lymphoma and obtain material for ancillary studies such as FISH. However, the performance of FISH in small biopsies has not been thoroughly evaluated or compared to surgical biopsies.
METHODS
We describe the results of and FISH in a series of 222 biopsy specimens, including FNAB with cell blocks, CNBs, and surgical excisional or incisional biopsies from 208 unique patients aggregated from 6 academic medical centers. A subset of patients had FNAB followed by a surgical biopsy (either CNB or excisional biopsy) obtained from the same or contiguous anatomic site as part of the same clinical workup; FISH results were compared for these paired specimens.
RESULTS
FISH had a low hybridization failure rate of around 1% across all specimen types. FISH identified concurrent and rearrangements in 20 of 197 (10%) specimens and concurrent and rearrangements in 3 of 182 (1.6%) specimens. The paired FNAB and surgical biopsy specimens did not show any discrepancies for or FISH; of the 17 patients with 34 paired cytology and surgical specimens, only 2 of the 49 FISH probes compared (4% of all comparisons) showed any discrepancy and both were at the locus. One discrepancy was due to necrosis of the CNB specimen causing a false negative FISH result when compared to the FNAB cell block that demonstrated a rearrangement.
DISCUSSION
FISH showed a similar hybridization failure rate in all biopsy types. Ultimately, , or FISH showed 96% concordance when compared across paired cytology and surgical specimens, suggesting FNAB with cell block is equivalent to other biopsy alternatives for evaluation of DLBCL or HGBCL FISH testing.
PubMed: 38903717
DOI: 10.3389/fonc.2024.1408238