Integrating imaging and genomic data for the discovery of distinct glioblastoma subtypes: a joint learning approach

Glioblastoma is a highly heterogeneous disease, with variations observed at both phenotypical and molecular levels. Personalized therapies would be facilitated by non-invasive in vivo approaches for characterizing this heterogeneity. In this study, we developed unsupervised joint machine learning between radiomic and genomic data, thereby identifying distinct glioblastoma subtypes. A retrospective cohort of 571 IDH-wildtype glioblastoma patients were included in the study, and pre-operative multi-parametric MRI scans and targeted next-generation sequencing (NGS) data were collected. L21-norm minimization was used to select a subset of 12 radiomic features from the MRI scans, and 13 key driver genes from the five main signal pathways most affected in glioblastoma were selected from the genomic data. Subtypes were identified using a joint learning approach called Anchor-based Partial Multi-modal Clustering on both radiomic and genomic modalities. Kaplan-Meier analysis identified three distinct glioblastoma subtypes: high-risk, medium-risk, and low-risk, based on overall survival outcome (p < 0.05, log-rank test; Hazard Ratio = 1.64, 95% CI 1.17-2.31, Cox proportional hazard model on high-risk and low-risk subtypes). The three subtypes displayed different phenotypical and molecular characteristics in terms of imaging histogram, co-occurrence of genes, and correlation between the two modalities. Our findings demonstrate the synergistic value of integrated radiomic signatures and molecular characteristics for glioblastoma subtyping. Joint learning on both modalities can aid in better understanding the molecular basis of phenotypical signatures of glioblastoma, and provide insights into the biological underpinnings of tumor formation and progression.

NIMG-82. RADIOGENOMIC SIGNATURES OF KEY DRIVER GENES IN GBM REVEAL MOLECULAR HETEROGENEITY OF THE TUMOR MICROENVIRONMENT LINKED TO SPATIAL DISTRIBUTION: IMPACT ON THE TRAJECTORY OF GLIOMA EVOLUTION

Somatic genomic alterations acquired during GBM growth enhance adaptation of tumor cells to their microenvironment and give rise to molecular heterogeneity. Radiogenomics could facilitate exploration of the underlying pathobiology of tumor growth in specific microenvironments and thereby, promote precision medicine for the patients. We derived radiogenomic signatures of key driver genes and evaluated molecular compositions of tumor groups with predisposition to specific brain regions. Pre-operative multiparametric conventional MRI scans of 357 IDH-wildtype GBM patients with available targeted NGS data were jointly segmented and registered into a common template. We constructed spatial distribution atlases for tumors harboring mutations in driver genes and identified four distinct groups of tumor locations with predilection to the left frontal cingulate region (Group1), right temporal (Group2), right parietal (Group3), and occipital pole (Group4). Evaluation of the differences in molecular features of the tumor groups included: (1) exploring similarities of genomic profiles across all four groups by evaluating cosine similarity metric (CSM) between mutational signatures; (2) quantification of molecular heterogeneity based on Mutant Allele Tumor Heterogeneity (MATH) scores; and (3) inference of the evolutionary trajectories. Groups 1 and 4 were the most different, and Groups 2 and 3 were the most similar tumors, molecularly. The mutational signatures between Groups 1 and 4 revealed a CSM of 0.35. Group1 showed significantly lower MATH score (less heterogeneity) compared to Group4 (p&lt; 0.05). Evaluation of evolutionary patterns suggested NF1 mutation as an early event in Group1, without subsequent gain of function or mutation in EGFR. In contrast, in Group4, EGFR mutations were early events triggering PTEN mutations later in the evolutionary trajectory. Radiogenomic signatures revealed distinct molecular underpinnings for the tumors with predilection towards specific brain regions that may suggest existence of different tumor microenvironments in different brain regions that cause intra- and inter-patient heterogeneity in the molecular tumor composition.

NIMG-22. AN AI-BASED COORDINATE SYSTEM ELUCIDATES RADIOGENOMIC HETEROGENEITY OF GLIOBLASTOMA VIA DEEP LEARNING AND MANIFOLD EMBEDDINGS

PURPOSE

There is evidence that molecular heterogeneity of glioblastoma is associated with heterogeneity of MR imaging signatures. Modern machine learning models, such as deep neural networks, provide a tool for capturing such complex relationships in high-dimensional datasets. This study leverages recent advances in visualizing neural networks to construct a radiogenomics coordinate system whose axes reflect the expression of imaging signatures of genetic mutations commonly found in glioblastoma.

METHODS

Multi-parametric MRI (mpMRI) scans (T1, T1-Gd, T2, T2-FLAIR, DSC, DTI) of 254 subjects with glioblastoma were retrospectively collected. Radiomics features, including histograms, morphologic and textural descriptors, were derived. Genetic markers were obtained through next generation sequencing (NGS) panel. A multi-label classification deep neural network was trained for predicting mutation status in key driver genes, EGFR, PTEN, NF1, TP53 and RB1. We utilized a nonlinear manifold learning method called Intensive Principal Component Analysis (InPCA), to visualize the output probability distributions from the trained model. The first three principal components (PCs) were selected for constructing the coordinate system.

RESULTS

The axes derived from InPCA analysis were associated with molecular pathways known to be implicated in glioblastoma: (1) Increasing values of PC1 were associated with primary involvement of P53 then RB1 then MAPK then RTK/PI3K; (2) Increasing values of PC2 were associated with primary involvement of RTK then RB1/P53/MAPK then PI3K; (3) Increasing values of PC3 were associated with primary involvement of MAPK then RB1/P53/RTK/PI3K. Imaging features significantly associated with each of three PCs (p&lt; 0.05) were identified by Pearson correlation analysis.

CONCLUSION

Deep learning followed by nonlinear manifold embedding identifies a radiogenomics coordinate system spanned by three components which were associated with different molecular pathways of glioblastoma. The heterogeneity of radiogenomic signatures captured by this coordinate system offers in vivo biomarkers of the molecular heterogeneity of glioblastoma.

NIMG-37. JOINT LEARNING OF IMAGING AND GENOMIC DATA REVEALS DISTINCT GLIOBLASTOMA SUBTYPES

PURPOSE

The significant heterogeneity of glioblastoma is typically displayed on both phenotypical and molecular levels. Non-invasive in vivo approaches to characterize this heterogeneity would potentially facilitate personalized therapies. Here we leverage advanced unsupervised machine learning to integrate radiomic imaging features and genomics to identify distinct subtypes of glioblastoma.

METHODS

A retrospective cohort of 571 IDH-wildtype glioblastoma patients were collected with pre-operative multi-parametric MRI (T1, T1CE, T2, T2-FLAIR, DSC, DTI) scans (available in 462/571 patients) and targeted next-generation sequencing (NGS) data (available in 355/571 patients). Radiomic features (n= 971) were extracted from these MRI scans and a subset of 12 features were selected by L21-norm minimization. A total of 14 key driver genes in the 5 main pathways that are most frequently altered in glioblastoma were chosen. Subtypes were identified by a joint learning approach called Anchor-based Partial Multi-modal Clustering (APMC) on both radiomic and genomic modalities.

RESULTS

Three distinct glioblastoma subtypes were discovered by APMC based on 14-dimension NGS data together with 12 selected radiomic features representing characteristics from histograms, shape, and volumetric measures for different tumor sub-regions. The identified subtypes were 1) high-risk; 2) medium-risk; and 3) low-risk, in terms of their overall survival outcome in Kaplan-Meier analysis (p= 5.52e-6, log-rank test; HR= 1.51, 95%CI:1.20-1.74, Cox proportional hazard model). The three subtypes also displayed different molecular characteristics: subtype 1 exhibited increased frequency of mutation in [EGFR, PIK3CA, PTEN, NF1], subtype 3 showed frequently mutated [PDGFRA, ATRX], while subtype 2 did not show significant differences for mutations in any of these genes.

CONCLUSION

Our results revealed the synergistic value of integrated radiomic signatures and molecular characteristics for glioblastoma subtyping. Joint learning on both modalities could help better understand the molecular basis of phenotypical signatures of glioblastoma and further provide insights into the biologic underpinnings of tumor formation and progression.

EPCO-25. MULTI-OMICS DISEASE STRATIFICATION IN PATIENTS WITH IDH-WILDTYPE GLIOBLASTOMA: SYNERGISTIC VALUE OF CLINICAL MEASURES, CONVENTIONAL AND DEEP RADIOMICS, AND GENOMICS FOR PREDICTION OF OVERALL SURVIVAL

PURPOSE

Multi-omics data integration captures tumor characteristics at multiple scales [i.e., microscopic (genomics and epigenetics), macroscopic (radiomics), clinical manifestation], provides a more comprehensive assessment of patient’s risk, and facilitates personalized therapies. In this work, we investigated the synergistic value of such multiple data sources for risk stratification and prediction of overall survival in IDH-wildtype glioblastoma tumors.

METHODS

Quantitative conventional and deep radiomics were extracted from pre-operative multi-parametric structural MRI (T1, T1Gd, T2, T2-FLAIR) of 501 patients with newly diagnosed glioblastoma. 389/501 and 112/501 patients formed our discovery and replication cohorts, respectively. Conventional radiomics were extracted from CaPTk, and deep radiomics from a pre-trained VGG-19 model. Multivariate SVM classification was performed on the discovery cohort to stratify patients in high, medium, and low-risk groups, using recursive feature elimination and 5-fold cross-validation. This model was independently tested on the replication cohort, and a radiomic-based survival prediction index (SPIradiomics) was calculated for each patient. Multi-stage integration of omics data, i.e., clinical (age, gender, extent of resection (EOR)), SPIradiomics, epigenetics (MGMT promoter methylation), and genomics (27 clinically relevant gene mutations via next-generation sequencing (NGS)), was performed using multivariate Cox proportional hazards (Cox-PH) model for stratification of the risk in the replication cohort.

RESULTS

Cox-PH modeling resulted in a concordance index (c-index) of 0.65 (95% CI:0.6–0.7) for clinical data, 0.67 (95% CI:0.62–0.72) for clinical and epigenetics, 0.70 (95% CI:0.65–0.75) for clinical and radiomics, 0.72 (95% CI:0.68–0.77) for clinical, epigenetics, and radiomics, and 0.75 (95% CI:0.71 – 0.78) for the multi-omics combination of all data; highlighting the added value of each layer of information in prediction of the patient’s risk.

CONCLUSION

Our results reinforce the synergistic value of integrated diagnostic methods for improving risk assessment of patients with glioblastoma that may pave the path towards a more personalized treatment planning.

NIMG-58. CANONICAL CORRELATION ANALYSIS IN GLIOBLASTOMA REVEALS ASSOCIATIONS BETWEEN EXPRESSION OF RADIOMIC SIGNATURES AND GENOMICS

PURPOSE

Understanding the molecular underpinnings of imaging signatures of glioblastoma can provide insights into the biologic basis of tumor formation and progression as well as in vivo surrogate markers of molecular events driving the tumor’s phenotype. Through machine learning (ML), this study demonstrates that distinct imaging subtypes of glioblastoma are related to specific molecular alterations.

METHODS

Pre-operative multi-parametric MRI (T1, T2, T1CE, T2-FLAIR, DSC-MRI, DTI-MRI) of 669 IDH-wildtype subjects with glioblastoma were retrospectively collected and radiomic features, including descriptors of morphology, intensity, histogram, and texture, were extracted. Imaging subtypes were identified by a feature selection and clustering approach. Genomic markers, obtained using next generation sequencing (NGS) panel of 27 key glioblastoma genes, were available in 358/669 patients. Canonical correlation analysis (CCA) was conducted within each imaging subtype between the selected imaging features and genetic variables to seek maximum correlations between combinations of variables in imaging and genomic sets, and hence elucidate the molecular drivers of respective subtypes.

RESULTS

Three distinct imaging subtypes were identified by clustering on 50 selected features, representing characteristics of morphology, tumor neo-angiogenesis (DSC-derived features), and cellular density (DTI-derived features). These subtypes yielded differentiable overall survival based on Kaplan-Meier analysis. The canonical coefficients of each subtype revealed the distinction of the underlying genomic characteristics: one exhibited frequently mutated [ARID2, NTRK1], another subtype showed increased frequency of mutation in [ATRX, EGFR, PIK3R1], while the third was associated with all these genes and [NF1, PIK3CA, RB1], additionally.

CONCLUSION

We derived three distinct radiomic MRI subtypes for glioblastoma that highly correlate with the patients' survival and molecular genetic characteristics. Investigating the relationship between imaging and genomic information may enable identification of molecularly- and phenotypically-consistent tumor subtypes, which would offer non-invasive approaches for characterizing heterogeneity of glioblastoma, further facilitating patient stratification and treatment planning.

NIMG-73. CAPTURING GLIOBLASTOMA HETEROGENEITY USING IMAGING AND DEEP LEARNING: APPLICATION TO MGMT PROMOTER METHYLATION

PURPOSE

Intratumor heterogeneity is frequent in glioblastoma (GB), giving rise to the tumor’s resistance to standard therapies and, ultimately, poorer clinical outcomes. Yet heterogeneity is often not quantified when assessing the genomic or methylomic profile of a tumor, when a single tissue sample is analyzed. This study proposes a novel approach to non-invasively characterize heterogeneity across glioblastoma using deep learning analysis MRI scans, using MGMT promoter methylation (MGMTpm) as a test-case, and validates the imaging-derived heterogeneity maps with MGMTpm heterogeneity measured via multiple tissue samples.

METHODS

Multi-parametric MRI (mpMRI) scans (T1, T1-Gd, T2, T2-FLAIR) of 181 patients with newly diagnosed glioblastoma, who underwent surgical tumor resection and had MGMT methylation assessment results, were retrospectively collected. We trained a 5-fold cross-validated deep convolutional neural network with six convolutional layers for a discovery cohort of 137 patients by placing overlapping regional patches over the whole tumor on mpMRI scans to capture spatial heterogeneity of MGMTpm status in different regions within the tumor. Our approach effectively hypothesized that despite heterogeneity in the training examples, dominant imaging patterns would be captured by deep learning. Trained model was independently applied to an unseen replication cohort of 44 patients, with multiple tissue specimens chosen from different spatial regions within the tumor, allowing us to compare imaging- and tissue-based MGMTpm estimates.

RESULTS

Our model yielded AUC of 0.75 (95% CI: 0.65–0.79) for global MGMT status prediction, which reflected the heterogeneity in MGMTpm, but also that a dominant imaging pattern of MGMT methylation seemed to emerge. In methylated patients with multiple tissue samples, a significant Pearson's correlation coefficient of 0.64 (p&lt; 0.05) was found between imaging-based heterogeneity maps and MGMTpm heterogeneity.

CONCLUSION

A novel method based on mpMRI and deep neural networks yielded imaging-based heterogeneity maps that strongly associated with intratumor molecular heterogeneity in MGMT promoter methylated tumors.

NIMG-52. RADIOGENOMICS SIGNATURES IN KEY DRIVER GENES IN GLIOBLASTOMA EVALUATED WITH AND WITHOUT THE PRESENCE OF CO-OCCURRING MUTATIONS

PURPOSE

Glioblastomas display significant heterogeneity on the molecular level, typically harboring several co-occurring mutations, which likely contributes to failure of molecularly targeted therapeutic approaches. Radiogenomics has emerged as a promising tool for in vivo characterization of this heterogeneity. We derive radiogenomic signatures of four mutations via machine learning (ML) analysis of multiparametric MRI (mpMRI) and evaluate them in the presence and absence of other co-occurring mutations.

METHODS

We identified a retrospective cohort of 359 IDH-wildtype glioblastoma patients, with available pre-operative mpMRI (T1, T1Gd, T2, T2-FLAIR) scans and targeted next generation sequencing (NGS) data. Radiomic features, including morphologic, histogram, texture, and Gabor wavelet descriptors, were extracted from the mpMRI. Multivariate predictive models were trained using cross-validated SVM with LASSO feature selection to predict mutation status in key driver genes, EGFR, PTEN, TP53, and NF1. ML models and spatial population atlases of genetic mutations were generated for stratification of the tumors (1) with co-occurring mutations versus wildtypes, (2) with exclusive mutations in each driver gene versus the tumors without any mutations in the pathways associated with these genes.

RESULTS

ML models yielded AUCs of 0.75 (95%CI:0.62-0.88) / 0.87 (95%CI:0.70-1) for co-occurring / exclusive EGFR mutations, 0.69 (95%CI:0.58-0.80) / 0.80 (95%CI:0.61-0.99) for co-occurring / exclusive PTEN mutations, and 0.77 (95%CI:0.65-0.88) / 0.86 (95%CI:0.69-1) for co-occurring / exclusive TP53 cases. Spatial atlases revealed a predisposition of left temporal lobe for NF1 and right frontotemporal region for TP53 in mutually exclusive tumors, which was not observed in the co-occurring mutation atlases.

CONCLUSION

Our results suggest the presence of distinct radiogenomic signatures of several glioblastoma mutations, which become even more pronounced when respective mutations do not co-occur with other mutations. These in vivo signatures can contribute to pre-operative stratification of patients for molecular targeted therapies, and potentially longitudinal monitoring of mutational changes during treatment.

Contrasting spectroscopic response of human hemoglobin in presence of graphene oxides and its reduced form: Comparative approach with carbon quantum dots

Recently, a considerable amount of research is being directed towards study of graphene oxide (GO) and its reduced form (RGO) since their exposed functional groups make them better candidates in nanobiotechnolgy. In order to assess their biocompatibility, the nature of interactions between Human Hemoglobin (HHb) and GO/RGO are monitored since a comparative spectroscopic approach towards understanding their nature of interactions has not been investigated previously. UV-vis spectroscopy reveals hyperchromicity for HHb-GO system and hypochromicity for HHb-RGO system in the region of absorption of tryptophan/tyrosine residues. Notably, although steady-state fluorescence static quenching of HHb for GO and enhancement of fluorescence for RGO is noticed, but average fluorescence-lifetime is remaining unchanged in presence of GO/RGO. Calorimetric data illustrates three-site and five-site binding model to be the best-fit model for GO and RGO respectively. Also, synchronous fluorescence quenching corresponding to alterations in microenvironment of tryptophan/ tyrosine residues is observed only in presence of GO. Likewise FTIR spectroscopy elucidates involvement of both amide I and amide II bond of HHb backbone through H-bonding interaction only for GO. Furthermore RLS spectra demonstrate an increase and a decrease in signal for GO and RGO respectively. Surprisingly, secondary structure of HHb is maintained upon interaction with both GO/RGO, as revealed by CD spectroscopy, thus supporting their potential application in biological microenvironment. Thus it appears that the spectroscopic properties of HHb upon interaction with GO is altered upon its reduction to RGO. Furthermore the role of HHb as good candidate for bimolecular interaction has been highlighted.

NIMG-40. RADIOGENOMIC SIGNATURES OF DRIVER GENES IN NEWLY DIAGNOSED GLIOBLASTOMA PATIENTS BASED ON PRE-OPERATIVE MULTI-PARAMETRIC MRI

PURPOSE

Non-invasive and quantitative biomarkers of somatic mutations derived from multi-parametric MRI (MP-MRI) could potentially help in predicting the response of patients to therapy, leading to development of targeted and personalized treatments. In this study, we developed radiogenomic signatures of multiple driver genes using artificial intelligence (AI) methods.

METHODS

In this study, 2740 radiomic features, including shape and volumetric measures computed for different tumorous regions, and characteristics derived from histograms and gray-level co-occurrence matrix (GLCM), were extracted from pre-operative MP-MRI (T1, T1Gd, T2, T2-FLAIR, DTI, and DSC-MRI) scans of 161 patients with newly diagnosed glioblastoma. The tumor samples, collected surgically from these patients, were sequenced using an in-house targeted next generation sequencing (NGS) panel of genes. We constructed quantitative imaging signatures of somatic mutations in several genes from 161 IDH-wildtype glioblastoma patients, including ATRX, FGFR2, EGFR, MET, NF1, PDGFRA, PIK3CA, PTEN, RB1, TP53, using cross-validated SVM classifiers.

RESULTS

The cross-validated classification performance for each signature was assessed by area under the receiver operating characteristic (ROC) curve (AUC), indicating the following results: PTEN (n = 69, AUC = 0.64), EGFR (n = 52, AUC = 0.72), TP53 (n = 51, AUC = 0.67), NF1 (n = 33, AUC = 0.74), ATRX (n = 22; AUC = 0.74), FGFR2 (n = 6, AUC = 0.82), MET (n = 26, AUC = 0.77), PDGFRA (n = 14, AUC = 0.82), PIK3CA (n = 14, AUC = 0.78), RB1 (n = 14, AUC = 0.81).

CONCLUSION

Using multi-parametric MRI, we developed quantitative non-invasive in vivo signatures with the potential for pre-operative assessment of a glioblastoma’s molecular characteristics. These non-invasive radiogenomic biomarkers may be useful for understanding the molecular composition of a glioblastoma prior to surgical resection, thus enabling earlier selection of patients for targeted therapy trials and possible neoadjuvant treatment.

Fluorescence enhancement via aggregation effect due to microenvironmental alterations in human hemoglobin protein in presence of carbon quantum dots (CQD): Comparative spectroscopic approach

CQDs have emerged with outstanding properties as a star member of carbon nanomaterial family and in order to reveal its wide-range of application in biological microenvironment the interactions between human hemoglobin (HHb) and CQD and also with ethylenediamine-functionalized CQD (NCQD) are assessed using several techniques. Firstly, UV-vis absorption spectra of HHb reveal hyperchromic effect in the region of absorbance of tryptophan and tyrosine residues and also hypochromicity of Soret band in presence of CQD and NCQD. Interestingly, steady-state fluorescence spectroscopy reveal distinct fluorescence enhancement of HHb with significant red shift thereby indicating exposures of tryptophan and tyrosine residues to a more hydrophilic environment. However synchronous fluorescence spectra reveal that the microenvironment of tryptophan and tyrosine residues is altered in opposite manner, i.e. exposure of tryptophan residues to a more hydrophilic environment and the tyrosine residues to a more hydrophobic environment. Moreover the fluorescence enhancement is observed to be accompanied by increase in average fluorescence-lifetime and decrease in steady-state anisotropy thus signifying a decrease in restriction of rotational motion. Furthermore tryptophan residues within HHb appear to interact more with CQD compared to NCQD. Thermodynamic parameters as revealed by Isothermal Titration Calorimetry (ITC) demonstrate that electrostatic, hydrogen bonding and hydrophobic interactions are the predominant modes of interactions in presence of CQD. Whereas hydrophobic and hydrogen bonding interactions are the major interacting forces in presence of NCQD with five-site sequential binding as best-fit model in both the cases. Such interactions also appear to be associated with an increase in aggregation of HHb as evident from the measurements by atomic force microscopy (AFM) and dynamic light scattering (DLS) study. Although FT-IR spectra display alteration of amide I band, but the overall secondary structure of HHb seems to be nearly retained even in presence of CQDs, as evident in the CD spectra. These observations thus highlight the potential biomedical application of CQDs in biological microenvironment of human especially as drug-delivery system. Also bimolecular interaction of HHb as a model protein with other nanoparticles at the nano bio-interface has been outlined.

Molecular diagnosis of somatic overgrowth conditions: A single-center experience

Background

Somatic overgrowth conditions, including Proteus syndrome, Sturge–Weber syndrome, and PIK3CA‐related overgrowth spectrum, are caused by post‐zygotic pathogenic variants, result in segmental mosaicism, and give rise to neural, cutaneous and/or lipomatous overgrowth. These variants occur in growth‐promoting pathways leading to cellular proliferation and expansion of tissues that arise from the affected cellular lineage.

Methods

We report on 80 serial patients evaluated for somatic overgrowth conditions in a diagnostic laboratory setting, including three prenatal patients. In total, 166 tissues from these 80 patients were subjected to targeted sequencing of an 8‐gene panel capturing 10.2 kb of sequence containing known pathogenic variants associated with somatic overgrowth conditions. Deep next‐generation sequencing was performed with the IonTorrent PGM platform at an average depth typically >5,000×.

Results

Likely pathogenic or pathogenic variants were identified in 36 individuals and variants of unknown significance in four. The overall molecular diagnostic yield was 45% but was highly influenced by both submitted tissue type and phenotype. In the prenatal setting, two patients had pathogenic variants identified in cultured amniocytes but in a third patient, the pathogenic variant was only present in post‐natal tissues. Finally, expanding the test to include full gene sequencing of PIK3CA in contrast to targeted sequencing identified likely pathogenic variants in 3 of 7 patients that tested negative on the original panel.

Conclusion

Next‐generation sequencing has enabled sensitive detection of somatic pathogenic variants associated with overgrowth conditions. However, as the pathogenic variant allele frequency varies by tissue type within an individual, submission of affected tissue(s) greatly increases the chances of a molecular diagnosis.

Interactions of Fluorescein Dye with Spherical and Star Shaped Gold Nanoparticles

UV-vis absorption, FT-IR, steady state fluorescence and fluorescence lifetime measurements were made on Fluorescein dye (Fl dye) molecules in presence of gold nanoparticles of different morphologies: spherical gold nanoparticles (GNP) and star shaped gold nanoparticles (GNS). The experimental observations demonstrate that Fl dye molecules form dimers when adsorbed on nanosurface of spherical gold particles. On the other hand possibly due to lack of adsorption on the surface of GNS the dye molecules were unable to form dimers. The projected tips on the surface of GNS may possibly hinder the dyes to adsorb on the surface of this nanoparticle. From the spectral analysis and measurements of thermodynamic parameters it is inferred that two different types of ground state interactions occur between Fl-dye-GNP and Fl dye-GNS systems. Both the observed negative values of the thermodynamic parameters ΔH and ΔS in the case of the former system predict the possibility of occurrences of hydrogen bonding interactions between two neighboring Fl dye molecules when adsorbed on the nanosurface of GNP. On the other hand in Fl dye-GNS system electrostatic interactions appear to occur, as evidenced from negative ΔH and positive value of ΔS, between the positive charges residing on the tips of the nanoparticles and anionic form of Fl dye. It has been concluded that as the adsorption of organic dyes on solid surfaces is prerequisite for the degradation of dye pollutants, the present experimental observations demonstrate that GNP could be used as a better candidate than GNS in degradation mechanism of the xanthenes dyes.

A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression

Background

Though Illumina has largely dominated the RNA-Seq field, the simultaneous availability of Ion Torrent has left scientists wondering which platform is most effective for differential gene expression (DGE) analysis. Previous investigations of this question have typically used reference samples derived from cell lines and brain tissue, and do not involve biological variability. While these comparisons might inform studies of tissue-specific expression, marked by large-scale transcriptional differences, this is not the common use case.

Results

Here we employ a standard treatment/control experimental design, which enables us to evaluate these platforms in the context of the expression differences common in differential gene expression experiments. Specifically, we assessed the hepatic inflammatory response of mice by assaying liver RNA from control and IL-1β treated animals with both the Illumina HiSeq and the Ion Torrent Proton sequencing platforms. We found the greatest difference between the platforms at the level of read alignment, a moderate level of concordance at the level of DGE analysis, and nearly identical results at the level of differentially affected pathways. Interestingly, we also observed a strong interaction between sequencing platform and choice of aligner. By aligning both real and simulated Illumina and Ion Torrent data with the twelve most commonly-cited aligners in the literature, we observed that different aligner and platform combinations were better suited to probing different genomic features; for example, disentangling the source of expression in gene-pseudogene pairs.

Conclusions

Taken together, our results indicate that while Illumina and Ion Torrent have similar capacities to detect changes in biology from a treatment/control experiment, these platforms may be tailored to interrogate different transcriptional phenomena through careful selection of alignment software.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-4011-0) contains supplementary material, which is available to authorized users.

Abstract 3689: Jak3 mutations in colorectal neoplasia- Preliminary data on a not so silent minority

As a tumorigenesis model, colorectal cancer is associated with multiple gene mutations accumulating progressively but also has mutations that may alter disease course and provide a therapeutic target. Good examples of this are EGFR and VEGF. In melanoma, PD-1 interactions involving the immunobiome are therapeutically important. We conducted a study to detect potential mutations that might enhance therapy in colorectal cancer guided by expression of p87, a product of innate immune system Paneth cells. Methods: Adnab-9 immunohistochemistry or ELISA was used to define significant p87 Adenoma-associated antigen field effects (FE) in 10 patients with &gt;1cm large high grade dysplastic adenomas (LHiGDA) and 3 with smaller high grade dysplastic adenomas (SHiGDA). We postulated that SHiGDA are not immunologically recognized by host defenses leading to negative outcomes. We used Ion Torrent™ sequencing (ITS) to find mutations in DNA (QiaAmp kit) extracted from 4 normal-appearing colonic segments taken from 1 patient in each group. Novel mutations found on ITS would then be sought using PCR with appropriate primers and subsequent sequencing of the PCR product circulating DNA extracted from available serum samples. These samples were taken from the Large- and SHiGDA groups described above and from 17 patients undergoing colonoscopy for diverse indications. Results: p87 FE were found in 40% of 10 LHiGDA and 0% of 3 SHiGDA patients. The ITS in the 2 representative patients showed unique mutational fields in: KRAS, APC, p53 in the LHiGDA and Jak3, PIK3Ca, p53, APC in the SHiGDA patient, both of whom lacked p87 FE. PCR using the Jak3 primers used in the ITS and subsequent sequencing revealed the same non-synonymous mutation in the serum of a FAP patient after colonic resection and an additional colonic segment of the selected ShiGDA patient but not in his serum. Other Jak3 mutations were found in 1 of 8 LHiGDA, 1 (the selected patient) of 3 SHiGDA, 1 of 7 patients with FAP and 1 of 10 colonoscopy patients with a family history of colorectal cancer with a FE and an untoward outcome. The selected SHiGDA patient subsequently contracted and died of NSCLC adenocarcinoma. The positive LHiGDA and FAP patients had a severely dysplastic anal condyloma and severe pancreatitis, respectively. Overall, the non-synonymous mutation occurring in the non-FAP SHiGDA patient occurred in the absence of p87 FE. Conclusions: In this pilot study we demonstrate the presence of Jak3 mutations likely associated with the lack of p87 expression in patients with high grade dysplastic adenomas and 1 FAP patient. Most of these patients had a clinical course which may have differed from their group members suggesting an altered immune system milieu. If confirmed in SHiGDA and FAP, Jak 3 mutations, associated with the SCID and late onset combined immunodeficiency, may allow for intervention with currently available medications to potentially avert a deleterious clinical outcome.

Citation Format: Martin Tobi, Xiaoping Zhao, Darshana Jhala, Rebecca Rodriguez, Fadi Antaki, Edi Levi, Paula Sochacki, John Lieb, MaryAnn Rambus, Tapan Ganguly, Martin Bluth, Michael J. Lawson. Jak3 mutations in colorectal neoplasia- Preliminary data on a not so silent minority [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3689. doi:10.1158/1538-7445.AM2017-3689

Designing of an artificial light energy converter in the form of short-chain dyad when combined with core-shell gold/silver nanocomposites

UV-vis absorption, steady state and time resolved fluorescence and absorption spectroscopic investigations demonstrate that the short chain dyad MNTMA when combined with gold-silver core-shell (Au@Ag) nanocomposite , forms elongated conformers in the excited state whereas for the dyad - Ag (spherical) system the majority of dyads remains in a folded conformation. In the dyad-core-shell nanocomposite system, energy wasting charge recombination rate slows down primarily due to elongated conformation and thus it may be anticipated that this hybrid nanocomposite system may serve as a better light energy conversion device.

Use of Spectroscopic Techniques to Reveal the Nature of the Interactions of Two Sialic Acid Specific Lectins with Gold Nanoparticles

From UV-vis absorption, steady state and time resolved fluorescence measurements coupled with circular dichroism (CD) spectral studies, it was revealed that among the two lectins: Sambucus nigra agglutinin (SNA) and Saraca indica (saracin II), SNA forms stronger binding complex in the ground state with gold nanoparticles (GNPs). From the measurements of Stern-Volmer (SV) constants Ksv, and binding constants K(A) and number of binding sites two important inferences could be drawn. Firstly, the fluorescence quenching is primarily due to static quenching and secondly SNA forms stronger binding with GNPs relative to the other lectin saracin II. Synchronous fluorescence spectral measurements further substantiate this proposition of exhibiting the fully exposed tryptophan residue in case of SNA. It appears that the lectin SNA adopted a relatively looser conformation with the extended polypeptide structures leading to the exposure of the hydrophobic cavities which favoured stronger binding with GNPs. CD measurements demonstrate that gold nanoparticles when interact with the lectins (glycoproteins), no significant distortion in the structural pattern of the later occurs. The unaltered identity in the secondary structural pattern of both SNA and saracin II in presence of gold nanoparticles hints that GNPs may be used as useful drug or drug delivery systems.

Time Resolved Spectroscopic Studies on a Novel Synthesized Photo-Switchable Organic Dyad and Its Nanocomposite Form in Order to Develop Light Energy Conversion Devices

UV-vis absorption, steady state and time resolved spectroscopic investigations in pico and nanosecond time domain were made in the different environments on a novel synthesized dyad, 3-(2-methoxynaphthalen-1-yl)-1-(4-methoxyphenyl)prop-2-en-1-one (MNTMA) in its pristine form and when combined with gold (Au) nanoparticles i.e., in its nanocomposite structure. Both steady state and time resolved measurements coupled with the DFT calculations performed by using Gaussian 03 suit of software operated in the linux operating system show that though the dyad exhibits mainly the folded conformation in the ground state but on photoexcitation the nanocomposite form of dyad prefers to be in elongated structure in the excited state indicating its photoswitchable nature. Due to the predominancy of elongated isomeric form of the dyad in the excited state in presence of Au Nps, it appears that the dyad MNTMA may behave as a good light energy converter specially in its nanocomposite form. As larger charge separation rate (kcs ~ 4 x 10(8) s-1) is found relative to the rate associated with the energy wasting charge recombination processes (kcR ~ 3 x 10(5) s-1) in the nanocomposite form of the dyad, it demonstrates the suitability of constructing the efficient light energy conversion devices with Au-dyad hybrid nanomaterials.

Improved Methods to Generate Spheroid Cultures from Tumor Cells, Tumor Cells & Fibroblasts or Tumor-Fragments: Microenvironment, Microvesicles and MiRNA

Diagnostic and prognostic indicators are key components to achieve the goal of personalized cancer therapy. Two distinct approaches to this goal include predicting response by genetic analysis and direct testing of possible therapies using cultures derived from biopsy specimens. Optimally, the latter method requires a rapid assessment, but growing xenograft tumors or developing patient-derived cell lines can involve a great deal of time and expense. Furthermore, tumor cells have much different responses when grown in 2D versus 3D tissue environments. Using a modification of existing methods, we show that it is possible to make tumor-fragment (TF) spheroids in only 2–3 days. TF spheroids appear to closely model characteristics of the original tumor and may be used to assess critical therapy-modulating features of the microenvironment such as hypoxia. A similar method allows the reproducible development of spheroids from mixed tumor cells and fibroblasts (mixed-cell spheroids). Prior literature reports have shown highly variable development and properties of mixed-cell spheroids and this has hampered the detailed study of how individual tumor-cell components interact. In this study, we illustrate this approach and describe similarities and differences using two tumor models (U87 glioma and SQ20B squamous-cell carcinoma) with supporting data from additional cell lines. We show that U87 and SQ20B spheroids predict a key microenvironmental factor in tumors (hypoxia) and that SQ20B cells and spheroids generate similar numbers of microvesicles. We also present pilot data for miRNA expression under conditions of cells, tumors, and TF spheroids.

Chromosome 3 status combined with BAP1 and EIF1AX mutation profiles are associated with metastasis in uveal melanoma

PURPOSE

Somatic mutations in GNAQ, GNA11, SF3B1, EIF1AX, and BAP1 have been identified in uveal melanoma (UM). The aim of this study was to determine whether mutations in these genes in primary tumors were associated with metastases in individuals diagnosed with UM.

METHODS

A total of 63 UM cases who developed a metastasis within 48 months of primary treatment and 53 UM controls who were metastasis-free over a similar time period were selected for the study. Primary UM cases were screened for mutations in GNAQ, GNA11, SF3B1, EIF1AX, and BAP1. The association of these mutations with tumor characteristics, chromosome 3 copy number, and metastatic status was analyzed by logistic regression to estimate the odds of developing metastasis within 48 months.

RESULTS

As expected, tumor diameter, thickness, cilio-choroidal location, and chromosome 3 monosomy were all significantly (P < 0.02) associated with the presence of metastasis. In univariate analysis, GNA11 (odds ratio [OR] 2.5, 95% confidence interval [CI] 1.1-5.5) and BAP1 (OR 6.3, 95% CI 2.7-14.4) mutations were positively associated and EIF1AX mutation (OR 0.13, 95% CI 0.034-0.47) was inversely associated with metastatic status at 48 months after UM treatment. After adjustment for covariates, a chromosome 3 monosomy/BAP1-mutation/EIF1AX-wild-type (WT) mutation profile was strongly associated (OR 37.5, 95% CI 4.3-414) with the presence of metastasis compared with a chromosome 3 disomy/BAP1-WT/EIF1AX mutation profile.

CONCLUSIONS

The results suggest that knowledge of mutations in BAP1 and EIF1AX can enhance prognostication of UM beyond that determined by chromosome 3 and tumor characteristics. Tumors with chromosome 3 disomy/BAP1-WT/EIF1AX-WT have a 10-fold increased risk of metastasis at 48 months compared with disomy-3/BAP1-WT/EIF1AX mutant tumors.

Absence of WNT4 gene mutation in a patient with MURCS association

MURCS (Mullerian duct aplasia, Renal anomalies, and Cervicothoracic Somite dysplasia) association is a group of congenital genito-urinary and skeletal malformations. We report an adolescent girl with the cardinal features of MURCS association, obesity, and clinical findings of hyperandrogenism who did not show any exonic mutation of the WNT4 gene. Our finding excludes WNT4 gene as a candidate for MURCS association and suggests the need for further genetic studies.

Filaggrin-2 variation is associated with more persistent atopic dermatitis in African American subjects

BACKGROUND

Atopic dermatitis (AD) is a common skin disease characterized by recurrent episodes of itching. Genetic variation associated with the persistence of AD has not been described for African American subjects.

OBJECTIVE

We sought to evaluate genetic variation of filaggrin-2 (FLG2) in African American subjects with AD.

METHODS

We evaluated a multiyear prospective cohort study of African American children with AD with respect to FLG2 variation based on whole-exome sequencing, followed by a targeted analysis. We ultimately evaluated the association of rs12568784 and rs16833974 with respect to the persistence of AD symptoms over time.

RESULTS

Whole-exome analysis was conducted on 60 subjects, revealing a premature stop codon in exon 3 at S2377X (rs12568784) and X2392S (rs150529054) and a large exon 3 deletion mutation, Q2053del224. On the basis of a priori criteria, we then studied rs12568784, rs16833974 (H1249R), and Q2053del224. We noted that patients with S2377X (odds ratio [OR], 0.44; 95% CI, 0.25-0.46) and H1249R (OR, 0.23; 05% CI, 0.12-0.46) were significantly less likely to be free of symptoms of AD, and Q2053del224 (OR, 0.54; 95% CI, 0.16-1.80) trended toward this outcome. S2377X and H1249R were in high linkage disequilibrium (D' = 0.95).

CONCLUSIONS

In an African American cohort with AD, FLG2 mutations were associated with more persistent AD. This is the first finding of genetic variation of a skin barrier protein in subjects of African ancestry with AD.

Enhanced sensitivity for detection of low-level germline mosaic RB1 mutations in sporadic retinoblastoma cases using deep semiconductor sequencing

Sporadic retinoblastoma (RB) is caused by de novo mutations in the RB1 gene. Often, these mutations are present as mosaic mutations that cannot be detected by Sanger sequencing. Next-generation deep sequencing allows unambiguous detection of the mosaic mutations in lymphocyte DNA. Deep sequencing of the RB1 gene on lymphocyte DNA from 20 bilateral and 70 unilateral RB cases was performed, where Sanger sequencing excluded the presence of mutations. The individual exons of the RB1 gene from each sample were amplified, pooled, ligated to barcoded adapters, and sequenced using semiconductor sequencing on an Ion Torrent Personal Genome Machine. Six low-level mosaic mutations were identified in bilateral RB and four in unilateral RB cases. The incidence of low-level mosaic mutation was estimated to be 30% and 6%, respectively, in sporadic bilateral and unilateral RB cases, previously classified as mutation negative. The frequency of point mutations detectable in lymphocyte DNA increased from 96% to 97% for bilateral RB and from 13% to 18% for unilateral RB. The use of deep sequencing technology increased the sensitivity of the detection of low-level germline mosaic mutations in the RB1 gene. This finding has significant implications for improved clinical diagnosis, genetic counseling, surveillance, and management of RB.

Synthesis, characterization, photophysical properties of a novel organic photoswitchable dyad in its pristine and hybrid nanocomposite forms

In the present paper the method of synthesis and characterization of a novel organic dyad, 3-(1-Methoxy-3,4-dihydro-naphthalyn-2-yl-)-1-p-chlorophenyl propenone, have been reported. In this paper our main thrust is to fabricate new hybrid nanocomposites by combining the organic dyad with different noble metals, semiconductor nanoparticle and noble metal-semiconductor core/shell nanocomposites. In this organic dyad, donor part is 1-Methoxy-3, 4-dihydro-naphthalen-2-carboxaldehyde with the acceptor p-chloroacetophenone. We have carried out steady state and time-resolved spectroscopic measurements on the dyad and its hybrid nanocomposite systems. Some quantum chemical calculations have also been done using Gaussian 03 software to support the experimental findings by theoretical point of view. Both from the theoretical predictions and NMR studies it reveals that in the ground state only extended (E-type or trans-type) conformation of the dyad exists whereas on photoexcitation these elongated conformers are converted into folded forms (Z- or cis-type) of the dyad, showing its photoswitchable character. Time resolved fluorescence spectroscopic (fluorescence lifetime by TCSPC method) measurements demonstrate that in chloroform medium all the organic-inorganic hybrid nanocomposites, studied in the present investigation, possess larger amount of extended conformers relative to folded ones, even in the excited singlet state. This indicates the possibility of slower energy destructive charge recombination rates relative to the rate processes associate with charge-separation within the dyad. It was found that in CHCl3 medium, the computed charge separation rate was found to be approximately 10(8) s(-1) for the dyad alone and other hybrid nanocomposite systems. The rate is found to be faster than the energy wasting charge recombination rate approximately 10(2)-10(1) s(-1), as observed from the transient absorption measurements for the corresponding hybrid systems. It indicates the conformational geometry has a great effect on the charge-separation and recombination rate processes. The suitability for the construction of efficient light energy conversion devices especially with Ag-Dyad nanocomposite of all the systems studied here is hinted from the observed long ion-pair lifetime.

The rates of charge separation and energy destructive charge recombination processes within an organic dyad in presence of metal-semiconductor core shell nanocomposites

Steady state and time resolved spectroscopic measurements were made at the ambient temperature on an organic dyad, 1-(4-Chloro-phenyl)-3-(4-methoxy-naphthalen-1-yl)-propenone (MNCA), where the donor 1-methoxynaphthalene (1 MNT) is connected with the acceptor p-chloroacetophenone (PCA) by an unsaturated olefinic bond, in presence of Ag@TiO2 nanoparticles. Time resolved fluorescence and absorption measurements reveal that the rate parameters associated with charge separation, k(CS), within the dyad increases whereas charge recombination rate k(CR) reduces significantly when the surrounding medium is changed from only chloroform to mixture of chloroform and Ag@TiO2 (noble metal-semiconductor) nanocomposites. The observed results indicate that the dyad being combined with core-shell nanocomposites may form organic-inorganic nanocomposite system useful for developing light energy conversion devices. Use of metal-semiconductor nanoparticles may provide thus new ways to modulate charge recombination processes in light energy conversion devices. From comparison with the results obtained in our earlier investigations with only TiO2 nanoparticles, it is inferred that much improved version of light energy conversion device, where charge-separated species could be protected for longer period of time of the order of millisecond, could be designed by using metal-semiconductor core-shell nanocomposites rather than semiconductor nanoparticles only.

Quantization of bovine serum albumin by fluorescence enhancement effects and corresponding binding of macrocyclic host-protein assembly

The present paper reports the investigations on the spectroscopic behavior of the binary complexes of the dye aurintricarboxylic acid (ATA) with protein bovine serum albumin (BSA) and 18-crown 6 (CW) (ATA·BSA, ATA·CW) and the ternary complex ATA·CW·BSA by using UV-vis steady state and time resolved fluorescence spectroscopy. The primary aim of the work is to determine the protein (BSA) quantization by fluorescence enhancement method and investigate the 'enhancer' activity of crown ether (CW) on it to increase the resolution. Steady state and time resolved fluorescence measurements demonstrated how fluorescence intensity of ATA could be used for the determination of the protein BSA in aqueous solution. The binding of dye (probe/fluorescent medicinal molecule) with protein and the denaturing effect in the polar environment of acetonitrile of the dye protein complex act as drug binding as well as drug release activity. Apart from its basic research point of view, the present study also possesses significant importance and applications in the field of medicinal chemistry.

Is dye mixture more suitable rather than single dye to fabricate dye sensitized solar cell?

The steady state and time resolved spectroscopic studies reveal that two xanthene dyes Rhodamine 6G (R6G) and Rhodamine B (RB), used in the present investigations, form ground state hydrogen -bonded complexes with meso-tetrakis(4-carboxyphenyl) porphyrin (TCPP). However, it is apparent that upon photoexcitation the H-bonding complexes formed in the ground state decompose into the individual reacting components. This presumption was confirmed from the observation of the presence of only static quenching mode in the steady state fluorescence of the dyes in presence of porphyrin. The photoelectrochemical properties of the free dyes and the mixtures of each dye with porphyrin are investigated by measuring incident photon-to-current conversion efficiency (IPCE) using ZnO electrode and also with TiO2 electrode. It is seen that Rhodamine B-porphyrin mixture has attained maximum IPCE among the four samples studied at approximately 550 nm using ZnO electrode. Using TiO2 electrode, slight improvement in the value of IPCE was found for the same mixture. Therefore Rhodamine B-porphyrin mixture may act as a good sensitizer for converting solar energy to electrical energy.

Interaction and photodegradation characteristics of fluorescein dye in presence of ZnO nanoparticles

The interaction between xanthene dye Fluorescein (Fl) and zinc oxide (ZnO) nanoparticles is investigated under physiological conditions. From the analysis of the steady state and time resolved spectroscopic studies in aqueous solution static mode is found to be responsible in the mechanism of fluorescence quenching of the dye Fl in presence of ZnO. ZnO nanoparticles are used as photocatalyst in order to degrade Fl dye. At pH 7, a maximum degradation efficiency of 44.4% of the dye has been achieved in presence of ZnO as a nanophotocatalyst and the photodegradation follows second-order kinetics.

Spectroscopic investigations on Naphthol and Tetrahydronaphthol. A theoretical approach

The computational efficiencies of the semi-empirical method have been compared with those of different ab-initio methods for positional isomers of Naphthol and Tetrahydro-naphthol type molecules. The efficiencies for computations in case of optimized structure, electronic absorption and emission properties are investigated. For that semi-empirical approach ZINDO and two different nature of ab-initio approaches such as TD-HF/6-311G(d,p) and TD-DFT/B3LYP/6-311G(d,p) were considered. The three main approaches are studied here to give the right direction of simulation. Semi-empirical AM1/ZINDO function itself can detect the trend of molecular transitions and the values obtained by simulations are more realistic than ab-initio methods. Ab-initio methods can reproduce exact values of first transitional energy with some scaling factor both in ground and in excited states of Tetrahydro-naphthol positional isomers whereas no solution or prediction could be inferred for Naphthol isomers.

Nonradiative inter- and intramolecular energy transfer from the aromatic donor anisole to a synthesized photoswitchable acceptor system

We report steady state and time resolved fluorescence measurements on acetonitrile (ACN) solutions of the model compounds, energy donor anisole (A) and a photoswitchable acceptor N,N'-1,2-phenylene di-p-tosylamide (B) and the multichromophore (M) where A and B are connected by a spacer containing both rigid triple (acetylenic) and flexible methylene bonds. Both steady state and time correlated single photon counting measurements demonstrate that though intermolecular energy transfer, of Forster type, between the donor and acceptor moieties occurs with rate 10(8)s(-1) but when these two reacting components are linked by a spacer (multichromophore, M) the observed transfer rate ( approximately 10(11)s(-1)) enhances. This seemingly indicates that the imposition of the spacer by inserting a triple bond may facilitate in the propagation of electronic excitation energy through bond. The time resolved fluorescence measurements along with the theoretical predictions using Configuration interaction singles (CIS) method by using 6-31G (d,p) basis set, implemented in the Gaussian package indicate the formations of the two excited conformers of B. The experimental findings made from the steady state and time resolved fluorescence measurements demonstrate that, though two different isomeric species of the acceptor B are formed in the excited singlet states, the prevailing singlet-singlet nonradiative energy transfer route was found from the donor A to the relatively longer-lived isomeric species of B.

Development of a nanocomposite system by combining an organic dyad 1-(4-chloro-phenyl)-3-(4-methoxy-naphthalen-1-yl)-Propenone with semiconductor TiO2 nanoparticles

Steady state and time resolved spectroscopic measurements on an organic dyad, 1-(4-chlorophenyl)-3-(4-methoxy-naphthalen-1-yl)-propenone, where the donor 1-methoxynaphthalene is connected with the acceptor p-chloroacetophenone by an unsaturated olefinic bond, in presence of TiO2 nanoparticles were made at the ambient temperature. Time resolved fluorescence measurements reveal that the rate parameters associated with charge separation, kCS, within the dyad increases whereas charge recombination rate reduces when the surrounding medium is changed from chloroform to TiO2 nanoparticles. The observed results indicate that the dyad being combined with TiO2 nanoparticles may form organic-inorganic nanocomposite systems useful for developing light energy conversion devices.

N-hetero atomic effect on the photophysics of 2,2'-dipyridylketone

Emission characteristics of 2,2'-dipyridylketone (DPK) have been studied in the rigid glass matrices of ethanol (EtOH) and methyl cyclohexane (MCH) at 77 K. As in the case of the aromatic analogue benzophenone (BOP), DPK is found to exhibit only phosphorescence emission. Although both BOP and DPK have the lowest triplet states chiefly of n pi* nature, the presence of other triplet states in the neighbourhood of the lowest triplet one is found to play some significant roles in determining the photophysical properties of DPK, specially in the non-polar solvent (MCH). All the photophysical properties including the polarization characteristics have been explored in both the molecules. Experimental observations are corroborated with necessary quantum chemical calculations.

Inactivation of indispensable bacterial proteins by early proteins of bacteriophages: implication in antibacterial drug discovery

Bacteriophages utilize host bacterial cellular machineries for their own reproduction and completion of life cycles. The early proteins that phage synthesize immediately after the entry of their genomes into bacterial cells participate in inhibiting host macromolecular biosynthesis, initiating phage-specific replication and synthesizing late proteins. Inhibition of synthesis of host macromolecules that eventually leads to cell death is generally performed by the physical and/or chemical modification of indispensable host proteins by early proteins. Interestingly, most modified bacterial proteins were shown to take part actively in phage-specific transcription and replication. Research on phages in last nine decades has demonstrated such lethal early proteins that interact with or chemically modify indispensable host proteins. Among the host proteins inhibited by lethal phage proteins, several are not inhibited by any chemical inhibitor available today. Under the context of widespread dissemination of antibiotic-resistant strains of pathogenic bacteria in recent years, the information of lethal phage proteins and cognate host proteins could be extremely invaluable as they may lead to the identification of novel antibacterial compounds. In this review, we summarize the current knowledge about some early phage proteins, their cognate host proteins and their mechanism of action and also describe how the above interacting proteins had been exploited in antibacterial drug discovery.