Analysis Of Various Molecules Research Articles

Zeolite reduces losses and minimizes fractionation of various flavor compounds during EA-IRMS analysis

Among the methods for confirming the natural origin of flavor compounds, δ13C measurements using IRMS technique are becoming increasingly important. EA-IRMS measures can suffer from errors caused by the volatility of the analyzed compounds and the consequent isotope fractionation. This work suggests a method involving the adsorption of volatile molecules in zeolite before the EA-IRMS analysis, minimizing the possible error due to the volatility of the structures analyzed. The stabilizing effect on any fractionation was proven during the analysis of various molecules which cover a wide range of volatility. The work demonstrates that, by operating with the advised method, the repeatability of EA-IRMS data is very high not only for samples prepared before analysis, but also for samples prepared in a time span of up to 6 h. The proposed method facilitates serial preparation and prevents erroneous results due to the natural volatility of the molecules under evaluation.

A digital SERS sensing platform using 3D nanolaminate plasmonic crystals coupled with Au nanoparticles for accurate quantitative detection of dopamine.

We report a digital surface-enhanced Raman spectroscopy (SERS) sensing platform using the arrays of 3D nanolaminate plasmonic crystals (NLPC) coupled with Au nanoparticles and digital (on/off) SERS signal analysis for the accurate quantitative detection of dopamine (DA) at ultralow concentrations. 3D NLPC SERS substrates were fabricated to support the optically dense arrays of vertically-stacked multi-nanogap hotspots and combined with Raman tag-conjugated Au nanoparticles for NLPC-based dual-recognition structures. We demonstrate that the 3D NLPC-based dual-recognition structures including Au nanoparticle-induced additional hotspots can enable more effective SERS enhancement through the molecular recognition of DA. For the accurate quantification of DA at ultralow concentrations, we conducted digital SERS analysis to reduce stochastic signal variation due to various microscopic effects, including molecular orientation/position variation and the spatial distribution of nanoparticle-coupled hotspots. The digital SERS analysis allowed the SERS mapping results from the DA-specific dual-recognition structures to be converted into binary "On/Off" states; the number of "On" events was directly correlated with low-abundance DA molecules down to 1 pM. Therefore, the digital SERS platform using the 3D NLPC-based dual-recognition structures coupled with Au nanoparticles and digital SERS signal analysis can be used not only for the ultrasensitive, accurate, and quantitative determination of DA, but also for the practical and rapid analysis of various molecules on nanostructured surfaces.

Insight into the effects of electrochemical factors on host-guest interaction induced signature events in a biological nanopore.

The signature events caused by host-guest interactions in the nanopore system can be used as a novel and characteristic signal in quantitative detection and analysis of various molecules. However, the effect of several electrochemical factors on the host-guest interactions in nanopore still remains unknown. Here, we systematically studied host-guest interactions, especially oscillation of DNA-azide adamantane@cucurbit[6] in α-Hemolysin nanopore under varying pH, concentration of electrolytes and counterions (Li+, Na+, K+). Our results indicate correlations between the change of pH and the duration of the oscillation signal. In addition, the asymmetric electrolyte concentration and the charge of the counterions affects the frequency of signature events in oscillation signals, and even the integrity of the protein nanopore. This study provides insight into the design of a future biosensing platform based on signature oscillation signals of the host-guest interaction within a nanopore.

Predicting Treatment Response of Multiple Myeloma Patients Using Tumor Specific cell-free DNA

Great progress achieved in treatment of multiple myeloma (MM) over the past decade changed overall perception of importance of minimal residual disease (MRD) assessment. Since new drugs induce deep responses, MRD must be evaluated using sensitive techniques, such as allele specific PCR (ASO-PCR), next-generation sequencing (NGS) or flow cytometry. MM is a genetically heterogeneous disease characterized by multiple focal lesions in the bone marrow (BM). BM samples are typically used for analysis, but currently an alternative approach called liquid biopsies, which utilize body fluids for analysis of various molecules and cells, is intensively studied.

Upregulation of intratumoral HLA class I and peritumoral Mx1 in ulcerated melanomas

ABSTRACTBefore the era of immune checkpoint blockade, a meta-analysis encompassing fifteen trials reported that adjuvant IFN-α significantly reduces the risk of relapse and improves survival of ulcerated melanoma (UM) with no benefit for higher doses compared to lower doses. IFNa2b affects many cell intrinsic features of tumor cells and modulates the host innate and cognate immune responses. To better understand the biological traits associated with ulceration that could explain the efficacy of prophylactic type 1 IFN, we performed immunohistochemical analysis of various molecules (major histocompatibility complex class I and class II, MX Dynamin Like GTPase 1 (MX1), inducible Nitric-Oxide Synthase (iNOS) or CD47) in two retrospective cohorts of melanoma patients, one diagnosed with a primary cutaneous melanoma (1995–2013, N = 172, among whom 49% were ulcerated melanoma (UM)) and a second one diagnosed with metastatic melanoma amenable to lymph node resection (EORTC 18952 and 18991 trials, N = 98, among whom 44% were UM). We found that primary and metastatic UM exhibit higher basal expression of MHC class I molecules, independently of Breslow thickness, histology and lymphocytic infiltration compared with NUM and that primary UM harbored higher constitutive levels of the antiviral protein Mx1 at the border of tumor beds than NUM. These findings suggest that UM expand in a tumor microenvironment where chronic exposure to type 1 IFN could favor a response to exogenous IFNs.

Tumor Specific cfDNA Predicts Treatment Response of Multiple Myeloma Patients

Introduction:Great progress achieved in treatment of multiple myeloma (MM) over the past decade changed overall perception of importance of minimal residual disease (MRD) assessment. Since new drugs induce deep responses, MRD must be evaluated using sensitive techniques, such as allele specific PCR (ASO-PCR), next-generation sequencing (NGS) or flow cytometry. MM is a genetically heterogeneous cancer of plasma cells characterized by multiple focal lesions in the bone marrow (BM). Hence, a single-site biopsy can create a sampling bias. In spite of this, BM samples are typically used for MRD analysis, but currently an alternative approach called liquid biopsies, which utilizes body fluids for analysis of various molecules and cells, is intensively studied. Cell-free DNA (cfDNA) as one type of the molecule which can be analyzed using liquid biopsy approach showed promising results previously.In our study, patient-specific, clonotypic rearrangement of immunoglobulin heavy chain (IgH) gene, identified in bone marrow samples, was used for qPCR analysis of cfDNA samples from peripheral blood. We demonstrate that dynamics and quantity of patient-specific, clonotypic IgH rearrangement found in cfDNA can predict the outcomes and response of MM patients.Methods:Total of 45 patients enrolled in the study. Samples of BM were collected at diagnosis, and CD138+ cell fraction was sorted using magnetic activated cell sorting. At diagnosis and at three-month intervals, samples of peripheral blood (PB) were collected for cfDNA extraction and analysis until a patient reached complete remission (CR). If CR was not reached, samples were collected for 24 months after diagnosis. Two more samples of PB were collected (CR+3, CR+6) if patients reached CR. Patient-specific VDJ rearrangement was identified using previously described PCR method from genomic DNA extracted from CD138+ cell fraction; based on the results, patient-specific primers and probes were designed for use in ASO-qPCR. Obtained data were evaluated by absolute and relative frequencies of categorical variables and median (minimum-maximum) of quantitative variables.Results:First, we assessed time to CR. Patients were classified according to the quantity of cfDNA measured at time of diagnosis into three groups: negative, PNQ (= positive non-quantifiable) and positive. As PNQ had a similar profile to negative-classified samples (in K-M plot), PNQ were grouped together with negative results except extremely high values (> 5, n = 2) which were reclassified from PNQ to positive group. The Kaplan-Meier estimates at 12 months were reported and supplemented by the 95% confidence interval derived using Greenwood formula. The results show that significantly higher number of patients classified as negative or PNQ with quantity < 5 have reached CR in contrast to patients classified as positive or PNQ with quantity > 5.The same trend applies to association of quantity of tumor-specific cfDNA with time to CR where Cox proportional-hazards model was adopted. Patients classified as negative or PNQ with quantity < 5 have significantly increased chance of achieving CR (2.7 times) in comparison to patients classified as positive or PNQ with quantity > 5.Conclusion:Our results demonstrate that MM patient-specific cfDNA fragments are released into the bloodstream and that patients either with no or very few DNA fragments have a higher chance of achieving better treatment response eventually.Work was supported by grant AZV 17-29343A DisclosuresHajek:Amgen: Consultancy, Honoraria, Research Funding; Bristol-Myers Squibb: Consultancy, Honoraria, Research Funding; Takeda: Consultancy, Honoraria, Research Funding; Janssen: Consultancy, Honoraria, Research Funding; Celgene: Consultancy, Honoraria, Research Funding.

Gold Nanoparticle-DNA conjugates enhanced determination of dopamine by aptamer-based microcantilever array sensor

Aptamer-based microcantilever (ML) array sensor is a recently development method for the analysis of various molecules with free-label, high sensitivity and selectivity. Since its signal-transducing principle is the changes of surface stress or resonance frequency caused by molecules binding on the surface, there have difficulties in determining some low molecular weight substances. Herein, a novel detecting dopamine (DA) method based on aptamers functionalized-ML array using gold nanoparticle (NP)-DNA conjugates as the signal-amplifying strategy was developed. In this method, thiolated DA aptamers were self-assembled on the surface of ML array and then Au NP-DNA conjugates which contained a stretch of complementary sequences for DA aptamers were hybridized to DA aptamers. When DA sample interacted with its aptamer and replaced the Au NP-DNA conjugates, the surface stress of ML array was enhanced about fifteen times and resulted in much more deflection. The deflection was linearly proportional to DA concentration in the range from 0.5 to 4 μM with a lowest limit of detection 77.3 nM (R2 = 0.993). Some structural and functional DA analogues did not cause interference for the detection of DA. These results proved that the functionalized-ML array sensor based on Au NP-DNA conjugates could be used as a promising tool to detect low-weight molecules with high sensitivity and selectivity.

Comprehensive molecular tumor profiling in radiation oncology: How it could be used for precision medicine

New technologies enabling the analysis of various molecules, including DNA, RNA, proteins and small metabolites, can aid in understanding the complex molecular processes in cancer cells. In particular, for the use of novel targeted therapeutics, elucidation of the mechanisms leading to cell death or survival is crucial to eliminate tumor resistance and optimize therapeutic efficacy. While some techniques, such as genomic analysis for identifying specific gene mutations or epigenetic testing of promoter methylation, are already in clinical use, other “omics-based” assays are still evolving. Here, we provide an overview of the current status of molecular profiling methods, including promising research strategies, as well as possible challenges, and their emerging role in radiation oncology.

Nanoparticle-assisted laser desorption/ionization for metabolite imaging.

Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) has enabled the spatial analysis of various molecules, including peptides, nucleic acids, lipids, and drug molecules. To expand the capabilities of MALDI-IMS, we have established an imaging technique using metal nanoparticles (NPs) to visualize metabolites, termed nanoparticle-assisted laser desorption/ionization imaging mass spectrometry (nano-PALDI-IMS). By utilizing Ag-, Fe-, Au-, and TiO2-derived NPs, we have succeeded in visualizing various metabolites, including fatty acid and glycosphingolipids, with higher sensitivity and spatial resolution than conventional techniques. Herein, we describe the practical experimental procedures and methods associated with nano-PALDI-IMS for the visualization of these molecules.

Surface-assisted laser desorption and ionization mass spectrometry using low-cost matrix-free substrates

Surface-assisted laser desorption/ionization (SALDI) substrates have been fabricated using nanospiked polyurethane (PU) substrates that are replicated by a low-cost soft nanolithography method from silicon nanospike structures formed with femtosecond laser irradiations. The strongest mass spectrometry (MS) signal of Angiotensin II was obtained on 45-nm Au-coated nanospiked PU substrates. The effective ionization appears to be due to surface plasmon excitation. Such low-cost and identical SALDI substrates can be used for MS analysis of various molecules with high reproducibility.

NANO CAPILLARY ELECTROPHORESIS IN MICROCHIPS: A NEED OF THE PRESENT CENTURY

Microchip based electrophoresis is also called Nano Capillary Electrophoresis (NCE) in microchips. It has been developed in the last decade and used for analyses of some species of biological and environmental importance. It is believed that this modality is a requirement of the present century as it deals with nano or low level detection. The present article describes state-of-the-art NCE for the separation and identification of different compounds. The discussed classes of compounds include amino acids, drug development and design, biological fluids, enzymes and hormones, proteomics, genomics, foods and beverages, viruses, bacteria, environmental analyses, and explosives. Additionally, attempts have been made to describe NCE optimization and mechanisms of separation. It has been observed that this modality has been used for analysis of various molecules at nano or low levels of detection limits, which is an asset in separation science. Briefly, NCE development in this century has been remarkable and will open many mysteries of science, especially in the research of proteomics, genomics, and viral infections.

Laser desorption/ionization—Mass spectrometry using mesoporous silicate as matrix for the analysis of various molecules

In this study, mesoporous silicate was applied as a matrix for the analysis of various molecules from small molecules to medium sized peptides in laser desorption/ionization mass spectrometry. In contrast with conventional matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS), the proposed approach desorption/ionization on mesoporous silicate mass spectrometry (DIOM-MS), significantly reduces the problem of matrix interference in low mass region and can be applied to the analysis of versatile chemicals including amino acids, synthetic drugs, peptides and others. In addition, distinctive advantage of DIOM-MS showed higher salt tolerance and could be applied to identify the proteins from the analysis of tryptically digested peptides. DIOM-MS has several availabilities such as easy sample preparation, rapid analysis of small molecules without noise, peptide analysis without organic matrix, high salt tolerance, versatile coupling with other separation techniques, and high throughput manner.

Phylogenetic Position of Blastocystis hominis and of Stramenopiles Inferred from Multiple Molecular Sequence Data

Blastocystis hominis, a parasite of the human intestine, has recently been positioned within stramenopiles by the small subunit rRNA phylogeny. To further confirm its phylogenetic position using multiple molecular sequence data, we determined the nucleotide sequences putatively encoding small subunit ribosomal RNA, cytosolic-type 70-kDa heat shock protein, translation elongation factor 2, and the non-catalytic 'B' subunit of vacuolar ATPase of B. hominis (HE87-1 strain). Moreover, we determined the translation elongation factor 2 sequence of an apicomplexan parasite, Plasmodium falciparum, that belongs to alveolates. The maximum likelihood analyses of small subunit rRNA and cytosolic-type 70-kDa heat shock protein clearly demonstrated that B. hominis (HE87-1 strain) is positioned within stramenopiles, being congruent with the previous small subunit rRNA analysis, including the sequences of B. hominis (Nand strain) and a Blastocystis isolate from guinea pig. Although no clear resolution among major eukaryotic groups was obtained by the individual phylogenies based on the four molecules analyzed here, a combined analysis of various molecules, including these, clearly indicated that Blastocystis/stramenopiles are the closest relatives of alveolates.