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1.  Single-Cell Quantification of Cytosine Modifications by Hyperspectral Dark-Field Imaging 
ACS nano  2015;9(12):11924-11932.
Epigenetic modifications on DNA, especially on cytosine, play a critical role in regulating gene expression and genome stability. It is known that the levels of different cytosine derivatives are highly dynamic and are regulated by a variety of factors that act on the chromatin. Here we report an optical methodology based on hyperspectral dark-field imaging (HSDFI) using plasmonic nanoprobes to quantify the recently identified cytosine modifications on DNA in single cells. Gold (Au) and silver (Ag) nanoparticles (NPs) functionalized with specific antibodies were used as contrast-generating agents due to their strong Local Surface Plasmon Resonance (LSPR) properties. With this powerful platform we have revealed the spatial distribution and quantity of 5-carboxylcytosine (5caC) at the different stages in cell cycle, and demonstrated that 5caC was a stably inherited epigenetic mark. We have also shown that the regional density of 5caC on a single chromosome can be mapped due to the spectral sensitivity of the nanoprobes in relation to the inter-particle distance. Notably, HSDFI enables an efficient removal of the scattering noises from non-specifically aggregated nanoprobes, to improve accuracy in the quantification of different cytosine modifications in single cells. Further, by separating the LSPR fingerprints of AuNPs and AgNPs, multiplex detection of two cytosine modifications was also performed. Our results demonstrate HSDFI as a versatile platform for spatial and spectroscopic characterization of plasmonic nanoprobe-labeled nuclear targets at the single-cell level for quantitative epigenetic screening.
doi:10.1021/acsnano.5b04451
PMCID: PMC4766098  PMID: 26505210
quantitative imaging; epigenetics; cytosine modification; hyperspectral dark-field microscopy; plasmonic nanoprobes
2.  A Study of Alterations in DNA Epigenetic Modifications (5mC and 5hmC) and Gene Expression Influenced by Simulated Microgravity in Human Lymphoblastoid Cells 
PLoS ONE  2016;11(1):e0147514.
Cells alter their gene expression in response to exposure to various environmental changes. Epigenetic mechanisms such as DNA methylation are believed to regulate the alterations in gene expression patterns. In vitro and in vivo studies have documented changes in cellular proliferation, cytoskeletal remodeling, signal transduction, bone mineralization and immune deficiency under the influence of microgravity conditions experienced in space. However microgravity induced changes in the epigenome have not been well characterized. In this study we have used Next-generation Sequencing (NGS) to profile ground-based “simulated” microgravity induced changes on DNA methylation (5-methylcytosine or 5mC), hydroxymethylation (5-hydroxymethylcytosine or 5hmC), and simultaneous gene expression in cultured human lymphoblastoid cells. Our results indicate that simulated microgravity induced alterations in the methylome (~60% of the differentially methylated regions or DMRs are hypomethylated and ~92% of the differentially hydroxymethylated regions or DHMRs are hyperhydroxymethylated). Simulated microgravity also induced differential expression in 370 transcripts that were associated with crucial biological processes such as oxidative stress response, carbohydrate metabolism and regulation of transcription. While we were not able to obtain any global trend correlating the changes of methylation/ hydroxylation with gene expression, we have been able to profile the simulated microgravity induced changes of 5mC over some of the differentially expressed genes that includes five genes undergoing differential methylation over their promoters and twenty five genes undergoing differential methylation over their gene-bodies. To the best of our knowledge, this is the first NGS-based study to profile epigenomic patterns induced by short time exposure of simulated microgravity and we believe that our findings can be a valuable resource for future explorations.
doi:10.1371/journal.pone.0147514
PMCID: PMC4731572  PMID: 26820575
3.  Decitabine Nano-conjugate Sensitizing Human Glioblastoma Cells to Temozolomide 
Molecular pharmaceutics  2015;12(4):1279-1288.
In this study we developed and characterized a delivery system for the epigenetic demethylating drug, decitabine, to sensitize temozolomide-resistant human glioblastoma multiforme (GBM) cells to alkylating chemotherapy. A poly(lactic-co-glycolic acid) (PLGA) and polyethylene glycol (PEG) based nano-conjugate was fabricated to encapsulate decitabine and achieved a better therapeutic response in GBM cells. After synthesis, the highly efficient uptake process and intracellular dynamics of this nano-conjugate was monitored by single-molecule fluorescence tools. Our experiments demonstrated that, under an acidic pH due to active glycolysis in cancer cells, the PLGA-PEG nano-vector could release the conjugated decitabine at a faster rate, after which the hydrolyzed lactic acid and glycolic acid would further acidify the intracellular microenvironment, thus providing a “positive feedback” to increase the effective drug concentration and realize growth inhibition. In temozolomide-resistant GBM cells, decitabine can potentiate the cytotoxic DNA alkylation by counteracting cytosine methylation and reactivating tumor suppressor genes, such as p53 and p21. Owing to excellent internalization and endo-lysosomal escape enabled by the PLGA-PEG backbone, the encapsulated decitabine exhibited a better anti-GBM potential than free drug molecules. Hence, the synthesized nano-conjugate and temozolomide could act in synergy to deliver a more potent and long-term anti-proliferation effect against malignant GBM cells.
doi:10.1021/mp500815b
PMCID: PMC4689316  PMID: 25751281
Decitabine; Temozolomide; Glioblastoma Multiforme; Single-molecule Spectroscopy; Drug delivery; Nano-conjugate
4.  Second Harmonic Super-resolution Microscopy for Quantification of mRNA at Single Copy Sensitivity 
ACS Nano  2014;8(12):12418-12427.
Cell-specific information on the quantity and localization of key mRNAs at single copy sensitivity in single cells is critical for evaluating basic cellular process, disease risk, and efficacy of therapy. Quantification of overexpressed mRNAs beyond the diffraction limit is constrained by the optical property of the probes and microscopy techniques. In this report, nanosized barium titanium oxide (BaTiO3, BTO) crystals were utilized as probes for mRNA quantification by a second harmonic super-resolution microscopy (SHaSM). The SHaSM was able to detect a single copy of the human epidermal growth factor receptor 2 (Her2) mRNA at a resolution of 55.6 nm with the ability to resolve multiple mRNA copies in a diffraction-limited spot. Her2 mRNA per cell was counted in SK-BR-3, MCF-7, and HeLa cell lines as 595 ± 79.1, 38.9 ± 8.26, and 1.5 ± 2.8, respectively. Our single-cell quantification results were validated with the fluorescence in situ hybridization studies and quantitative PCR, showing better specificity and selectivity over current single-molecule approaches for transcript detection. The SHaSM is expected to have an upper limit of resolving ∼104 transcripts in a single cell with the ability to monitor intracellular transcriptional dynamics at video rate. The developed approach has strong potential in clinical research and in the early diagnosis of life-threatening diseases such as cancer.
doi:10.1021/nn505096t
PMCID: PMC4334232  PMID: 25494326
super-resolution microscopy; second harmonic generation; BaTiO3 nanocrystals; single-copy detection; mRNA quantification; diagnostics
5.  Quantification of 5-methylcytosine, 5-hydroxymethylcytosine and 5-carboxylcytosine from the blood of cancer patients by an Enzyme-based Immunoassay 
Analytica chimica acta  2014;852:212-217.
Background
Genome-wide aberrations of the classic epigenetic modification 5-methylcytosine (5mC), considered the hallmark of gene silencing, has been implicated to play a pivotal role in mediating carcinogenic transformation of healthy cells. Recently, three epigenetic marks derived from enzymatic oxidization of 5mC namely 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), have been discovered in the mammalian genome. Growing evidence suggests that these novel bases possess unique regulatory functions and may play critical roles in carcinogenesis.
Methods
To provide a quantitative basis for these rare epigenetic marks, we have designed a biotin-avidin mediated Enzyme-based Immunoassay (EIA) and evaluated its performance in genomic DNA isolated from blood of patients diagnosed with metastatic forms of lung, pancreatic and bladder cancer, as well as healthy controls. The proposed EIA incorporates spatially optimized biotinylated antibody and a high degree of horseradish-peroxidase (HRP) labeled streptavidin, facilitating signal amplification and sensitive detection.
Results
We report that the percentages of 5mC, 5hmC and 5caC present in the genomic DNA of blood in healthy controls as 1.025 + 0.081, 0.023 + 0.006 and 0.001 + 0.0002 respectively. We observed a significant (p<0.05) decrease in the mean global percentage of 5hmC in blood of patients with malignant lung cancer (0.013 + 0.003 %) in comparison to healthy controls.
Conclusion
The precise biological roles of these epigenetic modifications in cancers are still unknown but in the past two years it has become evident that the global 5hmC content is drastically reduced in a variety of cancers. To the best of our knowledge, this is the first report of decreased 5hmC content in the blood of metastatic lung cancer patients and the clinical utility of this observation needs to be further validated in larger sample datasets.
doi:10.1016/j.aca.2014.09.020
PMCID: PMC4254572  PMID: 25441900
5-methylcytosine (5mC); 5-hydroxymethylcytosine (5hmC); 5-formylcytosine (5fC); 5-carboxylcytosine (5caC); Enzyme-based Immunoassay (EIA); Cancer; Epigenetic modifications
6.  Graphene laminated gold bipyramids as sensitive detection platforms of antibiotic molecules 
Atomic layers of graphene were optomechanically laminated onto gold bipyramids (length of ~95±3 nm and sharp tips radius is less than 10 nm) using laser induced shock pressure. Fabricated graphene-gold bipyramid hybrids were employed as surface enhanced Raman scattering (SERS)-active substrates for the detection of tetracycline, an antibiotic, at very low concentration.
doi:10.1039/c5cc04890g
PMCID: PMC4605881  PMID: 26340316
7.  Trichloroethylene sensing in water based on SERS with multifunctional Au/TiO2 core-shell nanocomposites 
The Analyst  2015;140(19):6625-6630.
Herein we report on a rapid and highly sensitive scheme to detect trichloroethylene (TCE), an environmental contaminant, by surface enhanced Raman scattering (SERS) with multifunctional Au/TiO2 core-shell nanocomposites as SERS substrates. A facile approach to fabricate TiO2 shell around gold core nanocomposites is proposed as sensors for TCE detection by SERS. During detection, TCE was first oxidized due to the photocatalytic activity of the TiO2 shell and the increase in SERS intensity due to the product of TCE photooxidation can be used to determine the concentration of TCE. It should be noted that the SERS of the Raman label, 4-mercaptopyridine (4-MPy) modified onto the gold nanoparticle (GNP) core is in proportion to the product of TCE photooxidation. After optimizing the sample pH, enrichment of the analyte, and the UV exposure time, the methodology developed accomplishes an excellent limit of detection (LOD) (0.038 μM, ie. ~5 ppb) for TCE in water. Our unique approach based on the synthesized SERS composite to detect TCE, a chlorinated environmental contaminant directly in water could pave the way for the development of a multifunctional nanosensor platform to monitor TCE and the catalytic reactions in a multiplex format.
doi:10.1039/c5an01294e
PMCID: PMC4571490  PMID: 26332451
8.  Selective increase in subtelomeric DNA methylation: an epigenetic biomarker for malignant glioma 
Clinical Epigenetics  2015;7:107.
Background
Subtelomeric regions dynamically change their epigenetic pattern during development and progression of several malignancies and degenerative disorders. However, DNA methylation of human subtelomeres and their correlation to telomere length (TL) remain undetermined in glioma.
Results
Herein, we report on the selective changes in subtelomeric DNA methylation at the end of five chromosomes (Chr.) (7q, 8q. 18p, 21q, and XpYp) and ascertain their correlation with TL in patients with glioma. Subtelomeric methylation level was invariably higher in glioma patients compared to the control group, irrespective of their age and tumor grade. In particular, a significant increase in methylation was observed at the subtelomeric CpG sites of Chr. 8q, 21q, and XpYp in tissues, obtained from the brain tumor of glioma patients. In contrast, no significant change in methylation was observed at the subtelomere of Chr. 7q and 18p. Selective changes in the subtelomeric methylation level, however, did not show any significant correlation to the global TL. This observed phenomenon was validated in vitro by inducing demethylation in a glioblastoma cell line (SF-767) using 5-azacytidine (AZA) treatment. AZA treatment caused significant changes in the subtelomeric methylation pattern but did not alter the TL, which supports our hypothesis.
Conclusions
DNA methylation level dramatically increased at the subtelomere of Chr.8q, 21q, and XpYp in malignant glioma, which could be used as an early epigenetic diagnostic biomarker of the disease. Alterations in subtelomeric methylation, however, have no effects on the TL.
Electronic supplementary material
The online version of this article (doi:10.1186/s13148-015-0140-y) contains supplementary material, which is available to authorized users.
doi:10.1186/s13148-015-0140-y
PMCID: PMC4597615  PMID: 26451167
Subtelomeric DNA methylation; Telomere length; Glioma; Epigenetic biomarker
9.  Quantitative real-time kinetics of optogenetic proteins CRY2 and CIB1/N using single-molecule tools 
Analytical biochemistry  2014;458:58-60.
In this work we evaluate the interaction of two optogenetic protein variants (CIB1, CIBN) with their complementary protein CRY2 by single-molecule tools in cell-free extracts. After validating the blue light induced co-localization of CRY2 and CIB1/N by Förster resonance energy transfer (FRET) in live cells, a fluorescence correlation spectroscopy (FCS) based method was developed to quantitatively determine the in vitro association of the extracted proteins. Our experiments suggest that CIB1, in comparison with CIBN, possesses a better coupling efficiency with CRY2 due to its intact protein structure and lower diffusion rate within 300 s detection window.
doi:10.1016/j.ab.2014.04.023
PMCID: PMC4341968  PMID: 24780222
Optogenetic protein; CIB1; CIBN; CRY2; FRET; FCS
10.  Quantifying local density of optical states of nanorods by fluorescence lifetime imaging 
New journal of physics  2014;16:063069-.
In this letter, we demonstrate a facile far-field approach to quantify the near-field local density of optical states (LDOS) of a nanorod using CdTe quantum dots (QDs) emitters tethered to the surface of nanorods as beacons for optical read-outs. Radiative decay rate was extracted to quantify the LDOS; our analysis indicates that the LDOS of the nanorod enhance both the radiative and nonradiative decay of QD, particularly radiative decay of QDs at the end of nanorod is enhanced by 1.17 times greater than that at the waist, while the nonradiative decay was uniformly enhanced over the nanorod. To the best of our knowledge, our effort constitutes the first to map the LDOS of a nanostructure via far-field method, to provide clarity on the interaction mechanism between emitters and the nanostructure, and to be potentially employed in the LDOS mapping of high-throughput nanostructures.
doi:10.1088/1367-2630/16/6/063069
PMCID: PMC4232967  PMID: 25408619
LDOS; FLIM; Quantum Dots; Far field
11.  Quantitative Imaging of Single mRNA Splice Variants in Living Cells 
Nature nanotechnology  2014;9(6):474-480.
Alternative mRNA splicing is a fundamental process of gene regulation via the precise control of the post-transcriptional step that occurs before mRNA translation. Errors in RNA splicing have been known to correlate with different diseases; however, a key limitation is the lack of technologies for live cell monitoring and quantification to understand the process of alternative splicing. Here, we report a spectroscopic strategy for quantitative imaging of mRNA splice variants in living cells, using nanoplasmonic dimer antennas. The spatial and temporal distribution of three selected splice variants of the breast cancer susceptibility gene, BRCA1 were monitored at single copy resolution by measuring the hybridization dynamics of nanoplasmonic antennas targeting complementary mRNA sequences in live cells. Our study provides valuable insights on RNA and its transport in living cells, which has the potential to enhance our understanding of cellular protein complex, pharmacogenomics, genetic diagnosis, and gene therapies.
doi:10.1038/nnano.2014.73
PMCID: PMC4426190  PMID: 24747838
mRNA detection; splicing; single molecule detection; hyperspectral intracellular imaging; transcript quantification; single cell/molecule imaging
12.  Dissecting the behavior and function of MBD3 in DNA methylation homeostasis by single-molecule spectroscopy and microscopy 
Nucleic Acids Research  2015;43(6):3046-3055.
The detailed mechanism for DNA methylation homeostasis relies on an intricate regulatory network with a possible contribution from methyl-CpG-binding domain protein 3 (MBD3). In this study we examine the single-molecule behavior of MBD3 and its functional implication in balancing the activity of DNA methyltransferases (DNMTs). Besides a localization tendency to DNA demethylating sites, MBD3 experiences a concurrent transcription with DNMTs in cell cycle. Fluorescence lifetime correlation spectroscopy (FLCS) and photon counting histogram (PCH) were applied to characterize the chromatin binding kinetics and stoichiometry of MBD3 in different cell phases. In the G1-phase, MBD3, in the context of the Mi-2/NuRD (nucleosome remodeling deacetylase) complex, could adopt a salt-dependent homodimeric association with its target epigenomic loci. Along with cell cycle progression, utilizing fluorescence lifetime imaging microscopy-based Förster resonance energy transfer (FLIM-FRET) we revealed that a proportion of MBD3 and MBD2 would co-localize with DNMT1 during DNA maintenance methylation, providing a proofreading and protective mechanism against a possible excessive methylation by DNMT1. In accordance with our hypothesis, insufficient MBD3 induced by small interfering RNA (siRNA) was found to result in a global DNA hypermethylation as well as increased methylation in the promoter CpG islands (CGIs) of a number of cell cycle related genes.
doi:10.1093/nar/gkv098
PMCID: PMC4381056  PMID: 25753672
13.  One-stop Genomic DNA Extraction by Salicylic Acid Coated Magnetic Nanoparticles 
Analytical biochemistry  2013;442(2):249-252.
Salicylic acid coated magnetic nanoparticles were prepared via a modified, one-step synthesis and used for a one-stop extraction of genomic DNA from mammalian cells. The synthesized magnetic particles were used for magnetic separation of cells from the media by non-specific binding of the particles, as well as extraction of genomic DNA from the lysate. The quantity and quality were confirmed by agarose gel electrophoresis and polymerase chain reaction. The entire process of extraction and isolation can be completed within 30 min. Compared to traditional methods based on centrifugation and filtration, the established method is fast, simple, reliable, and environmentally-friendly.
doi:10.1016/j.ab.2013.07.030
PMCID: PMC4281273  PMID: 23911528
Salicylic acid; Magnetic nanoparticles; genomic DNA; extraction; simple and rapid
14.  Real-time dynamics of methyl-CpG-binding domain protein 3 and its role in DNA demethylation by fluorescence correlation spectroscopy 
Epigenetics  2013;8(10):1089-1100.
With unprecedented development in technology, epigenetics is recognized as a substantial and flexible regulatory pathway for phenotyping. Cytosine methylation and its subsequent oxidization have attracted significant attention due to their direct impact on gene regulation, in association with methyl-CpG-binding domain proteins (MBDs) and transcription related factors. In this study we record the dynamics of DNA demethylation using the recombinant MBD3-GFP protein in living cells under hypoxia and Decitabine treatment using Fluorescence Correlation Spectroscopy (FCS) by monitoring the diffusion dynamics of MBD3. Our study shows a DNA-replication-independent decrease of 5-methylcytosine (5mC)/5-hydroxymethylcytosine (5hmC) under hypoxia vs. a dependent decrease under Decitabine treatment. Further, we define a significantly faster diffusion of MBD3 in the nucleus as a precursory event for active demethylation rather than the Decitabine induced passive demethylation. By monitoring the diffusion of bound and unbound MBD3 in the nucleus we were able to identify and characterize hypoxia-sensitive cells from insensitive/tolerant cells, as well as the respective contribution to active demethylation in a time-dependent manner. Last, we quantitatively describe the concurrent decreasing trend in all of the three oxidized products of 5mC, which points to the potential involvement of ten-eleven-translocation proteins (TETs) in hypoxia induced active demethylation. Overall, for the first time we correlate the dynamic process of DNA demethylation with the biophysical properties of the corresponding DNA binding proteins in live single cells by single molecule spectroscopy.
doi:10.4161/epi.25958
PMCID: PMC3891690  PMID: 23974971
DNA demethylation; methyl-CpG-binding domain protein 3 (MBD3); ten-eleven-translocation proteins (TETs); dynamics; nuclear protein; fluorescence correlation spectroscopy (FCS); biophysics
15.  NuMA promotes homologous recombination repair by regulating the accumulation of the ISWI ATPase SNF2h at DNA breaks 
Nucleic Acids Research  2014;42(10):6365-6379.
Chromatin remodeling factors play an active role in the DNA damage response by shaping chromatin to facilitate the repair process. The spatiotemporal regulation of these factors is key to their function, yet poorly understood. We report that the structural nuclear protein NuMA accumulates at sites of DNA damage in a poly[ADP-ribose]ylation-dependent manner and functionally interacts with the ISWI ATPase SNF2h/SMARCA5, a chromatin remodeler that facilitates DNA repair. NuMA coimmunoprecipitates with SNF2h, regulates its diffusion in the nucleoplasm and controls its accumulation at DNA breaks. Consistent with NuMA enabling SNF2h function, cells with silenced NuMA exhibit reduced chromatin decompaction after DNA cleavage, lesser focal recruitment of homologous recombination repair factors, impaired DNA double-strand break repair in chromosomal (but not in episomal) contexts and increased sensitivity to DNA cross-linking agents. These findings reveal a structural basis for the orchestration of chromatin remodeling whereby a scaffold protein promotes genome maintenance by directing a remodeler to DNA breaks.
doi:10.1093/nar/gku296
PMCID: PMC4041463  PMID: 24753406
16.  Fluorescence lifetime imaging of biosensor peptide phosphorylation in single live cells 
doi:10.1002/anie.201209303
PMCID: PMC3779901  PMID: 23450802
fluorescence lifetime imaging microscopy; Abl kinase; inhibitors; fluorescent probes; kinase biosensor
17.  Diversity of two forms of DNA methylation in the brain 
DNA methylation 5-methylcytosine (5mC) predicts a compacting chromatin inaccessible to transcription. The discovery of 5-hydroxymethylcytosine (5hmC), which is derived from 5mC, adds a new dimension to the mechanism and role of DNA methylation in epigenetics. Genomic evidence indicates that the 5hmC is located in the alternate regions to 5mC. However, the nature of 5hmC, as compared with classical 5mC remains unclear. Observing the mouse brain through embryonic development to the adult, first, we found that 5hmC is not merely an intermediate metabolite of demethylation, but is long lasting, chromatically distinct, and dynamically changing during neurodevelopment. Second, we found that 5hmC distinctly differs from 5mC in its chromatin affiliation during neural stem cell (NSC) development. Thirdly, we found both 5mC and 5hmC to be uniquely polarized and dynamic through the NSC development. 5mC was found to progressively polarize with MBD1 and MeCP2, and recruits H3K9me3 and H3K27me3; while 5hmC progressively co-localizes with MBD3 and recruits H3K4me2. Critical differential binding of 5mC with MBD1, and 5hmC with MBD3 was validated by Resonance Energy Transfer technique FLIM-FRET. This transition and polarization coincides with neuroprogenitor differentiation. Finally, at the time of synaptogenesis, 5mC gradually accumulates in the heterochromatin while 5hmC accumulates in the euchromatin, which is consistent with the co-localization of 5hmC with PolII, which mediates RNA transcription. Our data indicate that 5mC and 5hmC are diverse in their functional interactions with chromatin. This diversity is likely to contribute to the versatile epigenetic control of transcription mediating brain development and functional maintenance of adult brain.
doi:10.3389/fgene.2014.00046
PMCID: PMC3948076  PMID: 24653733
epigenetics; 5-methylcytosine; 5-hydroxymethylcytosine; chromatin remodeling; histone code; confocal microscopy; FLIM-FRET
18.  Surface-enhanced Raman spectroscopy at single-molecule scale and its implications in biology 
Single-molecule (SM) spectroscopy has been an exciting area of research offering significant promise and hope in the field of sensor development to detect targets at ultra-low levels down to SM resolution. To the experts and developers in the field of surface-enhanced Raman spectroscopy (SERS), this has often been a challenge and a significant opportunity for exploration. Needless to say, the opportunities and excitement of this multidisciplinary area impacts span the fields of physics, chemistry and engineering, along with a significant thrust in applications constituting areas in medicine, biology, environment and agriculture among others. In this review, we will attempt to provide a quick snapshot of the basics of SM-SERS, nanostructures and devices that can enable SM Raman measurement. We will conclude with a discussion on SERS implications in biomedical sciences.
doi:10.1098/rstb.2012.0026
PMCID: PMC3538429  PMID: 23267180
single molecule; surface-enhanced Raman spectroscopy; nanotechnology; hot spot; biological sciences
19.  Intracellularly grown gold nanoislands as SERS substrates for monitoring chromate, sulfate and nitrate localization sites in remediating bacteria biofilms by Raman chemical imaging 
Analytica chimica acta  2012;745C:1-9.
Understanding the chemical composition of biofilm matrices is vital in different fields of biology such as surgery, dental medicine, synthetic grafts and bioremediation. The knowledge of biofilm development, composition, active reduction sites and remediation efficacy will help in the development of effective solutions and evaluation of remediating approaches prior to implementation. Surface-enhanced Raman spectroscopy (SERS) based imaging is an invaluable tool to obtain an understanding of the remediating efficacy of microorganisms and its role in the formation of organic and inorganic compounds in biofilms. We demonstrate for the first time, the presence of chromate, sulfate, nitrate and reduced trivalent chromium in soil biofilms. In addition, we demonstrate that SERS imaging was able to validate two observations made by previous studies on chromate/sulfate and chromate/nitrate interactions in Shewanella oneidensis MR-1 biofilms. Additionally, we show a detailed Raman mapping based evidence of the existence of chromate-sulfate competition for cellular entry. Subsequently, we use Raman mapping to study the effect of nitrate on chromate reduction. The findings presented in this paper are among the first to report- detection of multiple metallic ions in bacterial biofilms using intracellular SERS substrates. Such a detailed characterization of biofilms using gold nanoislands based SERS mapping substrate can be extended to study cellular localization of other metallic ions and chemical species of biological and toxicological significance and their effect on reduction reactions in bacterial biofilms.
doi:10.1016/j.aca.2012.07.037
PMCID: PMC3432932  PMID: 22938600
Surface-enhanced Raman spectroscopy (SERS); Chemical Imaging; Hexavalent Chromate; Sulfate; Nitrate; Bioremediation; Shewanella oneidensis MR-1
21.  Gold nanoprobes for theranostics 
Nanomedicine (London, England)  2011;6(10):1787-1811.
Gold nanoprobes have become attractive diagnostic and therapeutic agents in medicine and life sciences research owing to their reproducible synthesis with atomic level precision, unique physical and chemical properties, versatility of their morphologies, flexibility in functionalization, ease of targeting, efficiency in drug delivery and opportunities for multimodal therapy. This review highlights some of the recent advances and the potential for gold nanoprobes in theranostics.
doi:10.2217/nnm.11.155
PMCID: PMC3236610  PMID: 22122586
diagnostics; gold nanoparticles; imaging; therapeutics; toxicity
22.  FTIR nanobiosensors for Escherichia coli detection 
Summary
Infections due to enterohaemorrhagic E. coli (Escherichia coli) have a low incidence but can have severe and sometimes fatal health consequences, and thus represent some of the most serious diseases due to the contamination of water and food. New, fast and simple devices that monitor these pathogens are necessary to improve the safety of our food supply chain. In this work we report on mesoporous titania thin-film substrates as sensors to detect E. coli O157:H7. Titania films treated with APTES ((3-aminopropyl)triethoxysilane) and GA (glutaraldehyde) were functionalized with specific antibodies and the absorption properties monitored. The film-based biosensors showed a detection limit for E. coli of 1 × 102 CFU/mL, constituting a simple and selective method for the effective screening of water samples.
doi:10.3762/bjnano.3.55
PMCID: PMC3458592  PMID: 23019542
biosensors; E. coli; FTIR spectroscopy; foodborne pathogens; nanomaterials
23.  Raman Chemical Imaging of Chromate Reduction Sites in a Single Bacterium Using Intracellularly Grown Gold Nanoislands 
ACS nano  2011;5(6):4729-4736.
Imagingon act live molecular events within micro-organisms at single cell resolution would deliver valuable mechanistic information much needed in understanding key biological processes. We present a surface-enhanced Raman (SERS) chemical imaging strategy as a first step towards exploring the intracellular bioreduction pockets of toxic chromate in Shewanella. In order to achieve this, we take advantage of an innate reductive mechanism in bacteria of reducing gold ions into intracellular gold nanoislands which provide the necessary enhancement for SERS imaging. We show that SERS has the sensitivity and selectivity not only to identify, but also to differentiate between the two stable valence forms of chromate in cells. The imaging platform was used to understand intracellular metal reductiivities in a ubiquitous metal-reducing organism Shewanella oneidensis MR-1, by mapping Chromate reduction.
doi:10.1021/nn201105r
PMCID: PMC3140767  PMID: 21634405
Surface Enhanced Raman Spectroscopy; Shewanella oneidensis MR-1; Single Cell Raman Imaging; Hexavalent Chromate; Bioremediation
24.  Single Molecule In Vivo Analysis of Toll-Like Receptor 9 and CpG DNA Interaction 
PLoS ONE  2011;6(4):e17991.
Toll-like receptor 9 (TLR9) activates the innate immune system in response to oligonucleotides rich in CpG whereas DNA lacking CpG could inhibit its activation. However, the mechanism of how TLR9 interacts with nucleic acid and becomes activated in live cells is not well understood. Here, we report on the successful implementation of single molecule tools, constituting fluorescence correlation/cross-correlation spectroscopy (FCS and FCCS) and photon count histogram (PCH) with fluorescence lifetime imaging (FLIM) to study the interaction of TLR9-GFP with Cy5 labeled oligonucleotide containing CpG or lacking CpG in live HEK 293 cells. Our findings show that i) TLR9 predominantly forms homodimers (80%) before binding to a ligand and further addition of CpG or non CpG DNA does not necessarily increase the proportion of TLR9 dimers, ii) CpG DNA has a lower dissociation constant (62 nM±9 nM) compared to non CpG DNA (153 nM±26 nM) upon binding to TLR9, suggesting that a motif specific binding affinity of TLR9 could be an important factor in instituting a conformational change-dependant activation, and iii) both CpG and non CpG DNA binds to TLR9 with a 1∶2 stoichiometry in vivo. Collectively, through our findings we establish an in vivo model of TLR9 binding and activation by CpG DNA using single molecule fluorescence techniques for single cell studies.
doi:10.1371/journal.pone.0017991
PMCID: PMC3070698  PMID: 21483736
25.  Surface-Enhanced Raman Imaging of Intracellular Bioreduction of Chromate in Shewanella oneidensis 
PLoS ONE  2011;6(2):e16634.
This proposed research aims to use novel nanoparticle sensors and spectroscopic tools constituting surface-enhanced Raman spectroscopy (SERS) and Fluorescence Lifetime imaging (FLIM) to study intracellular chemical activities within single bioremediating microorganism. The grand challenge is to develop a mechanistic understanding of chromate reduction and localization by the remediating bacterium Shewanella oneidensis MR-1 by chemical and lifetime imaging. MR-1 has attracted wide interest from the research community because of its potential in reducing multiple chemical and metallic electron acceptors. While several biomolecular approaches to decode microbial reduction mechanisms exist, there is a considerable gap in the availability of sensor platforms to advance research from population-based studies to the single cell level. This study is one of the first attempts to incorporate SERS imaging to address this gap. First, we demonstrate that chromate-decorated nanoparticles can be taken up by cells using TEM and Fluorescence Lifetime imaging to confirm the internalization of gold nanoprobes. Second, we demonstrate the utility of a Raman chemical imaging platform to monitor chromate reduction and localization within single cells. Distinctive differences in Raman signatures of Cr(VI) and Cr(III) enabled their spatial identification within single cells from the Raman images. A comprehensive evaluation of toxicity and cellular interference experiments conducted revealed the inert nature of these probes and that they are non-toxic. Our results strongly suggest the existence of internal reductive machinery and that reduction occurs at specific sites within cells instead of at disperse reductive sites throughout the cell as previously reported. While chromate-decorated gold nanosensors used in this study provide an improved means for the tracking of specific chromate interactions within the cell and on the cell surface, we expect our single cell imaging tools to be extended to monitor the interaction of other toxic metal species.
doi:10.1371/journal.pone.0016634
PMCID: PMC3045368  PMID: 21364911

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