Nanoscale mechanism of molecular transport through the nuclear pore complex as studied by scanning electrochemical microscopy

Probing the disordered domain of the nuclear pore complex through coarse-grained molecular dynamics simulations

The distribution of disordered proteins (FG-nups) that line the transport channel of the nuclear pore complex (NPC) is investigated by means of coarse-grained molecular dynamics simulations. A one-bead-per-amino-acid model is presented that accounts for the hydrophobic/hydrophilic and electrostatic interactions between different amino acids, polarity of the solvent, and screening of free ions. The results indicate that the interaction of the FG-nups forms a high-density, doughnut-like distribution inside the NPC, which is rich in FG-repeats. We show that the obtained distribution is encoded in the amino-acid sequence of the FG-nups and is driven by both electrostatic and hydrophobic interactions. To explore the relation between structure and function, we have systematically removed different combinations of FG-nups from the pore to simulate inviable and viable NPCs that were previously studied experimentally. The obtained density distributions show that the maximum density of the FG-nups inside the pore does not exceed 185 mg/mL in the inviable NPCs, whereas for the wild-type and viable NPCs, this value increases to 300 mg/mL. Interestingly, this maximum density is not correlated to the total mass of the FG-nups, but depends sensitively on the specific combination of essential Nups located in the central plane of the NPC.

Size-dependent and real-time effect of SiO2 nanoparticles on a single living HeLa Cell's membrane permeability

Low toxic and biocompatible SiO₂ NPs of different sizes show different effects on cell membrane permeability.

Real-time monitoring of quorum sensing in 3D-printed bacterial aggregates using scanning electrochemical microscopy

Microbes frequently live in nature as small, densely packed aggregates containing ∼10(1)-10(5) cells. These aggregates not only display distinct phenotypes, including resistance to antibiotics, but also, serve as building blocks for larger biofilm communities. Aggregates within these larger communities display nonrandom spatial organization, and recent evidence indicates that this spatial organization is critical for fitness. Studying single aggregates as well as spatially organized aggregates remains challenging because of the technical difficulties associated with manipulating small populations. Micro-3D printing is a lithographic technique capable of creating aggregates in situ by printing protein-based walls around individual cells or small populations. This 3D-printing strategy can organize bacteria in complex arrangements to investigate how spatial and environmental parameters influence social behaviors. Here, we combined micro-3D printing and scanning electrochemical microscopy (SECM) to probe quorum sensing (QS)-mediated communication in the bacterium Pseudomonas aeruginosa. Our results reveal that QS-dependent behaviors are observed within aggregates as small as 500 cells; however, aggregates larger than 2,000 bacteria are required to stimulate QS in neighboring aggregates positioned 8 μm away. These studies provide a powerful system to analyze the impact of spatial organization and aggregate size on microbial behaviors.

Development of a versatile in vitro platform for studying biological systems using micro-3D printing and scanning electrochemical microscopy

We report a novel strategy for studying a broad range of cellular behaviors in real time by combining two powerful analytical techniques, micro-3D printing and scanning electrochemical microscopy (SECM). This allows one, in microbiological studies, to isolate a known number of cells in a micrometer-sized chamber with a roof and walls that are permeable to small molecules and observe metabolic products. In such studies, the size and spatial organization of a population play a crucial role in cellular group behaviors, such as intercellular interactions and communication. Micro-3D printing, a photolithographic method for constructing cross-linked protein microstructures, permits one to compartmentalize a small population of microbes by forming a porous roof and walls around cells in situ. Since the roof and walls defining the microchamber are porous, any small molecules can freely diffuse from the chamber to be detected and quantified using SECM. The size of the chamber and the roof permeability can be obtained by SECM using a small probe molecule, ferrocenemethanol (FcMeOH). The chamber permeability to FcMeOH can be tuned by varying printing parameters that influence the cross-linking density of the proteinaceous material. These analyses establish a versatile strategy as a sensitive platform to quantitatively monitor small molecules produced by microbes.

Exosomes in cancer development, metastasis, and drug resistance: a comprehensive review

Trafficking of biological material across membranes is an evolutionary conserved mechanism and is part of any normal cell homeostasis. Such transport is composed of active, passive, export through microparticles, and vesicular transport (exosomes) that collectively maintain proper compartmentalization of important micro- and macromolecules. In pathological states, such as cancer, aberrant activity of the export machinery results in expulsion of a number of key proteins and microRNAs resulting in their misexpression. Exosome-mediated expulsion of intracellular drugs could be another barrier in the proper action of most of the commonly used therapeutics, targeted agents, and their intracellular metabolites. Over the last decade, a number of studies have revealed that exosomes cross-talk and/or influence major tumor-related pathways, such as hypoxia-driven epithelial-to-mesenchymal transition, cancer stemness, angiogenesis, and metastasis involving many cell types within the tumor microenvironment. Emerging evidence suggests that exosome-secreted proteins can also propel fibroblast growth, resulting in desmoplastic reaction, a major barrier in effective cancer drug delivery. This comprehensive review highlights the advancements in the understanding of the biology of exosomes secretions and the consequence on cancer drug resistance. We propose that the successful combination of cancer treatments to tackle exosome-mediated drug resistance requires an interdisciplinary understanding of these cellular exclusion mechanisms, and how secreted biomolecules are involved in cellular cross-talk within the tumor microenvironment.

Quantitative and real-time effects of carbon quantum dots on single living HeLa cell membrane permeability

The interaction between carbon quantum dots (CQDs) and a single living cell was explored in real time. Here, we provide the quantitative data on the permeability of the HeLa cell membrane in the presence of CQDs with different surface functional groups (CQDs terminated with -OH/-COOH (CQD-OH), -PEG (CQD-PEG), and -NH2 (CQD-NH2)). Although these CQDs have very low toxicity towards HeLa cells, they still increase the cell membrane permeability by 8%, 13%, and 19% for CQD-PEG, CQD-OH, and CQD-NH2, respectively, and this kind of permeability was irreversible. These observations are valuable for promoting the bio-applications of carbon nanostructures in living systems.

Nuclear pore complex protein sequences determine overall copolymer brush structure and function

The transport of cargo across the nuclear membrane is highly selective and accomplished by a poorly understood mechanism involving hundreds of nucleoporins lining the inside of the nuclear pore complex (NPC). Currently, there is no clear picture of the overall structure formed by this collection of proteins within the pore, primarily due to their disordered nature. We perform coarse-grained simulations of both individual nucleoporins and grafted rings of nups mimicking the in vivo geometry of the NPC and supplement this with polymer brush modeling. Our results indicate that different regions or blocks of an individual NPC protein can have distinctly different forms of disorder and that this property appears to be a conserved functional feature. Furthermore, this block structure at the individual protein level is critical to the formation of a unique higher-order polymer brush architecture that can exist in distinct morphologies depending on the effective interaction energy between the phenylalanine glycine (FG) domains of different nups. Because the interactions between FG domains may be modulated by certain forms of transport factors, our results indicate that transitions between brush morphologies could play an important role in regulating transport across the NPC, suggesting novel forms of gated transport across membrane pores with wide biomimetic applicability.

Response of microRNAs to in vitro treatment with graphene oxide

Graphene oxide (GO) can be potentially used in biomedical and nonbiomedical products. The in vivo studies have demonstrated that GO is predominantly deposited in the lung. In the present study, we employed SOLiD sequencing technique to investigate the molecular control of in vitro GO toxicity in GLC-82 pulmonary adenocarcinoma cells by microRNAs (miRNAs), a large class of short noncoding RNAs acting to post-transcriptionally inhibit gene expression. In GLC-82 cells, GO exposure at concentrations more than 50 mg/L resulted in severe reduction in cell viability, induction of lactate dehydrogenase leakage, reactive oxygen species production and apoptosis, and dysregulation of cell cycle. GO was localized in cytosol, mitochondria, endoplasmic reticulum, and nucleus of cells. Based on SOLiD sequencing, we identified 628 up-regulated and 25 down-regulated miRNAs in GO-exposed GLC-82 cells. Expression of some selected dysregulated miRNAs was concentration-dependent in GO-exposed GLC-82 cells. The dysregulated miRNAs and their predicted targeted genes were involved in many biological processes. By combining both information on targeted genes for dysregulated miRNAs and known signaling pathways for apoptosis control, we hypothesize that the dysregulated miRNAs could activate both a death receptor pathway by influencing functions of tumor necrosis factor α receptor and caspase-3 and a mitochondrial pathway by affecting functions of p53 and Bcl-2 in GO-exposed GLC-82 cells. Our results provide an important molecular basis at the miRNA level for explaining in vitro GO toxicity. Our data will be also useful for developing new strategies to reduce GO toxicity such as surface chemical modification.

Karyopherins: potential biological elements involved in the delayed graft function in renal transplant recipients

Background

Immediately after renal transplantation, patients experience rapid and significant improvement of their clinical conditions and undergo considerable systemic and cellular modifications. However, some patients present a slow recovery of the renal function commonly defined as delayed graft function (DGF). Although clinically well characterized, the molecular mechanisms underlying this condition are not totally defined, thus, we are currently missing specific clinical markers to predict and to make early diagnosis of this event.

Methods

We investigated, using a pathway analysis approach, the transcriptomic profile of peripheral blood mononuclear cells (PBMC) from renal transplant recipients with DGF and with early graft function (EGF), before (T0) and 24 hours (T24) after transplantation.

Results

Bioinformatics/statistical analysis showed that 15 pathways (8 up-regulated and 7 down-regulated) and 11 pathways (5 up-regulated and 6 down-regulated) were able to identify DGF patients at T0 and T24, respectively. Interestingly, the most up-regulated pathway at both time points was NLS-bearing substrate import into nucleus, which includes genes encoding for several subtypes of karyopherins, a group of proteins involved in nucleocytoplasmic transport. Signal transducers and activators of transcription (STAT) utilize karyopherins-alpha (KPNA) for their passage from cytoplasm into the nucleus. In vitro functional analysis demonstrated that in PBMCs of DGF patients, there was a significant KPNA-mediated nuclear translocation of the phosphorylated form of STAT3 (pSTAT3) after short-time stimulation (2 and 5 minutes) with interleukin-6.

Conclusions

Our study suggests the involvement, immediately before transplantation, of karyopherin-mediated nuclear transport in the onset and development of DGF. Additionally, it reveals that karyopherins could be good candidates as potential DGF predictive clinical biomarkers and targets for pharmacological interventions in renal transplantation. However, because of the low number of patients analyzed and some methodological limitations, additional studies are needed to validate and to better address these points.

Ion permeability of the nuclear pore complex and ion-induced macromolecular permeation as studied by scanning electrochemical and fluorescence microscopy

Efficient delivery of therapeutic macromolecules and nanomaterials into the nucleus is imperative for gene therapy and nanomedicine. Nucleocytoplasmic molecular transport, however, is tightly regulated by the nuclear pore complex (NPC) with the hydrophobic transport barriers based on phenylalanine and glycine repeats. Herein, we apply scanning electrochemical microscopy (SECM) to quantitatively study the permeability of the NPCs to small probe ions with a wide range of hydrophobicity as a measure of their hydrophobic interactions with the transport barriers. Amperometric detection of the redox-inactive probe ions is enabled by using the ion-selective SECM tips based on the micropipet- or nanopipet-supported interfaces between two immiscible electrolyte solutions. The remarkably high ion permeability of the NPCs is successfully measured by SECM and theoretically analyzed. This analysis demonstrates that the ion permeability of the NPCs is determined by the dimensions and density of the nanopores without a significant effect of the transport barriers on the transported ions. Importantly, the weak ion-barrier interactions become significant at sufficiently high concentrations of extremely hydrophobic ions, i.e., tetraphenylarsonium and perfluorobutylsulfonate, to permeabilize the NPCs to naturally impermeable macromolecules. Dependence of ion-induced permeabilization of the NPC on the pathway and mode of macromolecular transport is studied by using fluorescence microscopy to obtain deeper insights into the gating mechanism of the NPC as the basis of a new transport model.

Origins of nanoscale damage to glass-sealed platinum electrodes with submicrometer and nanometer size

Glass-sealed Pt electrodes with submicrometer and nanometer size have been successfully developed and applied for nanoscale electrochemical measurements such as scanning electrochemical microscopy (SECM). These small electrodes, however, are difficult to work with because they often lose a current response or give a low SECM feedback in current-distance curves. Here we report that these problems can be due to the nanometer-scale damage that is readily and unknowingly made to the small tips in air by electrostatic discharge or in electrolyte solution by electrochemical etching. The damaged Pt electrodes are recessed and contaminated with removed electrode materials to lower their current responses. The recession and contamination of damaged Pt electrodes are demonstrated by scanning electron microscopy and X-ray energy dispersive spectroscopy. The recessed geometry is noticeable also by SECM but is not obvious from a cyclic voltammogram. Characterization of a damaged Pt electrode with recessed geometry only by cyclic voltammetry may underestimate electrode size from a lower limiting current owing to an invalid assumption of inlaid disk geometry. Significantly, electrostatic damage can be avoided by grounding a Pt electrode and nearby objects, most importantly, an operator as a source of electrostatic charge. Electrochemical damage can be avoided by maintaining potentiostatic control of a Pt electrode without internally disconnecting the electrode from a potentiostat between voltammetric measurements. Damage-free Pt electrodes with submicrometer and nanometer sizes are pivotal for reliable and quantitative nanoelectrochemical measurements.