Force modulation and electrochemical gating of conductance in a cytochrome

NASA Astrophysics Data System (ADS)

Davis, Jason J.; Peters, Ben; Xi, Wang

2008-09-01

Scanning probe methods have been used to measure the effect of electrochemical potential and applied force on the tunnelling conductance of the redox metalloprotein yeast iso-1-cytochrome c (YCC) at a molecular level. The interaction of a proximal probe with any sample under test will, at this scale, be inherently perturbative. This is demonstrated with conductive probe atomic force microscopy (CP-AFM) current-voltage spectroscopy in which YCC, chemically adsorbed onto pristine Au(111) via its surface cysteine residue, is observed to become increasingly compressed as applied load is increased, with concomitant decrease in junction resistance. Electrical contact at minimal perturbation, where probe-molecule coupling is comparable to that in scanning tunnelling microscopy, brings with it the observation of negative differential resistance, assigned to redox-assisted probe-substrate tunnelling. The role of the redox centre in conductance is also resolved in electrochemical scanning tunnelling microscopy assays where molecular conductance is electrochemically gateable through more than an order of magnitude.

New molecular markers and cytogenetic probes enable chromosome identification of wheat-Thinopyrum intermedium introgression lines for improving protein and gluten contents.

PubMed

Li, Guangrong; Wang, Hongjin; Lang, Tao; Li, Jianbo; La, Shixiao; Yang, Ennian; Yang, Zujun

2016-10-01

New molecular markers were developed for targeting Thinopyrum intermedium 1St#2 chromosome, and novel FISH probe representing the terminal repeats was produced for identification of Thinopyrum chromosomes. Thinopyrum intermedium has been used as a valuable resource for improving the disease resistance and yield potential of wheat. A wheat-Th. intermedium ssp. trichophorum chromosome 1St#2 substitution and translocation has displayed superior grain protein and wet gluten content. With the aim to develop a number of chromosome 1St#2 specific molecular and cytogenetic markers, a high throughput, low-cost specific-locus amplified fragment sequencing (SLAF-seq) technology was used to compare the sequences between a wheat-Thinopyrum 1St#2 (1D) substitution and the related species Pseudoroegneria spicata (St genome, 2n = 14). A total of 5142 polymorphic fragments were analyzed and 359 different SLAF markers for 1St#2 were predicted. Thirty-seven specific molecular markers were validated by PCR from 50 randomly selected SLAFs. Meanwhile, the distribution of transposable elements (TEs) at the family level between wheat and St genomes was compared using the SLAFs. A new oligo-nucleotide probe named Oligo-pSt122 from high SLAF reads was produced for fluorescence in situ hybridization (FISH), and was observed to hybridize to the terminal region of 1St#L and also onto the terminal heterochromatic region of Th. intermedium genomes. The genome-wide markers and repetitive based probe Oligo-pSt122 will be valuable for identifying Thinopyrum chromosome segments in wheat backgrounds.

In vivo targeted molecular magnetic resonance imaging of free radicals in diabetic cardiomyopathy within mice.

PubMed

Towner, R A; Smith, N; Saunders, D; Carrizales, J; Lupu, F; Silasi-Mansat, R; Ehrenshaft, M; Mason, R P

2015-01-01

Free radicals contribute to the pathogenesis of diabetic cardiomyopathy. We present a method for in vivo observation of free radical events within murine diabetic cardiomyopathy. This study reports on in vivo imaging of protein/lipid radicals using molecular MRI (mMRI) and immuno-spin trapping (IST) in diabetic cardiac muscle. To detect free radicals in diabetic cardiomyopathy, streptozotocin (STZ)-exposed mice were given 5,5-dimethyl-pyrroline-N-oxide (DMPO) and administered an anti-DMPO probe (biotin-anti-DMPO antibody-albumin-Gd-DTPA). For controls, non-diabetic mice were given DMPO (non-disease control), and administered an anti-DMPO probe; or diabetic mice were given DMPO but administered a non-specific IgG contrast agent instead of the anti-DMPO probe. DMPO administration started at 7 weeks following STZ treatment for 5 days, and the anti-DMPO probe was administered at 8 weeks for MRI detection. MRI was used to detect a significant increase (p < 0.001) in MRI signal intensity (SI) from anti-DMPO nitrone adducts in diabetic murine left-ventricular (LV) cardiac tissue, compared to controls. Regional increases in MR SI in the LV were found in the apical and upper-left areas (p < 0.01 for both), compared to controls. The biotin moiety of the anti-DMPO probe was targeted with fluorescently-labeled streptavidin to locate the anti-DMPO probe in excised cardiac tissues, which indicated elevated fluorescence only in cardiac muscle of mice administered the anti-DMPO probe. Oxidized lipids and proteins were also found to be significantly elevated (p < 0.05 for both) in diabetic cardiac muscle compared to controls. It can be concluded that diabetic mice have more heterogeneously distributed radicals in cardiac tissue than non-diabetic mice.

Cleavable DNA-protein hybrid molecular beacon: A novel efficient signal translator for sensitive fluorescence anisotropy bioassay.

PubMed

Hu, Pan; Yang, Bin

2016-01-15

Due to its unique features such as high sensitivity, homogeneous format, and independence on fluorescent intensity, fluorescence anisotropy (FA) assay has become a hotspot of study in oligonucleotide-based bioassays. However, until now most FA probes require carefully customized structure designs, and thus are neither generalizable for different sensing systems nor effective to obtain sufficient signal response. To address this issue, a cleavable DNA-protein hybrid molecular beacon was successfully engineered for signal amplified FA bioassay, via combining the unique stable structure of molecular beacon and the large molecular mass of streptavidin. Compared with single DNA strand probe or conventional molecular beacon, the DNA-protein hybrid molecular beacon exhibited a much higher FA value, which was potential to obtain high signal-background ratio in sensing process. As proof-of-principle, this novel DNA-protein hybrid molecular beacon was further applied for FA bioassay using DNAzyme-Pb(2+) as a model sensing system. This FA assay approach could selectively detect as low as 0.5nM Pb(2+) in buffer solution, and also be successful for real samples analysis with good recovery values. Compatible with most of oligonucleotide probes' designs and enzyme-based signal amplification strategies, the molecular beacon can serve as a novel signal translator to expand the application prospect of FA technology in various bioassays. Copyright © 2015 Elsevier B.V. All rights reserved.

Targeted next generation sequencing for the detection of ciprofloxacin resistance markers using molecular inversion probes

DTIC Science & Technology

2016-07-06

1 Targeted next-generation sequencing for the detection of ciprofloxacin resistance markers using molecular inversion probes Christopher P...development and evaluation of a panel of 44 single-stranded molecular inversion probes (MIPs) coupled to next-generation sequencing (NGS) for the...padlock and molecular inversion probes as upfront enrichment steps for use with NGS showed the specificity and multiplexability of these techniques

Membrane Insertion Profiles of Peptides Probed by Molecular Dynamics Simulations

DTIC Science & Technology

2008-07-17

Membrane insertion profiles of peptides probed by molecular dynamics simulations In-Chul Yeh,* Mark A. Olson,# Michael S. Lee,*#§ and Anders...a methodology based on molecular dynamics simulation techniques to probe the insertion profiles of small peptides across the membrane interface. The...profiles of peptides probed by molecular dynamics simulations 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d

Molecular probes and microarrays for the detection of toxic algae in the genera Dinophysis and Phalacroma (Dinophyta).

PubMed

Edvardsen, Bente; Dittami, Simon M; Groben, René; Brubak, Sissel; Escalera, Laura; Rodríguez, Francisco; Reguera, Beatriz; Chen, Jixin; Medlin, Linda K

2013-10-01

Dinophysis and Phalacroma species containing diarrheic shellfish toxins and pectenotoxins occur in coastal temperate waters all year round and prevent the harvesting of mussels during several months each year in regions in Europe, Chile, Japan, and New Zealand. Toxicity varies among morphologically similar species, and a precise identification is needed for early warning systems. Molecular techniques using ribosomal DNA sequences offer a means to identify and detect precisely the potentially toxic species. We designed molecular probes targeting the 18S rDNA at the family and genus levels for Dinophysis and Phalacroma and at the species level for Dinophysis acuminata, Dinophysis acuta, and Dinophysis norvegica, the most commonly occurring, potentially toxic species of these genera in Western European waters. Dot blot hybridizations with polymerase chain reaction (PCR)-amplified rDNA from 17 microalgae were used to demonstrate probe specificity. The probes were modified along with other published fluorescence in situ hybridization and PCR probes and tested for a microarray platform within the MIDTAL project ( http://www.midtal.com ). The microarray was applied to field samples from Norway and Spain and compared to microscopic cell counts. These probes may be useful for early warning systems and monitoring and can also be used in population dynamic studies to distinguish species and life cycle stages, such as cysts, and their distribution in time and space.

78 FR 59040 - Center for Scientific Review; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-25

..., [email protected] . Name of Committee: Molecular, Cellular and Developmental Neuroscience Integrated... Scientific Review Special Emphasis Panel, RFA Panel: Molecular Probes. Date: October 18, 2013. Time: 8:00 a.m... Assistance Program Nos. 93.306, Comparative Medicine; 93.333, Clinical Research, 93.306, 93.333, 93.337, 93...

[Magnetic Resonance Imaging Tracing the Biodistribution of SPIO-shRNA Molecular Probe in vivo].

PubMed

Deng, Xiao-Lin; Wu, Xiao-Feng; Liao, Rui-Kun; Zeng, Dan-Ni; Wen, Ming; Li, Shao-Lin

2016-07-01

To investigate the biodistribution of superparamagnetic iron oxide (SPIO)-shRNA molecular probe by magnetic resonance imaging (MRI) in vivo . Six New Zealand white rabbits were injected intravenously with SPIO-shRNA molecular probe (9.6 mg Fe/kg) via ear edge vein. The blood samples were collected to analyse the pharmacokinetic parameters through measuring the iron content by atomic absorption spectrometry (AAS) method at 30 min before and 1 min, 3 min, 5 min, 10 min, 15 min, 30 min and at 1, 2, 3, 6, 12, and 24 h after the injection. Six Kun Ming (KM) mice were injected intravenously with SPIO-shRNA molecular probe (4.8 mg Fe/kg). The biodistribution of SPIO-shRNA molecular probe was traced by MRI in vivo . Ninety six KM mice were randomly divided into control group and experimental group: each mouse in experimental group was injected intravenously with SPIO-shRNA molecular probe (4.8 mg Fe/kg). The liver, spleen, kidney, brain and muscle of the control group and the experimental group on 1, 3, 5, 7, 9, 11 and 14 d after the injection were collected. The organ iron content were measured by AAS method and Prussian blue staining in order to observe the distribution of the SPIO-shRNA molecular probe in the main organ. Our results demonstrated that the pharmacokinetics of the molecular probe complied with two-compartment model, and the blood half-life was (3.692±0.196) h. The data of MRI showed that the probe were distributed in liver and spleen, and the signs were reduced in accord with the increase of probe's doses in liver and spleen. The probe's metabolism was slow, and the probe was cleared from liver and spleen at 2 weeks after the injection. The results of AAS and Prussian blue staining further testified the results of MRI. Our data showed the biodistribution of SPIO-shRNA molecular probe in main organs can be traced by MRI in vivo . Meanwhile, it provides important information for the effectiveness of the probe by MRI at tumor in vivo.

Construction of specific magnetic resonance imaging/optical dual-modality molecular probe used for imaging angiogenesis of gastric cancer.

PubMed

Yan, Xuejie; Song, Xiaoyan; Wang, Zhenbo

2017-05-01

The purpose of the study was to construct specific magnetic resonance imaging (MRI)/optical dual-modality molecular probe. Tumor-bearing animal models were established. MRI/optical dual-modality molecular probe was construed by coupling polyethylene glycol (PEG)-modified nano-Fe 3 O 4 with specific targeted cyclopeptide GX1 and near-infrared fluorescent dyes Cy5.5. MRI/optical imaging effects of the probe were observed and the feasibility of in vivo double-modality imaging was discussed. It was found that, the double-modality probe was of high stability; tumor signal of the experimental group tended to be weak after injection of the probe, but rose to a level which was close to the previous level after 18 h (p > 0.05). We successively completed the construction of an ideal MRI/optical dual-modality molecular probe. MRI/optical dual-modality molecular probe which can selectively gather in gastric cancer is expected to be a novel probe used for diagnosing gastric cancer in the early stage.

Detection of DNA damage based on metal-mediated molecular beacon and DNA strands displacement reaction.

PubMed

Xiong, Yanxiang; Wei, Min; Wei, Wei; Yin, Lihong; Pu, Yuepu; Liu, Songqin

2014-01-24

DNA hairpin structure probes are usually designed by forming intra-molecular duplex based on Watson-Crick hydrogen bonds. In this paper, a molecular beacon based on silver ions-mediated cytosine-Ag(+)-cytosine base pairs was used to detect DNA. The inherent characteristic of the metal ligation facilitated the design of functional probe and the adjustment of its binding strength compared to traditional DNA hairpin structure probes, which make it be used to detect DNA in a simple, rapid and easy way with the help of DNA strands displacement reaction. The method was sensitive and also possesses the good specificity to differentiate the single base mismatched DNA from the complementary DNA. It was also successfully applied to study the damage effect of classic genotoxicity chemicals such as styrene oxide and sodium arsenite on DNA, which was significant in food science, environmental science and pharmaceutical science. Copyright © 2013 Elsevier B.V. All rights reserved.

Cyanine-based probe\\tag-peptide pair fluorescence protein imaging and fluorescence protein imaging methods

DOEpatents

Mayer-Cumblidge, M. Uljana; Cao, Haishi

2013-01-15

A molecular probe comprises two arsenic atoms and at least one cyanine based moiety. A method of producing a molecular probe includes providing a molecule having a first formula, treating the molecule with HgOAc, and subsequently transmetallizing with AsCl.sub.3. The As is liganded to ethanedithiol to produce a probe having a second formula. A method of labeling a peptide includes providing a peptide comprising a tag sequence and contacting the peptide with a biarsenical molecular probe. A complex is formed comprising the tag sequence and the molecular probe. A method of studying a peptide includes providing a mixture containing a peptide comprising a peptide tag sequence, adding a biarsenical probe to the mixture, and monitoring the fluorescence of the mixture.

Cyanine-based probe\\tag-peptide pair for fluorescence protein imaging and fluorescence protein imaging methods

DOEpatents

Mayer-Cumblidge, M Uljana [Richland, WA; Cao, Haishi [Richland, WA

2010-08-17

A molecular probe comprises two arsenic atoms and at least one cyanine based moiety. A method of producing a molecular probe includes providing a molecule having a first formula, treating the molecule with HgOAc, and subsequently transmetallizing with AsCl.sub.3. The As is liganded to ethanedithiol to produce a probe having a second formula. A method of labeling a peptide includes providing a peptide comprising a tag sequence and contacting the peptide with a biarsenical molecular probe. A complex is formed comprising the tag sequence and the molecular probe. A method of studying a peptide includes providing a mixture containing a peptide comprising a peptide tag sequence, adding a biarsenical probe to the mixture, and monitoring the fluorescence of the mixture.

Measurement Of Molecular Mobilities Of Polymers

NASA Technical Reports Server (NTRS)

Kim, Soon Sam; Tsay, Fun-Dow

1989-01-01

New molecular-probe technique used to measure molecular mobility of polymer. Method based on use of time-resolved electron-spin resonance (ESR) spectroscopy to monitor decay of transient nutation amplitudes from photoexcited triplet states of probe molecules with which polymer is doped. The higher molecular mobility of polymer matrix, the faster nutation amplitudes of the probe molecules decay.

A Direct, Quantitative Connection between Molecular Dynamics Simulations and Vibrational Probe Line Shapes.

PubMed

Xu, Rosalind J; Blasiak, Bartosz; Cho, Minhaeng; Layfield, Joshua P; Londergan, Casey H

2018-05-17

A quantitative connection between molecular dynamics simulations and vibrational spectroscopy of probe-labeled systems would enable direct translation of experimental data into structural and dynamical information. To constitute this connection, all-atom molecular dynamics (MD) simulations were performed for two SCN probe sites (solvent-exposed and buried) in a calmodulin-target peptide complex. Two frequency calculation approaches with substantial nonelectrostatic components, a quantum mechanics/molecular mechanics (QM/MM)-based technique and a solvatochromic fragment potential (SolEFP) approach, were used to simulate the infrared probe line shapes. While QM/MM results disagreed with experiment, SolEFP results matched experimental frequencies and line shapes and revealed the physical and dynamic bases for the observed spectroscopic behavior. The main determinant of the CN probe frequency is the exchange repulsion between the probe and its local structural neighbors, and there is a clear dynamic explanation for the relatively broad probe line shape observed at the "buried" probe site. This methodology should be widely applicable to vibrational probes in many environments.

A rational regulatory approach for positron emission tomography imaging probes: from "first in man" to NDA approval and reimbursement.

PubMed

Barrio, Jorge R; Marcus, Carol S; Hung, Joseph C; Keppler, Jennifer S

2004-01-01

We propose a new regulatory approach for positron emission tomography (PET) molecular imaging probes, essential tools in today's medicine. Even though the focus of this paper is on positron-emitting labeled probes, it is also justified to extend this proposed regulatory approach to other diagnostic nuclear medicine radiopharmaceuticals. Key aspects of this proposal include: (1) PET molecular imaging probes would be placed in a "no significant risk" category, similar to that category for devices in current Food and Drug Administration (FDA) regulations, based on overwhelming scientific evidence that demonstrates their faultless safety profile; (2) the FDA-sanctioned Radioactive Drug Research Committee (RDRC) will oversee all diagnostic research with these probes. The newly defined RDRC should approve "first in man" use; supervise a broader spectrum of diagnostic research protocols, including those looking to demonstrate initial efficacy, as well as multicenter clinical trials and the use of molecular imaging probes as a screening tool in drug discovery. The current investigational new drug (IND) mechanism is thus eliminated for these diagnostic probes; (3) when a molecular imaging probe has demonstrated diagnostic efficacy, FDA approval (i.e., NDA) will be sought. The review will be done by a newly constituted Radioactive Drug Advisory Committee (RDAC) composed of experts chosen by the professional societies, who would provide a binding assessment of the adequacy of the safety and efficacy data. When the RDAC recommends its diagnostic use on scientific and medical grounds, the molecular imaging probe becomes FDA approved. After a molecular imaging probe is approved for a diagnostic indication, the existing mechanism to seek reimbursement will be utilized; and (4) the FDA would retain its direct oversight function for traditional manufacturers engaged in commercial distribution of the approved diagnostic molecular imaging probes (i.e., under NDA) to monitor compliance with existing US Pharmacopeia (USP) requirements. With abbreviated and more appropriate regulations, new PET molecular imaging probes for diagnostic use would be then rapidly incorporated into the mainstream diagnostic medicine. Equally importantly, this approach would facilitate the use of molecular imaging in drug discovery and development, which would substantially reduce the costs and time required to bring new therapeutic drugs to market.

MTBDRplus and MTBDRsl Assays: Absence of Wild-Type Probe Hybridization and Implications for Detection of Drug-Resistant Tuberculosis

PubMed Central

Georghiou, Sophia B.; Catanzaro, Donald; Rodrigues, Camilla; Crudu, Valeriu; Victor, Thomas C.; Garfein, Richard S.; Catanzaro, Antonino; Rodwell, Timothy C.

2016-01-01

Accurate identification of drug-resistant Mycobacterium tuberculosis is imperative for effective treatment and subsequent reduction in disease transmission. Line probe assays rapidly detect mutations associated with resistance and wild-type sequences associated with susceptibility. Examination of molecular-level performance is necessary for improved assay result interpretation and for continued diagnostic development. Using data collected from a large, multisite diagnostic study, probe hybridization results from line probe assays, MTBDRplus and MTBDRsl, were compared to those of sequencing, and the diagnostic performance of each individual mutation and wild-type probe was assessed. Line probe assay results classified as resistant due to the absence of wild-type probe hybridization were compared to those of sequencing to determine if novel mutations were inhibiting wild-type probe hybridization. The contribution of absent wild-type probe hybridization to the detection of drug resistance was assessed via comparison to a phenotypic reference standard. In our study, mutation probes demonstrated significantly higher specificities than wild-type probes and wild-type probes demonstrated marginally higher sensitivities than mutation probes, an ideal combination for detecting the presence of resistance conferring mutations while yielding the fewest number of false-positive results. The absence of wild-type probe hybridization without mutation probe hybridization was determined to be primarily the result of failure of mutation probe hybridization and not the result of novel or rare mutations. Compared to phenotypic culture-based drug susceptibility testing, the absence of wild-type probe hybridization without mutation probe hybridization significantly contributed to the detection of phenotypic rifampin and fluoroquinolone resistance with negligible increases in false-positive results. PMID:26763971

Molecular Dynamics and Theoretical Chemistry

DTIC Science & Technology

2013-03-08

and structural stability compared to H-Si(111) • Air- and electrochemical-stability enables advanced sensors, fuel and solar cells , etc. • Probes...Diagnostics ARO – plasmonics AFOSR - Endo fuels, combustion, solar PNNL – Institute for Integrated Catalysis Navy, DTRA – Clusters AFRL, NASA, DoD...Propellants • Real-time probing of reactions • Hybrid Chemical Lasers • Sensors for Trace Detection Distribution A: Approved for public release

Molecular engineering of two-photon fluorescent probes for bioimaging applications

NASA Astrophysics Data System (ADS)

Liu, Hong-Wen; Liu, Yongchao; Wang, Peng; Zhang, Xiao-Bing

2017-03-01

During the past two decades, two-photon microscopy (TPM), which utilizes two near-infrared photons as the excitation source, has emerged as a novel, attractive imaging tool for biological research. Compared with one-photon microscopy, TPM offers several advantages, such as lowering background fluorescence in living cells and tissues, reducing photodamage to biosamples, and a photobleaching phenomenon, offering better 3D spatial localization, and increasing penetration depth. Small-molecule-based two-photon fluorescent probes have been well developed for the detection and imaging of various analytes in biological systems. In this review, we will give a general introduction of molecular engineering of two-photon fluorescent probes based on different fluorescence response mechanisms for bioimaging applications during the past decade. Inspired by the desired advantages of small-molecule two-photon fluorescent probes in biological imaging applications, we expect that more attention will be devoted to the development of new two-photon fluorophores and applications of TPM in areas of bioanalysis and disease diagnosis.

Factors determining electrostatic fields in molecular dynamics simulations of the Ras/effector interface.

PubMed

Ensign, Daniel L; Webb, Lauren J

2011-12-01

Using molecular dynamics simulations, we explore geometric and physical factors contributing to calculated electrostatic fields at the binding surface of the GTPase Ras with a spectroscopically labeled variant of a downstream effector, the Ras-binding domain of Ral guanine nucleotide dissociation stimulator (RalGDS). A related system (differing by mutation of one amino acid) has been studied in our group using vibrational Stark effect spectroscopy, a technique sensitive to electrostatic fields. Electrostatic fields were computed using the AMBER 2003 force field and averaged over snapshots from molecular dynamics simulation. We investigate geometric factors by exploring how the orientation of the spectroscopic probe changes on Ras-effector binding. In addition, we explore the physical origin of electrostatic fields at our spectroscopic probe by comparing contributions to the field from discrete components of the system, such as explicit solvent, residues on the Ras surface, and residues on the RalGDS surface. These models support our experimental hypothesis that vibrational Stark shifts are caused by Ras binding to its effector and not the structural rearrangements of the effector surface or probe reorientation on Ras-effector binding, for at least some of our experimental probes. These calculations provide physical insight into the origin, magnitude, and importance of electrostatic fields in protein-protein interactions and suggest new experiments to probe the field's role in protein docking. Copyright © 2011 Wiley-Liss, Inc.

In Vivo Imaging of Immuno-Spin Trapped Radicals With Molecular Magnetic Resonance Imaging in a Diabetic Mouse Model

PubMed Central

Towner, Rheal A.; Smith, Nataliya; Saunders, Debra; Henderson, Michael; Downum, Kristen; Lupu, Florea; Silasi-Mansat, Robert; Ramirez, Dario C.; Gomez-Mejiba, Sandra E.; Bonini, Marcelo G.; Ehrenshaft, Marilyn; Mason, Ronald P.

2012-01-01

Oxidative stress plays a major role in diabetes. In vivo levels of membrane-bound radicals (MBRs) in a streptozotocin-induced diabetic mouse model were uniquely detected by combining molecular magnetic resonance imaging (mMRI) and immunotrapping techniques. An anti-DMPO (5,5-dimethyl-1-pyrroline N-oxide) antibody (Ab) covalently bound to an albumin (BSA)-Gd (gadolinium)-DTPA (diethylene triamine penta acetic acid)-biotin MRI contrast agent (anti-DMPO probe), and mMRI, were used to detect in vivo levels of DMPO-MBR adducts in kidneys, livers, and lungs of diabetic mice, after DMPO administration. Magnetic resonance signal intensities, which increase in the presence of a Gd-based molecular probe, were significantly higher within the livers, kidneys, and lungs of diabetic animals administered the anti-DMPO probe compared with controls. Fluorescence images validated the location of the anti-DMPO probe in excised tissues via conjugation of streptavidin-Cy3, which targeted the probe biotin moiety, and immunohistochemistry was used to validate the presence of DMPO adducts in diabetic mouse livers. This is the first report of noninvasively imaging in vivo levels of MBRs within any disease model. This method can be specifically applied toward diabetes models for in vivo assessment of free radical levels, providing an avenue to more fully understand the role of free radicals in diabetes. PMID:22698922

Probing Massive Star Cluster Formation with ALMA

NASA Astrophysics Data System (ADS)

Johnson, Kelsey

2015-08-01

Observationally constraining the physical conditions that give rise to massive star clusters has been a long-standing challenge. Now with the ALMA Observatory coming on-line, we can finally begin to probe the birth environments of massive clusters in a variety of galaxies with sufficient angular resolution. In this talk I will give an overview of ALMA observations of galaxies in which candidate proto-super star cluster molecular clouds have been identified. These new data probe the physical conditions that give rise to super star clusters, providing information on their densities, pressures, and temperatures. In particular, the observations indicate that these clouds may be subject to external pressures of P/k > 108 K cm-3, which is consistent with the prevalence of optically observed adolescent super star clusters in interacting galaxy systems and other high pressure environments. ALMA observations also enable an assessement of the molecular cloud chemical abundances in the regions surrounding super star clusters. Molecular clouds associated with existing super star clusters are strongly correlated with HCO+ emission, but appear to have relatively low ratio of CO/HCO+ emission compared to other clouds, indicating that the super star clusters are impacting the molecular abundances in their vicinity.

Intraoperative Molecular Imaging of Lung Adenocarcinoma Can Identify Residual Tumor Cells at the Surgical Margins

PubMed Central

Keating, Jane J.; Okusanya, Olugbenga T.; De Jesus, Elizabeth; Judy, Ryan; Jiang, Jack; Deshpande, Charuhas; Nie, Shuming; Low, Philip; Singhal, Sunil

2017-01-01

Purpose During lung surgery, identification of surgical margins is challenging. We hypothesized that molecular imaging with a fluorescent probe to pulmonary adenocarcinomas could enhance residual tumor during resection. Procedures Mice with flank tumors received a contrast agent targeting folate receptor alpha. Optimal dose and time of injection was established. Margin detection was compared using traditional methods versus molecular imaging. A pilot study was then performed in 3 humans with lung adenocarcinoma. Results The peak tumor-to background ratio (TBR) of murine tumors was 3.9. Fluorescence peaked at 2 hours and was not improved beyond 0.1 mg/kg. Traditional inspection identified 30% of mice with positive margins. Molecular imaging identified an additional 50% of residual tumor deposits (P<0.05). The fluorescent probe visually enhanced all human tumors with a mean TBR of 3.5. Conclusions Molecular imaging is an important adjunct to traditional inspection to identify surgical margins after tumor resection. PMID:26228697

Oecomys catherinae (Sigmodontinae, Cricetidae): Evidence for chromosomal speciation?

PubMed

Malcher, Stella Miranda; Pieczarka, Julio Cesar; Geise, Lena; Rossi, Rogério Vieira; Pereira, Adenilson Leão; O'Brien, Patricia Caroline Mary; Asfora, Paulo Henrique; Fonsêca da Silva, Victor; Sampaio, Maria Iracilda; Ferguson-Smith, Malcolm Andrew; Nagamachi, Cleusa Yoshiko

2017-01-01

Among the Oryzomyini (Sigmodontinae), Oecomys is the most speciose, with 17 species. This genus presents high karyotypic diversity (2n = 54 to 2n = 86) and many taxonomic issues at the species level because of the presence of cryptic species and the overlap of morphological characters. For these reasons the real number of species of Oecomys may be underestimated. With the aim of verifying if the taxon Oecomys catherinae is composed of more than one species, we made comparative studies on two populations from two regions of Brazil, one from the Amazon and another from the Atlantic Forest using both classical cytogenetics (G- and C-banding) and comparative genomic mapping with whole chromosome probes of Hylaeamys megacephalus (HME), molecular data (cytochrome b mitochondrial DNA) and morphology. Our results confirm that Oecomys catherinae occurs in the southeast Amazon, and reveal a new karyotype for the species (2n = 62, FNa = 62). The comparative genomic analysis with HME probes identified chromosomal homeologies between both populations and rearrangements that are responsible for the different karyotypes. We compared our results in Sigmodontinae genera with other studies that also used HME probes. These chromosomal differences together with the absence of consistent differentiation between the two populations on morphological and molecular analyses suggest that these populations may represent cryptic species.

Activatable fluorescent probes in fluorescence-guided surgery: Practical considerations.

PubMed

Mochida, Ai; Ogata, Fusa; Nagaya, Tadanobu; Choyke, Peter L; Kobayashi, Hisataka

2018-02-15

Fluorescence-guided imaging during surgery is a promising technique that is increasingly used to aid surgeons in identifying sites of tumor and surgical margins. Of the two types of fluorescent probes, always-on and activatable, activatable probes are preferred because they produce higher target-to-background ratios, thus improving sensitivity compared with always-on probes that must contend with considerable background signal. There are two types of activatable probes: 1) enzyme-reactive probes that are normally quenched but can be activated after cleavage by cancer-specific enzymes (activity-based probes) and 2) molecular-binding probes which use cancer targeting moieties such as monoclonal antibodies to target receptors found in abundance on cancers and are activated after internalization and lysosomal processing (binding-based probes). For fluorescence-guided intraoperative surgery, enzyme-reactive probes are superior because they can react quickly, require smaller dosages especially for topical applications, have limited side effects, and have favorable pharmacokinetics. Enzyme-reactive probes are easier to use, fit better into existing work flows in the operating room and have minimal toxicity. Although difficult to prove, it is assumed that the guidance provided to surgeons by these probes results in more effective surgeries with better outcomes for patients. In this review, we compare these two types of activatable fluorescent probes for their ease of use and efficacy. Published by Elsevier Ltd.

High Resolution PET Imaging Probe for the Detection, Molecular Characterization and Treatment Monitoring of Prostate Cancer

DTIC Science & Technology

2010-07-01

W81XWH-09-1-0420 TITLE: High Resolution PET Imaging Probe for the Detection, Molecular Characterization and Treatment Monitoring of Prostate Cancer...4. TITLE AND SUBTITLE High-Resolution PET Imaging Probe for the Detection, Molecular Characterization and Treatment of Prostate Cancer... molecular imaging for diagnosis as well as treatment planning and monitoring in prostate cancer. This investigation hypothesizes that a dedicated

An ALuc-Based Molecular Tension Probe for Sensing Intramolecular Protein-Protein Interactions.

PubMed

Kim, Sung-Bae; Nishihara, Ryo; Suzuki, Koji

2016-01-01

Optical imaging of protein-protein interactions (PPIs) facilitates comprehensive elucidation of intracellular molecular events. The present protocol demonstrates an optical measure for visualizing molecular tension triggered by any PPI in mammalian cells. A unique design of single-chain probes was fabricated, in which a full-length artificial luciferase (ALuc(®)) was sandwiched between two model proteins of interest, e.g., FKBP and FRB. A molecular tension probe comprising ALuc23 greatly enhances the bioluminescence in response to varying concentrations of rapamycin, and named "tension probe (TP)." The basic probe design can be further modified towards eliminating the C-terminal end of ALuc and was found to improve signal-to-background ratios, named "combinational probe." TPs may become an important addition to the tool box of bioassays in the determination of protein dynamics of interest in mammalian cells.

NIR fluorescence lifetime sensing through a multimode fiber for intravascular molecular probing

NASA Astrophysics Data System (ADS)

Ingelberts, H.; Hernot, S.; Debie, P.; Lahoutte, T.; Kuijk, M.

2016-04-01

Coronary artery disease (CAD) contributes to millions of deaths each year. The identification of vulnerable plaques is essential to the diagnosis of CAD but is challenging. Molecular probes can improve the detection of these plaques using intravascular imaging methods. Fluorescence lifetime sensing is a safe and robust method to image these molecular probes. We present two variations of an optical system for intravascular near-infrared (NIR) fluorescence lifetime sensing through a multimode fiber. Both systems are built around a recently developed fast and efficient CMOS detector, the current-assisted photonic sampler (CAPS) that is optimized for sub-nanosecond NIR fluorescence lifetime sensing. One system mimics the optical setup of an epifluorescence microscope while the other uses a practical fiber optic coupler to separate fluorescence excitation and emission. We test both systems by measuring the lifetime of several NIR dyes in DMSO solutions and we show that these systems are capable of detecting lifetimes of solutions with concentrations down to 370 nM and this with short acquisition times. These results are compared with time-correlated single photon counting (TCSPC) measurements for reference.

Molecular galactose-galectin association in neuroblastoma cells: An unconventional tool for qualitative/quantitative screening.

PubMed

Pastorino, Fabio; Ponzoni, Mirco; Simone, Giuseppina

2017-05-01

Galectin decorates the cell membrane and forms an extracellular molecular association with galactoside units. Here, galactoside probes have been used to study galectin expression in neuroblastoma cells. The hypothesis behind this investigation has been that the molecular mechanisms by which glycans modulate neural metastatic cells involve a protein-carbohydrate association, galectin-galactose. Preliminary screening to validate the hypothesis has been performed with galactose moieties anchored to beads. The molecular association has been studied by FACS. In vitro experiments reveal the molecular binding preferences of the metastatic neuroblastoma cells. Ex vivo, the galactose probes discriminate healthy tissues. The unconventional assay in microfluidics used in this study displayed results analogous to the above (GI-LI-N cell capture efficiency overcomes IMR-32). At the point of equilibrium of shear and binding forces, the capture yield inside the chamber was measured to 60 ± 4.4% in GI-LI-N versus 40 ± 2.1% in IMR-32. Staining of the fished cells and subsequent conjugation with red beads bearing the galactose also have evidenced that microfluidics can be used to study and quantify the molecular association of galectin-galactose. Most importantly, a crucial insight for obtaining single-cell qualitative/quantitative glycome analysis has been achieved. Finally, the specificity of the assay performed in microfluidics is demonstrated by comparing GI-LI-N fishing efficiency in galactose and fucose environments. The residual adhesion to fucose confirmed the existence of receptors for this glycan and that its eventual unspecific binding (i.e. due to electrostatic interactions) is insignificant compared with the molecular binding. Identification and understanding of this mechanism of discrimination can be relevant for diagnostic monitoring and for producing probes tailored to interfere with galectin activities associated with the malignant phenotype. Besides, the given strategy has implications for the rational design of galectin-specific ligands. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Capillary levelling as a probe of rheology in polymer thin films

NASA Astrophysics Data System (ADS)

McGraw, Joshua D.; Jago, Nick M.; Dalnoki-Veress, Kari

2011-03-01

While measuring the rheology of bulk polymer systems is routine, when the size of a system becomes comparable to the molecular size, flow properties are poorly understood and hard to measure. Here, we present the results of experiments that are easily performed and can probe the rheological properties of polymer films that are mere tens of nanometres in thickness. We prepare glassy bilayer polymer films with height profiles well approximated by a step function. Upon annealing above the glass transition, broadening of the height profiles due to gradients in the Laplace pressure is observed. By validating the technique as a probe of the rheology with a range of molecular weights, we will show that this robust technique can be used to investigate the effects of confinement and interfaces on the rheology of ultrathin polymer films. Financial support from NSERC of Canada is gratefully acknowledged.

Dynamic-force spectroscopy measurement with precise force control using atomic-force microscopy probe

NASA Astrophysics Data System (ADS)

Takeuchi, Osamu; Miyakoshi, Takaaki; Taninaka, Atsushi; Tanaka, Katsunori; Cho, Daichi; Fujita, Machiko; Yasuda, Satoshi; Jarvis, Suzanne P.; Shigekawa, Hidemi

2006-10-01

The accuracy of dynamic-force spectroscopy (DFS), a promising technique of analyzing the energy landscape of noncovalent molecular bonds, was reconsidered in order to justify the use of an atomic-force microscopy (AFM) cantilever as a DFS force probe. The advantages and disadvantages caused, for example, by the force-probe hardness were clarified, revealing the pivotal role of the molecular linkage between the force probe and the molecular bonds. It was shown that the feedback control of the loading rate of tensile force enables us a precise DFS measurement using an AFM cantilever as the force probe.

Nitro stretch probing of a single molecular layer to monitor shock compression with picosecond time resolution

NASA Astrophysics Data System (ADS)

Berg, Christopher; Lagutchev, Alexei; Fu, Yuanxi; Dlott, Dana

2012-03-01

Ultrafast shock compression vibrational spectroscopy experiments with molecular monolayers provide atomic-scale time and space resolution, which enables critical testing of reactive molecular simulations. Since the origination of this project, we have greatly improved the ability to detect shocked monolayers by nonlinear coherent vibrational spectroscopy with nonresonant suppression. In this study, we show new results on a nitroaromatic monolayer, where the nitro symmetric stretch is probed. A small frequency blue-shift under shock conditions compared to measurements with static high pressure shows the shock is ~1 GPa. The ability to flash-preheat the monolayer by several hundred K is demonstrated. In order to observe shock monolayer chemistry in real time, along with pre-heating, the shock pressure needs to be increased and methods to do so are described.

Effect of molecular asymmetry on the charge transport physics of high mobility n-type molecular semiconductors investigated by scanning Kelvin probe microscopy.

PubMed

Hu, Yuanyuan; Berdunov, Nikolai; Di, Chong-an; Nandhakumar, Iris; Zhang, Fengjiao; Gao, Xike; Zhu, Daoben; Sirringhaus, Henning

2014-07-22

We have investigated the influence of the symmetry of the side chain substituents in high-mobility, solution processable n-type molecular semiconductors on the performance of organic field-effect transistors (OFETs). We compare two molecules with the same conjugated core, but either symmetric or asymmetric side chain substituents, and investigate the transport properties and thin film growth mode using scanning Kelvin probe microscopy (SKPM) and atomic force microscopy (AFM). We find that asymmetric side chains can induce a favorable two-dimensional growth mode with a bilayer structure, which enables ultrathin films with a single bilayer to exhibit excellent transport properties, while the symmetric molecules adopt an unfavorable three-dimensional growth mode in which transport in the first monolayer at the interface is severely hindered by high-resistance grain boundaries.

Dual-Modal Colorimetric/Fluorescence Molecular Probe for Ratiometric Sensing of pH and Its Application.

PubMed

Wu, Luling; Li, Xiaolin; Huang, Chusen; Jia, Nengqin

2016-08-16

As traditional pH meters cannot work well for minute regions (such as subcellular organelles) and in harsh media, molecular pH-sensitive devices for monitoring pH changes in diverse local heterogeneous environments are urgently needed. Here, we report a new dual-modal colorimetric/fluorescence merocyanine-based molecular probe (CPH) for ratiometric sensing of pH. Compared with previously reported pH probes, CPH bearing the benzyl group at the nitrogen position of the indolium group and the phenol, which is used as the acceptor for proton, could respond to pH changes immediately through both the ratiometric fluorescence signal readout and naked-eye colorimetric observation. The sensing process was highly stable and reversible. Most importantly, the suitable pKa value (6.44) allows CPH to presumably accumulate in lysosomes and become a lysosome-target fluorescent probe. By using CPH, the intralysosomal pH fluctuation stimulated by antimalaria drug chloroquine was successfully tracked in live cells through the ratiometric fluorescence images. Additionally, CPH could be immobilized on test papers, which exhibited a rapid and reversible colorimetric response to acid/base vapor through the naked-eye colorimetric analysis. This proof-of-concept study presents the potential application of CPH as a molecular tool for monitoring intralysosomal pH fluctuation in live cells, as well as paves the way for developing the economic, reusable, and fast-response optical pH meters for colorimetric sensing acid/base vapor with direct naked-eye observation.

Identification of Binding Modes for Amino Naphthalene 2-Cyanoacrylate (ANCA) Probes to Amyloid Fibrils from Molecular Dynamics Simulations.

PubMed

He, Huan; Xu, Juan; Cheng, Dan-Yang; Fu, Li; Ge, Yu-Shu; Jiang, Feng-Lei; Liu, Yi

2017-02-16

The amino naphthalene 2-cyanoacrylate (ANCA) probe is a kind of fluorescent amyloid binding probe that can report different fluorescence emissions when bound to various amyloid deposits in tissue, while their interactions with amyloid fibrils remain unclear due to the insoluble nature of amyloid fibrils. Here, all-atom molecular dynamics simulations were used to investigate the interaction between ANCA probes with three different amyloid fibrils. Two common binding modes of ANCA probes on Aβ40 amyloid fibrils were identified by cluster analysis of multiple simulations. The van der Waals and electrostatic interactions were found to be major driving forces for the binding. Atomic contacts analysis and binding free energy decomposition results suggested that the hydrophobic part of ANCA mainly interacts with aromatic side chains on the fibril surface and the hydrophilic part mainly interacts with positive charged residues in the β-sheet region. By comparing the binding modes with different fibrils, we can find that ANCA adopts different conformations while interacting with residues of different hydrophobicity, aromaticity, and electrochemical properties in the β-sheet region, which accounts for its selective mechanism toward different amyloid fibrils.

ProbeZT: Simulation of transport coefficients of molecular electronic junctions under environmental effects using Büttiker's probes

NASA Astrophysics Data System (ADS)

Korol, Roman; Kilgour, Michael; Segal, Dvira

2018-03-01

We present our in-house quantum transport package, ProbeZT. This program provides linear response coefficients: electrical and electronic thermal conductances, as well as the thermopower of molecular junctions in which electrons interact with the surrounding thermal environment. Calculations are performed based on the Büttiker probe method, which introduces decoherence, energy exchange and dissipation effects phenomenologically using virtual electrode terminals called probes. The program can realize different types of probes, each introducing various environmental effects, including elastic and inelastic scattering of electrons. The molecular system is described by an arbitrary tight-binding Hamiltonian, allowing the study of different geometries beyond simple one-dimensional wires. Applications of the program to study the thermoelectric performance of molecular junctions are illustrated. The program also has a built-in functionality to simulate electron transport in double-stranded DNA molecules based on a tight-binding (ladder) description of the junction.

Probing molecular potentials with an optical centrifuge.

PubMed

Milner, A A; Korobenko, A; Hepburn, J W; Milner, V

2017-09-28

We use an optical centrifuge to excite coherent rotational wave packets in N 2 O, OCS, and CS 2 molecules with rotational quantum numbers reaching up to J≈465, 690, and 1186, respectively. Time-resolved rotational spectroscopy at such ultra-high levels of rotational excitation can be used as a sensitive tool to probe the molecular potential energy surface at internuclear distances far from their equilibrium values. Significant bond stretching in the centrifuged molecules results in the growing period of the rotational revivals, which are experimentally detected using coherent Raman scattering. We measure the revival period as a function of the centrifuge-induced rotational frequency and compare it with the numerical calculations based on the known Morse-cosine potentials.

Probing molecular potentials with an optical centrifuge

NASA Astrophysics Data System (ADS)

Milner, A. A.; Korobenko, A.; Hepburn, J. W.; Milner, V.

2017-09-01

We use an optical centrifuge to excite coherent rotational wave packets in N2O, OCS, and CS2 molecules with rotational quantum numbers reaching up to J ≈465 , 690, and 1186, respectively. Time-resolved rotational spectroscopy at such ultra-high levels of rotational excitation can be used as a sensitive tool to probe the molecular potential energy surface at internuclear distances far from their equilibrium values. Significant bond stretching in the centrifuged molecules results in the growing period of the rotational revivals, which are experimentally detected using coherent Raman scattering. We measure the revival period as a function of the centrifuge-induced rotational frequency and compare it with the numerical calculations based on the known Morse-cosine potentials.

Pump-Probe Fragmentation Action Spectroscopy: A Powerful Tool to Unravel Light-Induced Processes in Molecular Photocatalysts.

PubMed

Imanbaew, Dimitri; Lang, Johannes; Gelin, Maxim F; Kaufhold, Simon; Pfeffer, Michael G; Rau, Sven; Riehn, Christoph

2017-05-08

We present a proof of concept that ultrafast dynamics combined with photochemical stability information of molecular photocatalysts can be acquired by electrospray ionization mass spectrometry combined with time-resolved femtosecond laser spectroscopy in an ion trap. This pump-probe "fragmentation action spectroscopy" gives straightforward access to information that usually requires high purity compounds and great experimental efforts. Results of gas-phase studies on the electronic dynamics of two supramolecular photocatalysts compare well to previous findings in solution and give further evidence for a directed electron transfer, a key process for photocatalytic hydrogen generation. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mechanistic and quantitative insight into cell surface targeted molecular imaging agent design.

PubMed

Zhang, Liang; Bhatnagar, Sumit; Deschenes, Emily; Thurber, Greg M

2016-05-05

Molecular imaging agent design involves simultaneously optimizing multiple probe properties. While several desired characteristics are straightforward, including high affinity and low non-specific background signal, in practice there are quantitative trade-offs between these properties. These include plasma clearance, where fast clearance lowers background signal but can reduce target uptake, and binding, where high affinity compounds sometimes suffer from lower stability or increased non-specific interactions. Further complicating probe development, many of the optimal parameters vary depending on both target tissue and imaging agent properties, making empirical approaches or previous experience difficult to translate. Here, we focus on low molecular weight compounds targeting extracellular receptors, which have some of the highest contrast values for imaging agents. We use a mechanistic approach to provide a quantitative framework for weighing trade-offs between molecules. Our results show that specific target uptake is well-described by quantitative simulations for a variety of targeting agents, whereas non-specific background signal is more difficult to predict. Two in vitro experimental methods for estimating background signal in vivo are compared - non-specific cellular uptake and plasma protein binding. Together, these data provide a quantitative method to guide probe design and focus animal work for more cost-effective and time-efficient development of molecular imaging agents.

Enzyme-less electrochemical displacement heterogeneous immunosensor for diclofenac detection.

PubMed

Nguyen, T T K; Vu, T T; Anquetin, G; Tran, H V; Reisberg, S; Noël, V; Mattana, G; Nguyen, Q V; Dai Lam, Tran; Pham, M C; Piro, B

2017-11-15

We describe an electrochemical immunosensor based on functionalization of a working electrode by electrografting two functional diazonium salts. The first one is a molecular probe, diclofenac, coupled with an arylamine onto which a specific antibody is immobilized by affinity interactions; the second is a redox probe (a quinone) also coupled with an arylamine, able to transduce the hapten-antibody association into a change in electroactivity. The steric hindrance induced by the antibody leads to a current decrease upon binding of the antibody on the grafted molecular probe; conversely, when diclofenac is present in solution, a displacement equilibrium occurs between the target diffusing into the solution and the grafted probe. This leads to dissociation of the antibody from the electrode surface, event which is transduced into a current increase ("signal-on" detection). The detection limit is ca. 20 fM, corresponding to 6pgL -1 diclofenac, which is competitive compared to other label-free immunosensors. We demonstrate that the sensor is selective and is able to quantify diclofenac in tap water. Copyright © 2017 Elsevier B.V. All rights reserved.

Enhancing in vivo tumor boundary delineation with structured illumination fluorescence molecular imaging and spatial gradient mapping

NASA Astrophysics Data System (ADS)

Sun, Jessica; Miller, Jessica P.; Hathi, Deep; Zhou, Haiying; Achilefu, Samuel; Shokeen, Monica; Akers, Walter J.

2016-08-01

Fluorescence imaging, in combination with tumor-avid near-infrared (NIR) fluorescent molecular probes, provides high specificity and sensitivity for cancer detection in preclinical animal models, and more recently, assistance during oncologic surgery. However, conventional camera-based fluorescence imaging techniques are heavily surface-weighted such that surface reflection from skin or other nontumor tissue and nonspecific fluorescence signals dominate, obscuring true cancer-specific signals and blurring tumor boundaries. To address this challenge, we applied structured illumination fluorescence molecular imaging (SIFMI) in live animals for automated subtraction of nonspecific surface signals to better delineate accumulation of an NIR fluorescent probe targeting α4β1 integrin in mice bearing subcutaneous plasma cell xenografts. SIFMI demonstrated a fivefold improvement in tumor-to-background contrast when compared with other full-field fluorescence imaging methods and required significantly reduced scanning time compared with diffuse optical spectroscopy imaging. Furthermore, the spatial gradient mapping enhanced highlighting of tumor boundaries. Through the relatively simple hardware and software modifications described, SIFMI can be integrated with clinical fluorescence imaging systems, enhancing intraoperative tumor boundary delineation from the uninvolved tissue.

Chromosomal evolution and phylogeny in the Nullicauda group (Chiroptera, Phyllostomidae): evidence from multidirectional chromosome painting.

PubMed

Gomes, Anderson José Baia; Nagamachi, Cleusa Yoshiko; Rodrigues, Luis Reginaldo Ribeiro; Ferguson-Smith, Malcolm Andrew; Yang, Fengtang; O'Brien, Patricia Caroline Mary; Pieczarka, Julio Cesar

2018-04-25

The family Phyllostomidae (Chiroptera) shows wide morphological, molecular and cytogenetic variation; many disagreements regarding its phylogeny and taxonomy remains to be resolved. In this study, we use chromosome painting with whole chromosome probes from the Phyllostomidae Phyllostomus hastatus and Carollia brevicauda to determine the rearrangements among several genera of the Nullicauda group (subfamilies Gliphonycterinae, Carolliinae, Rhinophyllinae and Stenodermatinae). These data, when compared with previously published chromosome homology maps, allow the construction of a phylogeny comparable to those previously obtained by morphological and molecular analysis. Our phylogeny is largely in agreement with that proposed with molecular data, both on relationships between the subfamilies and among genera; it confirms, for instance, that Carollia and Rhinophylla, previously considered as part of the same subfamily are, in fact, distant genera. The occurrence of the karyotype considered ancestral for this family in several different branches suggests that the diversification of Phyllostomidae into many subfamilies has occurred in a short period of time. Finally, the comparison with published maps using human whole chromosome probes allows us to track some syntenic associations prior to the emergence of this family.

Quantum Dot Platform for Single-Cell Molecular Profiling

NASA Astrophysics Data System (ADS)

Zrazhevskiy, Pavel S.

In-depth understanding of the nature of cell physiology and ability to diagnose and control the progression of pathological processes heavily rely on untangling the complexity of intracellular molecular mechanisms and pathways. Therefore, comprehensive molecular profiling of individual cells within the context of their natural tissue or cell culture microenvironment is essential. In principle, this goal can be achieved by tagging each molecular target with a unique reporter probe and detecting its localization with high sensitivity at sub-cellular resolution, primarily via microscopy-based imaging. Yet, neither widely used conventional methods nor more advanced nanoparticle-based techniques have been able to address this task up to date. High multiplexing potential of fluorescent probes is heavily restrained by the inability to uniquely match probes with corresponding molecular targets. This issue is especially relevant for quantum dot probes---while simultaneous spectral imaging of up to 10 different probes is possible, only few can be used concurrently for staining with existing methods. To fully utilize multiplexing potential of quantum dots, it is necessary to design a new staining platform featuring unique assignment of each target to a corresponding quantum dot probe. This dissertation presents two complementary versatile approaches towards achieving comprehensive single-cell molecular profiling and describes engineering of quantum dot probes specifically tailored for each staining method. Analysis of expanded molecular profiles is achieved through augmenting parallel multiplexing capacity with performing several staining cycles on the same specimen in sequential manner. In contrast to other methods utilizing quantum dots or other nanoparticles, which often involve sophisticated probe synthesis, the platform technology presented here takes advantage of simple covalent bioconjugation and non-covalent self-assembly mechanisms for straightforward probe preparation and specimen labeling, requiring no advanced technical skills and being directly applicable for a wide range of molecular profiling studies. Utilization of quantum dot platform for single-cell molecular profiling promises to greatly benefit both biomedical research and clinical diagnostics by providing a tool for addressing phenotypic heterogeneity within large cell populations, opening access to studying low-abundance events often masked or completely erased by batch processing, and elucidating biomarker signatures of diseases critical for accurate diagnostics and targeted therapy.

Mass amplifying probe for sensitive fluorescence anisotropy detection of small molecules in complex biological samples.

PubMed

Cui, Liang; Zou, Yuan; Lin, Ninghang; Zhu, Zhi; Jenkins, Gareth; Yang, Chaoyong James

2012-07-03

Fluorescence anisotropy (FA) is a reliable and excellent choice for fluorescence sensing. One of the key factors influencing the FA value for any molecule is the molar mass of the molecule being measured. As a result, the FA method with functional nucleic acid aptamers has been limited to macromolecules such as proteins and is generally not applicable for the analysis of small molecules because their molecular masses are relatively too small to produce observable FA value changes. We report here a molecular mass amplifying strategy to construct anisotropy aptamer probes for small molecules. The probe is designed in such a way that only when a target molecule binds to the probe does it activate its binding ability to an anisotropy amplifier (a high molecular mass molecule such as protein), thus significantly increasing the molecular mass and FA value of the probe/target complex. Specifically, a mass amplifying probe (MAP) consists of a targeting aptamer domain against a target molecule and molecular mass amplifying aptamer domain for the amplifier protein. The probe is initially rendered inactive by a small blocking strand partially complementary to both target aptamer and amplifier protein aptamer so that the mass amplifying aptamer domain would not bind to the amplifier protein unless the probe has been activated by the target. In this way, we prepared two probes that constitute a target (ATP and cocaine respectively) aptamer, a thrombin (as the mass amplifier) aptamer, and a fluorophore. Both probes worked well against their corresponding small molecule targets, and the detection limits for ATP and cocaine were 0.5 μM and 0.8 μM, respectively. More importantly, because FA is less affected by environmental interferences, ATP in cell media and cocaine in urine were directly detected without any tedious sample pretreatment. Our results established that our molecular mass amplifying strategy can be used to design aptamer probes for rapid, sensitive, and selective detection of small molecules by means of FA in complex biological samples.

Rational Design of in Vivo Tau Tangle-Selective Near-Infrared Fluorophores: Expanding the BODIPY Universe.

PubMed

Verwilst, Peter; Kim, Hye-Ri; Seo, Jinho; Sohn, Nak-Won; Cha, Seung-Yun; Kim, Yeongmin; Maeng, Sungho; Shin, Jung-Won; Kwak, Jong Hwan; Kang, Chulhun; Kim, Jong Seung

2017-09-27

The elucidation of the cause of Alzheimer's disease remains one of the greatest questions in neurodegenerative research. The lack of highly reliable low-cost sensors to study the structural changes in key proteins during the progression of the disease is a contributing factor to this lack of insight. In the current work, we describe the rational design and synthesis of two fluorescent BODIPY-based probes, named Tau 1 and Tau 2. The probes were evaluated on the molecular surface formed by a fibril of the PHF6 ( 306 VQIVYK 311 ) tau fragment using molecular docking studies to provide a potential molecular model to rationalize the selectivity of the new probes as compared to a homologous Aβ-selective probe. The probes were synthesized in a few steps from commercially available starting products and could thus prove to be highly cost-effective. We demonstrated the excellent photophysical properties of the dyes, such as a large Stokes shift and emission in the near-infrared window of the electromagnetic spectrum. The probes demonstrated a high selectivity for self-assembled microtubule-associated protein tau (Tau protein), in both solution and cell-based experiments. Moreover, the administration to an acute murine model of tauopathy clearly revealed the staining of self-assembled hyperphosphorylated tau protein in pathologically relevant hippocampal brain regions. Tau 1 demonstrated efficient blood-brain barrier penetrability and demonstrated a clear selectivity for tau tangles over Aβ plaques, as well as the capacity for in vivo imaging in a transgenic mouse model. The current work could open up avenues for the cost-effective monitoring of the tau protein aggregation state in animal models as well as tissue staining. Furthermore, these fluorophores could serve as the basis for the development of clinically relevant sensors, for example based on PET imaging.

DHA-fluorescent probe is sensitive to membrane order and reveals molecular adaptation of DHA in ordered lipid microdomains☆

PubMed Central

Teague, Heather; Ross, Ron; Harris, Mitchel; Mitchell, Drake C.; Shaikh, Saame Raza

2012-01-01

Docosahexaenoic acid (DHA) disrupts the size and order of plasma membrane lipid microdomains in vitro and in vivo. However, it is unknown how the highly disordered structure of DHA mechanistically adapts to increase the order of tightly packed lipid microdomains. Therefore, we studied a novel DHA-Bodipy fluorescent probe to address this issue. We first determined if the DHA-Bodipy probe localized to the plasma membrane of primary B and immortal EL4 cells. Image analysis revealed that DHA-Bodipy localized into the plasma membrane of primary B cells more efficiently than EL4 cells. We then determined if the probe detected changes in plasma membrane order. Quantitative analysis of time-lapse movies established that DHA-Bodipy was sensitive to membrane molecular order. This allowed us to investigate how DHA-Bodipy physically adapted to ordered lipid microdomains. To accomplish this, we employed steady-state and time-resolved fluorescence anisotropy measurements in lipid vesicles of varying composition. Similar to cell culture studies, the probe was highly sensitive to membrane order in lipid vesicles. Moreover, these experiments revealed, relative to controls, that upon incorporation into highly ordered microdomains, DHA-Bodipy underwent an increase in its fluorescence lifetime and molecular order. In addition, the probe displayed a significant reduction in its rotational diffusion compared to controls. Altogether, DHA-Bodipy was highly sensitive to membrane order and revealed for the first time that DHA, despite its flexibility, could become ordered with less rotational motion inside ordered lipid microdomains. Mechanistically, this explains how DHA acyl chains can increase order upon formation of lipid microdomains in vivo. PMID:22841541

Drying Affects the Fiber Network in Low Molecular Weight Hydrogels

PubMed Central

2017-01-01

Low molecular weight gels are formed by the self-assembly of a suitable small molecule gelator into a three-dimensional network of fibrous structures. The gel properties are determined by the fiber structures, the number and type of cross-links and the distribution of the fibers and cross-links in space. Probing these structures and cross-links is difficult. Many reports rely on microscopy of dried gels (xerogels), where the solvent is removed prior to imaging. The assumption is made that this has little effect on the structures, but it is not clear that this assumption is always (or ever) valid. Here, we use small angle neutron scattering (SANS) to probe low molecular weight hydrogels formed by the self-assembly of dipeptides. We compare scattering data for wet and dried gels, as well as following the drying process. We show that the assumption that drying does not affect the network is not always correct. PMID:28631478

Systematic validation and atomic force microscopy of non-covalent short oligonucleotide barcode microarrays.

PubMed

Cook, Michael A; Chan, Chi-Kin; Jorgensen, Paul; Ketela, Troy; So, Daniel; Tyers, Mike; Ho, Chi-Yip

2008-02-06

Molecular barcode arrays provide a powerful means to analyze cellular phenotypes in parallel through detection of short (20-60 base) unique sequence tags, or "barcodes", associated with each strain or clone in a collection. However, costs of current methods for microarray construction, whether by in situ oligonucleotide synthesis or ex situ coupling of modified oligonucleotides to the slide surface are often prohibitive to large-scale analyses. Here we demonstrate that unmodified 20mer oligonucleotide probes printed on conventional surfaces show comparable hybridization signals to covalently linked 5'-amino-modified probes. As a test case, we undertook systematic cell size analysis of the budding yeast Saccharomyces cerevisiae genome-wide deletion collection by size separation of the deletion pool followed by determination of strain abundance in size fractions by barcode arrays. We demonstrate that the properties of a 13K unique feature spotted 20 mer oligonucleotide barcode microarray compare favorably with an analogous covalently-linked oligonucleotide array. Further, cell size profiles obtained with the size selection/barcode array approach recapitulate previous cell size measurements of individual deletion strains. Finally, through atomic force microscopy (AFM), we characterize the mechanism of hybridization to unmodified barcode probes on the slide surface. These studies push the lower limit of probe size in genome-scale unmodified oligonucleotide microarray construction and demonstrate a versatile, cost-effective and reliable method for molecular barcode analysis.

Protein recognition by a pattern-generating fluorescent molecular probe.

PubMed

Pode, Zohar; Peri-Naor, Ronny; Georgeson, Joseph M; Ilani, Tal; Kiss, Vladimir; Unger, Tamar; Markus, Barak; Barr, Haim M; Motiei, Leila; Margulies, David

2017-12-01

Fluorescent molecular probes have become valuable tools in protein research; however, the current methods for using these probes are less suitable for analysing specific populations of proteins in their native environment. In this study, we address this gap by developing a unimolecular fluorescent probe that combines the properties of small-molecule-based probes and cross-reactive sensor arrays (the so-called chemical 'noses/tongues'). On the one hand, the probe can detect different proteins by generating unique identification (ID) patterns, akin to cross-reactive arrays. On the other hand, its unimolecular scaffold and selective binding enable this ID-generating probe to identify combinations of specific protein families within complex mixtures and to discriminate among isoforms in living cells, where macroscopic arrays cannot access. The ability to recycle the molecular device and use it to track several binding interactions simultaneously further demonstrates how this approach could expand the fluorescent toolbox currently used to detect and image proteins.

Protein recognition by a pattern-generating fluorescent molecular probe

NASA Astrophysics Data System (ADS)

Pode, Zohar; Peri-Naor, Ronny; Georgeson, Joseph M.; Ilani, Tal; Kiss, Vladimir; Unger, Tamar; Markus, Barak; Barr, Haim M.; Motiei, Leila; Margulies, David

2017-12-01

Fluorescent molecular probes have become valuable tools in protein research; however, the current methods for using these probes are less suitable for analysing specific populations of proteins in their native environment. In this study, we address this gap by developing a unimolecular fluorescent probe that combines the properties of small-molecule-based probes and cross-reactive sensor arrays (the so-called chemical 'noses/tongues'). On the one hand, the probe can detect different proteins by generating unique identification (ID) patterns, akin to cross-reactive arrays. On the other hand, its unimolecular scaffold and selective binding enable this ID-generating probe to identify combinations of specific protein families within complex mixtures and to discriminate among isoforms in living cells, where macroscopic arrays cannot access. The ability to recycle the molecular device and use it to track several binding interactions simultaneously further demonstrates how this approach could expand the fluorescent toolbox currently used to detect and image proteins.

How to get more from less. Comments on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar

NASA Astrophysics Data System (ADS)

Sachs, Frederick; Flomenbom, Ophir

2015-06-01

Measuring individual entities at room temperature has become routine due to improvements in technology. We can study ion channels (since the 70s), quantum dots (since the 80s), and receptors, molecular engines and enzymes (since the 90s). The inherent nature of these small systems is that the standard deviation of the measurement is comparable to the mean - the definition of a small system [1]. Individual probes are detected, measured, and the trajectories are then analyzed to extract the mean properties of the system. The review [2] provides links to many examples of single molecule studies, mostly those using optical probes.

Molecular simulation investigation of the nanorheology of an entangled polymer melt

NASA Astrophysics Data System (ADS)

Karim, Mir; Khare, Rajesh; Indei, Tsutomu; Schieber, Jay

2014-03-01

Knowledge of the ``local rheology'' is important for viscoelastic systems that contain significant structural and dynamic heterogeneities, such as cellular and extra-cellular crowded environments. For homogeneous viscoelastic media, a study of probe particle motion provides information on the microstructural evolution of the medium in response to the probe particle motion. Over the last two decades, probe particle rheology has emerged as a leading experimental technique for capturing local rheology of complex fluids. In recent work [M. Karim, S. C. Kohale, T. Indei, J. D. Schieber, and R. Khare, Phys. Rev. E86, 051501 (2012)], we showed that this approach can be used in molecular dynamics (MD) simulations to study the nanoscale viscoelastic properties of an unentangled polymer melt; an important conclusion of that work was that medium and particle inertia play a crucial role in analysis of the particle rheology simulation data. MD simulations have a natural advantage that they enable study of deformation and dynamics over a small length scale around the moving probe particle. In this work, the approach is extended to compare the motion of a nanoscale probe in melts of entangled and unentangled chains. The simulations will be used to elucidate the differences between the local responses of these media to the probe particle motion. In particular, results will be presented for the differences in the resultant velocity and stress fields as well as any possible structural asymmetry developed around the moving probe particle in the entangled and unentangled cases.

Domain of validity of the perturbative approach to femtosecond optical spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gelin, Maxim F.; Rao, B. Jayachander; Nest, Mathias

2013-12-14

We have performed numerical nonperturbative simulations of transient absorption pump-probe responses for a series of molecular model systems. The resulting signals as a function of the laser field strength and the pump-probe delay time are compared with those obtained in the perturbative response function formalism. The simulations and their theoretical analysis indicate that the perturbative description remains valid up to moderately strong laser pulses, corresponding to a rather substantial depopulation (population) of the initial (final) electronic states.

Molecular imaging needles: dual-modality optical coherence tomography and fluorescence imaging of labeled antibodies deep in tissue

PubMed Central

Scolaro, Loretta; Lorenser, Dirk; Madore, Wendy-Julie; Kirk, Rodney W.; Kramer, Anne S.; Yeoh, George C.; Godbout, Nicolas; Sampson, David D.; Boudoux, Caroline; McLaughlin, Robert A.

2015-01-01

Molecular imaging using optical techniques provides insight into disease at the cellular level. In this paper, we report on a novel dual-modality probe capable of performing molecular imaging by combining simultaneous three-dimensional optical coherence tomography (OCT) and two-dimensional fluorescence imaging in a hypodermic needle. The probe, referred to as a molecular imaging (MI) needle, may be inserted tens of millimeters into tissue. The MI needle utilizes double-clad fiber to carry both imaging modalities, and is interfaced to a 1310-nm OCT system and a fluorescence imaging subsystem using an asymmetrical double-clad fiber coupler customized to achieve high fluorescence collection efficiency. We present, to the best of our knowledge, the first dual-modality OCT and fluorescence needle probe with sufficient sensitivity to image fluorescently labeled antibodies. Such probes enable high-resolution molecular imaging deep within tissue. PMID:26137379

Detection of biological threats. A challenge for directed molecular evolution.

PubMed

Petrenko, Valery A; Sorokulova, Iryna B

2004-08-01

The probe technique originated from early attempts of Anton van Leeuwenhoek to contrast microorganisms under the microscope using plant juices, successful staining of tubercle bacilli with synthetic dyes by Paul Ehrlich and discovery of a stain for differentiation of gram-positive and gram-negative bacteria by Hans Christian Gram. The technique relies on the principle that pathogens have unique structural features, which can be recognized by specifically labeled organic molecules. A hundred years of extensive screening efforts led to discovery of a limited assortment of organic probes that are used for identification and differentiation of bacteria. A new challenge--continuous monitoring of biological threats--requires long lasting molecular probes capable of tight specific binding of pathogens in unfavorable conditions. To respond to the challenge, probe technology is being revolutionized by utilizing methods of combinatorial chemistry, phage display and directed molecular evolution. This review describes how molecular evolution methods are applied for development of peptide, antibody and phage probes, and summarizes the author's own data on development of landscape phage probes against Salmonella typhimurium. The performance of the probes in detection of Salmonella is illustrated by a precipitation test, enzyme-linked immunosorbent assay (ELISA), fluorescence-activated cell sorting (FACS) and fluorescent, optical and electron microscopy.

Excitation Spectra and Brightness Optimization of Two-Photon Excited Probes

PubMed Central

Mütze, Jörg; Iyer, Vijay; Macklin, John J.; Colonell, Jennifer; Karsh, Bill; Petrášek, Zdeněk; Schwille, Petra; Looger, Loren L.; Lavis, Luke D.; Harris, Timothy D.

2012-01-01

Two-photon probe excitation data are commonly presented as absorption cross section or molecular brightness (the detected fluorescence rate per molecule). We report two-photon molecular brightness spectra for a diverse set of organic and genetically encoded probes with an automated spectroscopic system based on fluorescence correlation spectroscopy. The two-photon action cross section can be extracted from molecular brightness measurements at low excitation intensities, while peak molecular brightness (the maximum molecular brightness with increasing excitation intensity) is measured at higher intensities at which probe photophysical effects become significant. The spectral shape of these two parameters was similar across all dye families tested. Peak molecular brightness spectra, which can be obtained rapidly and with reduced experimental complexity, can thus serve as a first-order approximation to cross-section spectra in determining optimal wavelengths for two-photon excitation, while providing additional information pertaining to probe photostability. The data shown should assist in probe choice and experimental design for multiphoton microscopy studies. Further, we show that, by the addition of a passive pulse splitter, nonlinear bleaching can be reduced—resulting in an enhancement of the fluorescence signal in fluorescence correlation spectroscopy by a factor of two. This increase in fluorescence signal, together with the observed resemblance of action cross section and peak brightness spectra, suggests higher-order photobleaching pathways for two-photon excitation. PMID:22385865

Investigating dye performance and crosstalk in fluorescence enabled bioimaging using a model system

PubMed Central

Arppe, Riikka; Carro-Temboury, Miguel R.; Hempel, Casper; Vosch, Tom

2017-01-01

Detailed imaging of biological structures, often smaller than the diffraction limit, is possible in fluorescence microscopy due to the molecular size and photophysical properties of fluorescent probes. Advances in hardware and multiple providers of high-end bioimaging makes comparing images between studies and between research groups very difficult. Therefore, we suggest a model system to benchmark instrumentation, methods and staining procedures. The system we introduce is based on doped zeolites in stained polyvinyl alcohol (PVA) films: a highly accessible model system which has the properties needed to act as a benchmark in bioimaging experiments. Rather than comparing molecular probes and imaging methods in complicated biological systems, we demonstrate that the model system can emulate this complexity and can be used to probe the effect of concentration, brightness, and cross-talk of fluorophores on the detected fluorescence signal. The described model system comprises of lanthanide (III) ion doped Linde Type A zeolites dispersed in a PVA film stained with fluorophores. We tested: F18, MitoTracker Red and ATTO647N. This model system allowed comparing performance of the fluorophores in experimental conditions. Importantly, we here report considerable cross-talk of the dyes when exchanging excitation and emission settings. Additionally, bleaching was quantified. The proposed model makes it possible to test and benchmark staining procedures before these dyes are applied to more complex biological systems. PMID:29176775

In vivo detection of free radicals in mouse septic encephalopathy using molecular MRI and immuno-spin trapping.

PubMed

Towner, Rheal A; Garteiser, Philippe; Bozza, Fernando; Smith, Nataliya; Saunders, Debra; d' Avila, Joana C P; Magno, Flora; Oliveira, Marcus F; Ehrenshaft, Marilyn; Lupu, Florea; Silasi-Mansat, Robert; Ramirez, Dario C; Gomez-Mejiba, Sandra E; Mason, Ronald P; Castro Faria-Neto, Hugo C

2013-12-01

Free radicals are known to play a major role in sepsis. Combined immuno-spin trapping and molecular magnetic resonance imaging (MRI) was used to detect in vivo and in situ levels of free radicals in murine septic encephalopathy after cecal ligation and puncture (CLP). DMPO (5,5-dimethyl pyrroline N-oxide) was injected over 6h after CLP, before administration of an anti-DMPO probe (anti-DMPO antibody bound to albumin-gadolinium-diethylene triamine pentaacetic acid-biotin MRI targeting contrast agent). In vitro assessment of the anti-DMPO probe in oxidatively stressed mouse astrocytes significantly decreased T1 relaxation (p < 0.0001) compared to controls. MRI detected the presence of anti-DMPO adducts via a substantial decrease in %T1 change within the hippocampus, striatum, occipital, and medial cortex brain regions (p < 0.01 for all) in septic animals compared to shams, which was sustained for over 60 min (p < 0.05 for all). Fluorescently labeled streptavidin was used to target the anti-DMPO probe biotin, which was elevated in septic brain, liver, and lungs compared to sham. Ex vivo DMPO adducts (qualitative) and oxidative products, including 4-hydroxynonenal and 3-nitrotyrosine (quantitative, p < 0.05 for both), were elevated in septic brains compared to shams. This is the first study that has reported on the detection of in vivo and in situ levels of free radicals in murine septic encephalopathy. Copyright © 2013 Elsevier Inc. All rights reserved.

Solid phase sequencing of biopolymers

DOEpatents

Cantor, Charles; Koster, Hubert

2010-09-28

This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include DNA or RNA in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

Nanoscale methods for single-molecule electrochemistry.

PubMed

Mathwig, Klaus; Aartsma, Thijs J; Canters, Gerard W; Lemay, Serge G

2014-01-01

The development of experiments capable of probing individual molecules has led to major breakthroughs in fields ranging from molecular electronics to biophysics, allowing direct tests of knowledge derived from macroscopic measurements and enabling new assays that probe population heterogeneities and internal molecular dynamics. Although still somewhat in their infancy, such methods are also being developed for probing molecular systems in solution using electrochemical transduction mechanisms. Here we outline the present status of this emerging field, concentrating in particular on optical methods, metal-molecule-metal junctions, and electrochemical nanofluidic devices.

Systematic Validation and Atomic Force Microscopy of Non-Covalent Short Oligonucleotide Barcode Microarrays

PubMed Central

Cook, Michael A.; Chan, Chi-Kin; Jorgensen, Paul; Ketela, Troy; So, Daniel; Tyers, Mike; Ho, Chi-Yip

2008-01-01

Background Molecular barcode arrays provide a powerful means to analyze cellular phenotypes in parallel through detection of short (20–60 base) unique sequence tags, or “barcodes”, associated with each strain or clone in a collection. However, costs of current methods for microarray construction, whether by in situ oligonucleotide synthesis or ex situ coupling of modified oligonucleotides to the slide surface are often prohibitive to large-scale analyses. Methodology/Principal Findings Here we demonstrate that unmodified 20mer oligonucleotide probes printed on conventional surfaces show comparable hybridization signals to covalently linked 5′-amino-modified probes. As a test case, we undertook systematic cell size analysis of the budding yeast Saccharomyces cerevisiae genome-wide deletion collection by size separation of the deletion pool followed by determination of strain abundance in size fractions by barcode arrays. We demonstrate that the properties of a 13K unique feature spotted 20 mer oligonucleotide barcode microarray compare favorably with an analogous covalently-linked oligonucleotide array. Further, cell size profiles obtained with the size selection/barcode array approach recapitulate previous cell size measurements of individual deletion strains. Finally, through atomic force microscopy (AFM), we characterize the mechanism of hybridization to unmodified barcode probes on the slide surface. Conclusions/Significance These studies push the lower limit of probe size in genome-scale unmodified oligonucleotide microarray construction and demonstrate a versatile, cost-effective and reliable method for molecular barcode analysis. PMID:18253494

Molecular imaging probe development: a chemistry perspective

PubMed Central

Nolting, Donald D; Nickels, Michael L; Guo, Ning; Pham, Wellington

2012-01-01

Molecular imaging is an attractive modality that has been widely employed in many aspects of biomedical research; especially those aimed at the early detection of diseases such as cancer, inflammation and neurodegenerative disorders. The field emerged in response to a new research paradigm in healthcare that seeks to integrate detection capabilities for the prediction and prevention of diseases. This approach made a distinct impact in biomedical research as it enabled researchers to leverage the capabilities of molecular imaging probes to visualize a targeted molecular event non-invasively, repeatedly and continuously in a living system. In addition, since such probes are inherently compact, robust, and amenable to high-throughput production, these probes could potentially facilitate screening of preclinical drug discovery, therapeutic assessment and validation of disease biomarkers. They could also be useful in drug discovery and safety evaluations. In this review, major trends in the chemical synthesis and development of positron emission tomography (PET), optical and magnetic resonance imaging (MRI) probes are discussed. PMID:22943038

Dendrimer probes for enhanced photostability and localization in fluorescence imaging.

PubMed

Kim, Younghoon; Kim, Sung Hoon; Tanyeri, Melikhan; Katzenellenbogen, John A; Schroeder, Charles M

2013-04-02

Recent advances in fluorescence microscopy have enabled high-resolution imaging and tracking of single proteins and biomolecules in cells. To achieve high spatial resolutions in the nanometer range, bright and photostable fluorescent probes are critically required. From this view, there is a strong need for development of advanced fluorescent probes with molecular-scale dimensions for fluorescence imaging. Polymer-based dendrimer nanoconjugates hold strong potential to serve as versatile fluorescent probes due to an intrinsic capacity for tailored spectral properties such as brightness and emission wavelength. In this work, we report a new, to our knowledge, class of molecular probes based on dye-conjugated dendrimers for fluorescence imaging and single-molecule fluorescence microscopy. We engineered fluorescent dendritic nanoprobes (FDNs) to contain multiple organic dyes and reactive groups for target-specific biomolecule labeling. The photophysical properties of dye-conjugated FDNs (Cy5-FDNs and Cy3-FDNs) were characterized using single-molecule fluorescence microscopy, which revealed greatly enhanced photostability, increased probe brightness, and improved localization precision in high-resolution fluorescence imaging compared to single organic dyes. As proof-of-principle demonstration, Cy5-FDNs were used to assay single-molecule nucleic acid hybridization and for immunofluorescence imaging of microtubules in cytoskeletal networks. In addition, Cy5-FDNs were used as reporter probes in a single-molecule protein pull-down assay to characterize antibody binding and target protein capture. In all cases, the photophysical properties of FDNs resulted in enhanced fluorescence imaging via improved brightness and/or photostability. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Development and characterization of a handheld hyperspectral Raman imaging probe system for molecular characterization of tissue on mesoscopic scales.

PubMed

St-Arnaud, Karl; Aubertin, Kelly; Strupler, Mathias; Madore, Wendy-Julie; Grosset, Andrée-Anne; Petrecca, Kevin; Trudel, Dominique; Leblond, Frédéric

2018-01-01

Raman spectroscopy is a promising cancer detection technique for surgical guidance applications. It can provide quantitative information relating to global tissue properties associated with structural, metabolic, immunological, and genetic biochemical phenomena in terms of molecular species including amino acids, lipids, proteins, and nucleic acid (DNA). To date in vivo Raman spectroscopy systems mostly included probes and biopsy needles typically limited to single-point tissue interrogation over a scale between 100 and 500 microns. The development of wider field handheld systems could improve tumor localization for a range of open surgery applications including brain, ovarian, and skin cancers. Here we present a novel Raman spectroscopy implementation using a coherent imaging bundle of fibers to create a probe capable of reconstructing molecular images over mesoscopic fields of view. Detection is performed using linear scanning with a rotation mirror and an imaging spectrometer. Different slits widths were tested at the entrance of the spectrometer to optimize spatial and spectral resolution while preserving sufficient signal-to-noise ratios to detect the principal Raman tissue features. The nonbiological samples, calcite and polytetrafluoroethylene (PTFE), were used to characterize the performance of the system. The new wide-field probe was tested on ex vivo samples of calf brain and swine tissue. Raman spectral content of both tissue types were validated with data from the literature and compared with data acquired with a single-point Raman spectroscopy probe. The single-point probe was used as the gold standard against which the new instrument was benchmarked as it has already been thoroughly validated for biological tissue characterization. We have developed and characterized a practical noncontact handheld Raman imager providing tissue information at a spatial resolution of 115 microns over a field of view >14 mm 2 and a spectral resolution of 6 cm -1 over the whole fingerprint region. Typical integration time to acquire an entire Raman image over swine tissue was set to approximately 100 s. Spectra acquired with both probes (single-point and wide-field) showed good agreement, with a Pearson correlation factor >0.85 over different tissue categories. Protein and lipid content of imaged tissue were manifested into the measured spectra which correlated well with previous findings in the literature. An example of quantitative molecular map is presented for swine tissue and calf brain based on the ratio of protein-to-lipid content showing clear delineations between white and gray matter as well as between adipose and muscle tissue. We presented the development of a Raman imaging probe with a field of view of a few millimeters and a spatial resolution consistent with standard surgical imaging methods using an imaging bundle. Spectra acquired with the newly developed system on swine tissue and calf brain correlated well with an establish single-point probe and observed spectral features agreed with previous finding in the literature. The imaging probe has demonstrated its ability to reconstruct molecular images of soft tissues. The approach presented here has a lot of potential for the development of surgical Raman imaging probe to guide the surgeon during cancer surgery. © 2017 American Association of Physicists in Medicine.

Pre-Assembly of Near-Infrared Fluorescent Multivalent Molecular Probes for Biological Imaging.

PubMed

Peck, Evan M; Battles, Paul M; Rice, Douglas R; Roland, Felicia M; Norquest, Kathryn A; Smith, Bradley D

2016-05-18

A programmable pre-assembly method is described and shown to produce near-infrared fluorescent molecular probes with tunable multivalent binding properties. The modular assembly process threads one or two copies of a tetralactam macrocycle onto a fluorescent PEGylated squaraine scaffold containing a complementary number of docking stations. Appended to the macrocycle periphery are multiple copies of a ligand that is known to target a biomarker. The structure and high purity of each threaded complex was determined by independent spectrometric methods and also by gel electrophoresis. Especially helpful were diagnostic red-shift and energy transfer features in the absorption and fluorescence spectra. The threaded complexes were found to be effective multivalent molecular probes for fluorescence microscopy and in vivo fluorescence imaging of living subjects. Two multivalent probes were prepared and tested for targeting of bone in mice. A pre-assembled probe with 12 bone-targeting iminodiacetate ligands produced more bone accumulation than an analogous pre-assembled probe with six iminodiacetate ligands. Notably, there was no loss in probe fluorescence at the bone target site after 24 h in the living animal, indicating that the pre-assembled fluorescent probe maintained very high mechanical and chemical stability on the skeletal surface. The study shows how this versatile pre-assembly method can be used in a parallel combinatorial manner to produce libraries of near-infrared fluorescent multivalent molecular probes for different types of imaging and diagnostic applications, with incremental structural changes in the number of targeting groups, linker lengths, linker flexibility, and degree of PEGylation.

Comparing in vivo pump–probe and multiphoton fluorescence microscopy of melanoma and pigmented lesions

PubMed Central

Wilson, Jesse W.; Degan, Simone; Gainey, Christina S.; Mitropoulos, Tanya; Simpson, Mary Jane; Zhang, Jennifer Y.; Warren, Warren S.

2014-01-01

Abstract. We demonstrate a multimodal approach that combines a pump–probe with confocal reflectance and multiphoton autofluorescence microscopy. Pump–probe microscopy has been proven to be of great value in analyzing thin tissue sections of pigmented lesions, as it produces molecular contrast which is inaccessible by other means. However, the higher optical intensity required to overcome scattering in thick tissue leads to higher-order nonlinearities in the optical response of melanin (e.g., two-photon pump and one-photon probe) that present additional challenges for interpreting the data. We show that analysis of pigment composition in vivo must carefully account for signal terms that are nonlinear with respect to the pump and probe intensities. We find that pump–probe imaging gives useful contrast for pigmented structures over a large range of spatial scales (100  μm to 1 cm), making it a potentially useful tool for tracking the progression of pigmented lesions without the need to introduce exogenous contrast agents. PMID:25415567

Restriction fragment length polymorphisms for growth hormone, prolactin, osteonectin, alpha crystallin, gamma crystallin, fibronectin and 21-steroid hydroxylase in cattle.

PubMed

Theilmann, J L; Skow, L C; Baker, J F; Womack, J E

1989-01-01

Genomic DNAs from animals representing six breeds of cattle (Angus, Brahman, Hereford, Holstein, Jersey and Texas Longhorn) were screened with cloned gene probes in a search for restriction fragment length polymorphisms (RFLPs). Eleven RFLPs were identified using seven different probes: growth hormone, prolactin, osteonectin, alpha A-crystallin, gamma crystallin, fibronectin and 21-steroid hydroxylase. The frequencies of the alleles identified by each probe were calculated and compared in a limited sampling of the six bovine breeds. These polymorphisms greatly enhance the pool of immunogenetic, biochemical and molecular markers available in cattle for linkage analysis, testing of parentage, and distinction of breeds.

Comparison of nine different real-time PCR chemistries for qualitative and quantitative applications in GMO detection.

PubMed

Buh Gasparic, Meti; Tengs, Torstein; La Paz, Jose Luis; Holst-Jensen, Arne; Pla, Maria; Esteve, Teresa; Zel, Jana; Gruden, Kristina

2010-03-01

Several techniques have been developed for detection and quantification of genetically modified organisms, but quantitative real-time PCR is by far the most popular approach. Among the most commonly used real-time PCR chemistries are TaqMan probes and SYBR green, but many other detection chemistries have also been developed. Because their performance has never been compared systematically, here we present an extensive evaluation of some promising chemistries: sequence-unspecific DNA labeling dyes (SYBR green), primer-based technologies (AmpliFluor, Plexor, Lux primers), and techniques involving double-labeled probes, comprising hybridization (molecular beacon) and hydrolysis (TaqMan, CPT, LNA, and MGB) probes, based on recently published experimental data. For each of the detection chemistries assays were included targeting selected loci. Real-time PCR chemistries were subsequently compared for their efficiency in PCR amplification and limits of detection and quantification. The overall applicability of the chemistries was evaluated, adding practicability and cost issues to the performance characteristics. None of the chemistries seemed to be significantly better than any other, but certain features favor LNA and MGB technology as good alternatives to TaqMan in quantification assays. SYBR green and molecular beacon assays can perform equally well but may need more optimization prior to use.

Combined molecular MRI and immuno-spin-trapping for in vivo detection of free radicals in orthotopic mouse GL261 gliomas.

PubMed

Towner, Rheal A; Smith, Nataliya; Saunders, Debra; De Souza, Patricia Coutinho; Henry, Leah; Lupu, Florea; Silasi-Mansat, Robert; Ehrenshaft, Marilyn; Mason, Ronald P; Gomez-Mejiba, Sandra E; Ramirez, Dario C

2013-12-01

Free radicals play a major role in gliomas. By combining immuno-spin-trapping (IST) and molecular magnetic resonance imaging (mMRI), in vivo levels of free radicals were detected within mice bearing orthotopic GL261 gliomas. The nitrone spin trap DMPO (5,5-dimethyl pyrroline N-oxide) was administered prior to injection of an anti-DMPO probe (anti-DMPO antibody covalently bound to a bovine serum albumin (BSA)-Gd (gadolinium)-DTPA (diethylene triamine penta acetic acid)-biotin MRI contrast agent) to trap tumor-associated free radicals. mMRI detected the presence of anti-DMPO adducts by either a significant sustained increase (p<0.001) in MR signal intensity or a significant decrease (p<0.001) in T1 relaxation, measured as %T1 change. In vitro assessment of the anti-DMPO probe indicated a significant decrease (p<0.0001) in T1 relaxation in GL261 cells that were oxidatively stressed with hydrogen peroxide, compared to controls. The biotin moiety of the anti-DMPO probe was targeted with fluorescently-labeled streptavidin to locate the anti-DMPO probe in excised brain tissues. As a negative control a non-specific IgG antibody covalently bound to the albumin-Gd-DTPA-biotin construct was used. DMPO adducts were also confirmed in tumor tissue from animals administered DMPO, compared to non-tumor brain tissue. GL261 gliomas were found to have significantly increased malondialdehyde (MDA) protein adducts (p<0.001) and 3-nitrotyrosine (3-NT) (p<0.05) compared to normal mouse brain tissue, indicating increased oxidized lipids and proteins, respectively. Co-localization of the anti-DMPO probe with either 3-NT or 4-hydroxynonenal was also observed. This is the first report regarding the detection of in vivo levels of free radicals from a glioma model. © 2013.

BODIPY-Based Fluorescent Probes for Sensing Protein Surface-Hydrophobicity.

PubMed

Dorh, Nethaniah; Zhu, Shilei; Dhungana, Kamal B; Pati, Ranjit; Luo, Fen-Tair; Liu, Haiying; Tiwari, Ashutosh

2015-12-18

Mapping surface hydrophobic interactions in proteins is key to understanding molecular recognition, biological functions, and is central to many protein misfolding diseases. Herein, we report synthesis and application of new BODIPY-based hydrophobic sensors (HPsensors) that are stable and highly fluorescent for pH values ranging from 7.0 to 9.0. Surface hydrophobic measurements of proteins (BSA, apomyoglobin, and myoglobin) by these HPsensors display much stronger signal compared to 8-anilino-1-naphthalene sulfonic acid (ANS), a commonly used hydrophobic probe; HPsensors show a 10- to 60-fold increase in signal strength for the BSA protein with affinity in the nanomolar range. This suggests that these HPsensors can be used as a sensitive indicator of protein surface hydrophobicity. A first principle approach is used to identify the molecular level mechanism for the substantial increase in the fluorescence signal strength. Our results show that conformational change and increased molecular rigidity of the dye due to its hydrophobic interaction with protein lead to fluorescence enhancement.

Thermopower of molecular junctions: Tunneling to hopping crossover in DNA

NASA Astrophysics Data System (ADS)

Korol, Roman; Kilgour, Michael; Segal, Dvira

2016-12-01

We study the electrical conductance G and the thermopower S of single-molecule junctions and reveal signatures of different transport mechanisms: off-resonant tunneling, on-resonant coherent (ballistic) motion, and multi-step hopping. These mechanisms are identified by studying the behavior of G and S while varying molecular length and temperature. Based on a simple one-dimensional model for molecular junctions, we derive approximate expressions for the thermopower in these different regimes. Analytical results are compared to numerical simulations, performed using a variant of Büttiker's probe technique, the so-called voltage-temperature probe, which allows us to phenomenologically introduce environmentally induced elastic and inelastic electron scattering effects, while applying both voltage and temperature biases across the junction. We further simulate the thermopower of GC-rich DNA sequences with mediating A:T blocks and manifest the tunneling-to-hopping crossover in both the electrical conductance and the thermopower, in accord with measurements by Li et al. [Nat. Commun. 7, 11294 (2016)].

Ultrafast time-resolved pump-probe spectroscopy of PYP by a sub-8 fs pulse laser at 400 nm.

PubMed

Liu, Jun; Yabushita, Atsushi; Taniguchi, Seiji; Chosrowjan, Haik; Imamoto, Yasushi; Sueda, Keiichi; Miyanaga, Noriaki; Kobayashi, Takayoshi

2013-05-02

Impulsive excitation of molecular vibration is known to induce wave packets in both the ground state and excited state. Here, the ultrafast dynamics of PYP was studied by pump-probe spectroscopy using a sub-8 fs pulse laser at 400 nm. The broadband spectrum of the UV pulse allowed us to detect the pump-probe signal covering 360-440 nm. The dependence of the vibrational phase of the vibrational mode around 1155 cm(-1) on the probe photon energy was observed for the first time to our knowledge. The vibrational mode coupled to the electronic transition observed in the probe spectral ranges of 2.95-3.05 and 3.15-3.35 eV was attributed to the wave packets in the ground state and the excited state, respectively. The frequencies in the ground state and excited state were determined to be 1155 ± 1 and 1149 ± 1 cm(-1), respectively. The frequency difference is due to change after photoexcitation. This means a reduction of the bond strength associated with π-π* excitation, which is related to the molecular structure change associated with the primary isomerization process in the photocycle in PYP. Real-time vibrational modes at low frequency around 138, 179, 203, 260, and 317 cm(-1) were also observed and compared with the Raman spectrum for the assignment of the vibrational wave packet.

Complexation of β-cyclodextrin with dual molecular probes bearing fluorescent and paramagnetic moieties linked by short polyether chains.

PubMed

Mocanu, S; Matei, I; Ionescu, S; Tecuceanu, V; Marinescu, G; Ionita, P; Culita, D; Leonties, A; Ionita, Gabriela

2017-10-18

Electron paramagnetic resonance (EPR) and fluorescence spectroscopies provide molecular-level insights on the interaction of paramagnetic and fluorescent species with the microenvironment. A series of dual molecular probes bearing fluorescent and paramagnetic moieties linked by flexible short polyether chains have been synthesized. These new molecular probes open the possibility to investigate various multi-component systems such as host-guest systems, polymeric micelles, gels and protein solutions by using EPR and fluorescence spectroscopies concertedly. The EPR and fluorescence spectra of these compounds show that the dependence of the rotational correlation time and fluorescence quantum yield on the chain length of the linker is not linear, due to the flexibility of the polyether linker. The quenching effect of the nitroxide moiety on the fluorescence intensity of the pyrene group varies with the linker length and flexibility. The interaction of these dual molecular probes with β-cyclodextrin, in solution and in polymeric gels, was evaluated and demonstrated by analysis of EPR and fluorescence spectra.

Nanoparticles for Biomedical Imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nune, Satish K.; Gunda, Padmaja; Thallapally, Praveen K.

2009-11-01

Background: Synthetic nanoparticles are emerging as versatile tools in biomedical applications, particularly in the area of biomedical imaging. Nanoparticles 1 to 100 nm in diameter possess dimensions comparable to biological functional units. Diverse surface chemistries, unique magnetic properties, tunable absorption and emission properties, and recent advances in the synthesis and engineering of various nanoparticles suggest their potential as probes for early detection of diseases such as cancer. Surface functionalization has further expanded the potential of nanoparticles as probes for molecular imaging. Objective: To summarize emerging research of nanoparticles for biomedical imaging with increased selectivity and reduced non-specific uptake with increasedmore » spatial resolution containing stabilizers conjugated with targeting ligands. Methods: This review summarizes recent technological advances in the synthesis of various nanoparticle probes, and surveys methods to improve the targeting of nanoparticles for their applications in biomedical imaging. Conclusion: Structural design of nanomaterials for biomedical imaging continues to expand and diversify. Synthetic methods have aimed to control the size and surface characteristics of nanoparticles to control distribution, half-life and elimination. Although molecular imaging applications using nanoparticles are advancing into clinical applications, challenges such as storage stability and long-term toxicology should continue to be addressed. Keywords: nanoparticle synthesis, surface modification, targeting, molecular imaging, and biomedical imaging.« less

Photoabsorption of acridine yellow and proflavin bound to human serum albumin studied by means of quantum mechanics/molecular dynamics.

PubMed

Aidas, Kęstutis; Olsen, Jógvan Magnus H; Kongsted, Jacob; Ågren, Hans

2013-02-21

Attempting to unravel mechanisms in optical probing of proteins, we have performed pilot calculations of two cationic chromophores-acridine yellow and proflavin-located at different binding sites within human serum albumin, including the two primary drug binding sites as well as a heme binding site. The computational scheme adopted involves classical molecular dynamics simulations of the ligands bound to the protein and subsequent linear response polarizable embedding density functional theory calculations of the excitation energies. A polarizable embedding potential consisting of point charges fitted to reproduce the electrostatic potential and isotropic atomic polarizabilities computed individually for every residue of the protein was used in the linear response calculations. Comparing the calculated aqueous solution-to-protein shifts of maximum absorption energies to available experimental data, we concluded that the cationic proflavin chromophore is likely not to bind albumin at its drug binding site 1 nor at its heme binding site. Although agreement with experimental data could only be obtained in qualitative terms, our results clearly indicate that the difference in optical response of the two probes is due to deprotonation, and not, as earlier suggested, to different binding sites. The ramifications of this finding for design of molecular probes targeting albumin or other proteins is briefly discussed.

Synthesis and Biological Evaluation of Water-soluble Progesterone-Conjugated Probes for Magnetic Resonance Imaging of Hormone Related Cancers

PubMed Central

Sukerkar, Preeti A.; MacRenaris, Keith W.; Townsend, Taryn R.; Ahmed, Roshan A.; Burdette, Joanna E.; Meade, Thomas J.

2011-01-01

Progesterone receptor (PR) is strongly associated with disease prognosis and therapeutic efficacy in hormone related diseases such as endometriosis and breast, ovarian, and uterine cancers. Receptor status is currently determined by immunohistochemistry assays. However, noninvasive PR imaging agents could improve disease detection and help elucidate pathological molecular pathways, leading to new therapies and animal disease models. A series of water-soluble PR-targeted magnetic resonance imaging (MRI) probes were synthesized using Cu(I)-catalyzed click chemistry and evaluated in vitro and in vivo. These agents demonstrated activation of PR in vitro and preferential accumulation in PR(+) compared to PR(−) human breast cancer cells with low toxicity. In xenograft tumor models, the agents demonstrated enhanced signal intensity in PR(+) tumors compared to PR(−) tumors. The results suggest that these agents may be promising MRI probes for PR(+) diseases. PMID:21972997

In vivo targeted peripheral nerve imaging with a nerve-specific nanoscale magnetic resonance probe.

PubMed

Zheng, Linfeng; Li, Kangan; Han, Yuedong; Wei, Wei; Zheng, Sujuan; Zhang, Guixiang

2014-11-01

Neuroimaging plays a pivotal role in clinical practice. Currently, computed tomography (CT), magnetic resonance imaging (MRI), ultrasonography, and positron emission tomography (PET) are applied in the clinical setting as neuroimaging modalities. There is no optimal imaging modality for clinical peripheral nerve imaging even though fluorescence/bioluminescence imaging has been used for preclinical studies on the nervous system. Some studies have shown that molecular and cellular MRI (MCMRI) can be used to visualize and image the cellular and molecular level of the nervous system. Other studies revealed that there are different pathological/molecular changes in the proximal and distal sites after peripheral nerve injury (PNI). Therefore, we hypothesized that in vivo peripheral nerve targets can be imaged using MCMRI with specific MRI probes. Specific probes should have higher penetrability for the blood-nerve barrier (BNB) in vivo. Here, a functional nanometre MRI probe that is based on nerve-specific proteins as targets, specifically, using a molecular antibody (mAb) fragment conjugated to iron nanoparticles as an MRI probe, was constructed for further study. The MRI probe allows for imaging the peripheral nerve targets in vivo. Copyright © 2014 Elsevier Ltd. All rights reserved.

Fluorescence-correlation spectroscopy study of molecular transport within reversed-phase chromatographic particles compared to planar model surfaces.

PubMed

Cooper, Justin; Harris, Joel M

2014-12-02

Reversed-phase liquid chromatography (RPLC) is a widely used technique for molecular separations. Stationary-phase materials for RPLC generally consist of porous silica-gel particles functionalized with n-alkane ligands. Understanding motions of molecules within the interior of these particles is important for developing efficient chromatographic materials and separations. To characterize these dynamics, time-resolved spectroscopic methods (photobleach recovery, fluorescence correlation, single-molecule imaging) have been adapted to measure molecular diffusion rates, typically at n-alkane-modified planar silica surfaces, which serve as models of chromatographic interfaces. A question arising from these studies is how dynamics of molecules on a planar surface relate to motions of molecules within the interior of a porous chromatographic particle. In this paper, imaging-fluorescence-correlation spectroscopy is used to measure diffusion rates of a fluorescent probe molecule 1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbocyanine perchlorate (DiI) within authentic RPLC porous silica particles and compared with its diffusion at a planar C18-modified surface. The results show that surface diffusion on the planar C18 substrate is much faster than the diffusion rate of the probe molecule through a chromatographic particle. Surface diffusion within porous particles, however, is governed by molecular trajectories along the tortuous contours of the interior surface of the particles. By accounting for the greater surface area that a molecule must explore to diffuse macroscopic distances through the particle, the molecular-scale diffusion rates on the two surfaces can be compared, and they are virtually identical. These results provide support for the relevance of surface-diffusion measurements made on planar model surfaces to the dynamic behavior of molecules on the internal surfaces of porous chromatographic particles.

Mapping Hydrophobicity on the Protein Molecular Surface at Atom-Level Resolution

PubMed Central

Nicolau Jr., Dan V.; Paszek, Ewa; Fulga, Florin; Nicolau, Dan V.

2014-01-01

A precise representation of the spatial distribution of hydrophobicity, hydrophilicity and charges on the molecular surface of proteins is critical for the understanding of the interaction with small molecules and larger systems. The representation of hydrophobicity is rarely done at atom-level, as this property is generally assigned to residues. A new methodology for the derivation of atomic hydrophobicity from any amino acid-based hydrophobicity scale was used to derive 8 sets of atomic hydrophobicities, one of which was used to generate the molecular surfaces for 35 proteins with convex structures, 5 of which, i.e., lysozyme, ribonuclease, hemoglobin, albumin and IgG, have been analyzed in more detail. Sets of the molecular surfaces of the model proteins have been constructed using spherical probes with increasingly large radii, from 1.4 to 20 Å, followed by the quantification of (i) the surface hydrophobicity; (ii) their respective molecular surface areas, i.e., total, hydrophilic and hydrophobic area; and (iii) their relative densities, i.e., divided by the total molecular area; or specific densities, i.e., divided by property-specific area. Compared with the amino acid-based formalism, the atom-level description reveals molecular surfaces which (i) present an approximately two times more hydrophilic areas; with (ii) less extended, but between 2 to 5 times more intense hydrophilic patches; and (iii) 3 to 20 times more extended hydrophobic areas. The hydrophobic areas are also approximately 2 times more hydrophobicity-intense. This, more pronounced “leopard skin”-like, design of the protein molecular surface has been confirmed by comparing the results for a restricted set of homologous proteins, i.e., hemoglobins diverging by only one residue (Trp37). These results suggest that the representation of hydrophobicity on the protein molecular surfaces at atom-level resolution, coupled with the probing of the molecular surface at different geometric resolutions, can capture processes that are otherwise obscured to the amino acid-based formalism. PMID:25462574

Profiling of the yak skeletal muscle tissue gene expression and comparison with the domestic cattle by genome array.

PubMed

Wang, H B; Zan, L S; Zhang, Y Y

2014-01-01

Of all the mammals of the world, the yak lives at the highest altitude area of more than 3000 m. Comparison between yak and cattle of the low-altitude areas will be informative in studying animal adaptation to higher altitudes. To investigate the molecular mechanism involved in meat quality differences between the two Chinese special varieties Qinghai yak and Qinchuan cattle, 12 chemical-physical characteristics of the longissimus dorsi muscle related to meat quality were compared at the age of 36 months, and the gene expression profiles were constructed by utilizing the bovine genome array. Significant analysis of microarrays was used to identify the differentially expressed genes. Gene ontology and pathway analysis were performed by a free Web-based Molecular Annotation System 2.0. The results reveal ~11 000 probes representing about 10 000 genes that were detected in both the Qinghai yak and Qinchuan cattle. A total of 1922 genes were shown to be differentially expressed, 633 probes were upregulated and 1259 probes were downregulated in the muscle tissue of Qinghai yak that were mainly involved in ubiquitin-mediated proteolysis, muscle growth regulation, glucose metabolism, immune response and so on. Quantitative real-time PCR (qRT-PCR) was performed to validate some differentially expressed genes identified by microarray. Further analysis implied that animals living at a high altitude may supply energy by more active protein catabolism and glycolysis compared with those living in the plain areas. Our results establish the groundwork for further studies on yaks' meat quality and will be beneficial in improving the yaks' breeding by molecular biotechnology.

WE-EF-210-07: Development of a Minimally Invasive Photo Acoustic Imaging System for Early Prostate Cancer Detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sano, M; Yousefi, S; Xing, L

Purpose: The objective of this work is to design, implement and characterize a catheter-based ultrasound/photoacoustic imaging probe for early-diagnosis of prostate cancer and to aid in image-guided radiation therapy. Methods: The need to image across 6–10cm of tissue to image the whole prostate gland limits the resolution achievable with a transrectal ultrasound approach. In contrast, the urethra bisects the prostate gland, providing a minimally invasive pathway for deploying a high resolution ultrasound transducer. Utilizing a high-frequency (20MHz) ultrasound/photoacoustic probe, high-resolution structural and molecular imaging of the prostate tissue is possible. A custom 3D printed probe containing a high-frequency single-element ultrasoundmore » transducer is utilized. The diameter of the probe is designed to fit inside a Foley catheter and the probe is rotated around the central axis to achieve a circular B-scan. A custom ultrasound amplifier and receiver was set up to trigger the ultrasound pulse transmission and record the reflected signal. The reconstructed images were compared to images generated by traditional 5 MHz ultrasound transducers. Results: The preliminary results using the high-frequency ultrasound probe show that it is possible to resolve finely detailed information in a prostate tissue phantom that was not achievable with previous low-frequency ultrasound systems. Preliminary ultrasound imaging was performed on tissue mimicking phantom and sensitivity and signal-to-noise ratio of the catheter was measured. Conclusion: In order to achieve non-invasive, high-resolution, structural and molecular imaging for early-diagnosis and image-guided radiation therapy of the prostate tissue, a transurethral catheter was designed. Structural/molecular imaging using ultrasound/photoacoustic of the prostate tissue will allow for localization of hyper vascularized areas for early-stage prostate cancer diagnosis.« less

Novel DNA probes with low background and high hybridization-triggered fluorescence.

PubMed

Lukhtanov, Eugeny A; Lokhov, Sergey G; Gorn, Vladimir V; Podyminogin, Mikhail A; Mahoney, Walt

2007-01-01

Novel fluorogenic DNA probes are described. The probes (called Pleiades) have a minor groove binder (MGB) and a fluorophore at the 5'-end and a non-fluorescent quencher at the 3'-end of the DNA sequence. This configuration provides surprisingly low background and high hybridization-triggered fluorescence. Here, we comparatively study the performance of such probes, MGB-Eclipse probes, and molecular beacons. Unlike the other two probe formats, the Pleiades probes have low, temperature-independent background fluorescence and excellent signal-to-background ratios. The probes possess good mismatch discrimination ability and high rates of hybridization. Based on the analysis of fluorescence and absorption spectra we propose a mechanism of action for the Pleiades probes. First, hydrophobic interactions between the quencher and the MGB bring the ends of the probe and, therefore, the fluorophore and the quencher in close proximity. Second, the MGB interacts with the fluorophore and independent of the quencher is able to provide a modest (2-4-fold) quenching effect. Joint action of the MGB and the quencher is the basis for the unique quenching mechanism. The fluorescence is efficiently restored upon binding of the probe to target sequence due to a disruption in the MGB-quencher interaction and concealment of the MGB moiety inside the minor groove.

Novel DNA probes with low background and high hybridization-triggered fluorescence

PubMed Central

Lukhtanov, Eugeny A.; Lokhov, Sergey G.; Gorn, Vladimir V.; Podyminogin, Mikhail A.; Mahoney, Walt

2007-01-01

Novel fluorogenic DNA probes are described. The probes (called Pleiades) have a minor groove binder (MGB) and a fluorophore at the 5′-end and a non-fluorescent quencher at the 3′-end of the DNA sequence. This configuration provides surprisingly low background and high hybridization-triggered fluorescence. Here, we comparatively study the performance of such probes, MGB-Eclipse probes, and molecular beacons. Unlike the other two probe formats, the Pleiades probes have low, temperature-independent background fluorescence and excellent signal-to-background ratios. The probes possess good mismatch discrimination ability and high rates of hybridization. Based on the analysis of fluorescence and absorption spectra we propose a mechanism of action for the Pleiades probes. First, hydrophobic interactions between the quencher and the MGB bring the ends of the probe and, therefore, the fluorophore and the quencher in close proximity. Second, the MGB interacts with the fluorophore and independent of the quencher is able to provide a modest (2–4-fold) quenching effect. Joint action of the MGB and the quencher is the basis for the unique quenching mechanism. The fluorescence is efficiently restored upon binding of the probe to target sequence due to a disruption in the MGB–quencher interaction and concealment of the MGB moiety inside the minor groove. PMID:17259212

An Elegant Biosensor Molecular Beacon Probe: Challenges and Recent Solutions

PubMed Central

Kolpashchikov, Dmitry M.

2012-01-01

Molecular beacon (MB) probes are fluorophore- and quencher-labeled short synthetic DNAs folded in a stem-loop shape. Since the first report by Tyagi and Kramer, it has become a widely accepted tool for nucleic acid analysis and triggered a cascade of related developments in the field of molecular sensing. The unprecedented success of MB probes stems from their ability to detect specific DNA or RNA sequences immediately after hybridization with no need to wash out the unbound probe (instantaneous format). Importantly, the hairpin structure of the probe is responsible for both the low fluorescent background and improved selectivity. Furthermore, the signal is generated in a reversible manner; thus, if the analyte is removed, the signal is reduced to the background. This paper highlights the advantages of MB probes and discusses the approaches that address the challenges in MB probe design. Variations of MB-based assays tackle the problem of stem invasion, improve SNP genotyping and signal-to-noise ratio, as well as address the challenges of detecting folded RNA and DNA. PMID:24278758

Recent Advances of Activatable Molecular Probes Based on Semiconducting Polymer Nanoparticles in Sensing and Imaging

PubMed Central

Lyu, Yan

2017-01-01

Molecular probes that change their signals in response to the target of interest have a critical role in fundamental biology and medicine. Semiconducting polymer nanoparticles (SPNs) have recently emerged as a new generation of purely organic photonic nanoagents with desirable properties for biological applications. In particular, tunable optical properties of SPNs allow them to be developed into photoluminescence, chemiluminescence, and photoacoustic probes, wherein SPNs usually serve as the energy donor and internal reference for luminescence and photoacoustic probes, respectively. Moreover, facile surface modification and intraparticle engineering provide the versatility to make them responsive to various biologically and pathologically important substances and indexes including small‐molecule mediators, proteins, pH and temperature. This article focuses on recent advances in the development of SPN‐based activatable molecular probes for sensing and imaging. The designs and applications of these probes are discussed in details, and the present challenges to further advance them into life science are also analyzed. PMID:28638783

Solid phase sequencing of double-stranded nucleic acids

DOEpatents

Fu, Dong-Jing; Cantor, Charles R.; Koster, Hubert; Smith, Cassandra L.

2002-01-01

This invention relates to methods for detecting and sequencing of target double-stranded nucleic acid sequences, to nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probe comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include nucleic acids in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated determination of molecular weights and identification of the target sequence.

Spatially Resolved Analysis of Amines Using a Fluorescence Molecular Probe: Molecular Analysis of IDPs

NASA Technical Reports Server (NTRS)

Clemett, S. J.; Messenger, S.; Thomas-Keprta, K. L.; Wentworth, S. J.; Robinson, G. A.; McKay, D. S.

2002-01-01

Some Interplanetary Dust Particles (IDPs) have large isotope anomalies in H and N. To address the nature of the carrier phase, we are developing a procedure to spatially resolve the distribution of organic species on IDP thin sections utilizing fluorescent molecular probes. Additional information is contained in the original extended abstract.

Probing the brain with molecular fMRI.

PubMed

Ghosh, Souparno; Harvey, Peter; Simon, Jacob C; Jasanoff, Alan

2018-06-01

One of the greatest challenges of modern neuroscience is to incorporate our growing knowledge of molecular and cellular-scale physiology into integrated, organismic-scale models of brain function in behavior and cognition. Molecular-level functional magnetic resonance imaging (molecular fMRI) is a new technology that can help bridge these scales by mapping defined microscopic phenomena over large, optically inaccessible regions of the living brain. In this review, we explain how MRI-detectable imaging probes can be used to sensitize noninvasive imaging to mechanistically significant components of neural processing. We discuss how a combination of innovative probe design, advanced imaging methods, and strategies for brain delivery can make molecular fMRI an increasingly successful approach for spatiotemporally resolved studies of diverse neural phenomena, perhaps eventually in people. Copyright © 2018 Elsevier Ltd. All rights reserved.

Simulating Energy Relaxation in Pump-Probe Vibrational Spectroscopy of Hydrogen-Bonded Liquids.

PubMed

Dettori, Riccardo; Ceriotti, Michele; Hunger, Johannes; Melis, Claudio; Colombo, Luciano; Donadio, Davide

2017-03-14

We introduce a nonequilibrium molecular dynamics simulation approach, based on the generalized Langevin equation, to study vibrational energy relaxation in pump-probe spectroscopy. A colored noise thermostat is used to selectively excite a set of vibrational modes, leaving the other modes nearly unperturbed, to mimic the effect of a monochromatic laser pump. Energy relaxation is probed by analyzing the evolution of the system after excitation in the microcanonical ensemble, thus providing direct information about the energy redistribution paths at the molecular level and their time scale. The method is applied to hydrogen-bonded molecular liquids, specifically deuterated methanol and water, providing a robust picture of energy relaxation at the molecular scale.

Modeling of coherent ultrafast magneto-optical experiments: Light-induced molecular mean-field model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hinschberger, Y.; Hervieux, P.-A.

2015-12-28

We present calculations which aim to describe coherent ultrafast magneto-optical effects observed in time-resolved pump-probe experiments. Our approach is based on a nonlinear semi-classical Drude-Voigt model and is used to interpret experiments performed on nickel ferromagnetic thin film. Within this framework, a phenomenological light-induced coherent molecular mean-field depending on the polarizations of the pump and probe pulses is proposed whose microscopic origin is related to a spin-orbit coupling involving the electron spins of the material sample and the electric field of the laser pulses. Theoretical predictions are compared to available experimental data. The model successfully reproduces the observed experimental trendsmore » and gives meaningful insight into the understanding of magneto-optical rotation behavior in the ultrafast regime. Theoretical predictions for further experimental studies are also proposed.« less

On the quantification of the dissolved hydroxyl radicals in the plasma-liquid system using the molecular probe method

NASA Astrophysics Data System (ADS)

Ma, Yupengxue; Gong, Xinning; He, Bangbang; Li, Xiaofei; Cao, Dianyu; Li, Junshuai; Xiong, Qing; Chen, Qiang; Chen, Bing Hui; Huo Liu, Qing

2018-04-01

Hydroxyl (OH) radical is one of the most important reactive species produced by plasma-liquid interactions, and the OH in liquid phase (dissolved OH radical, OHdis) takes effect in many plasma-based applications due to its high reactivity. Therefore, the quantification of the OHdis in a plasma-liquid system is of great importance, and a molecular probe method usually used for the OHdis detection might be applied. Herein, we investigate the validity of using the molecular probe method to estimate the [OHdis] in the plasma-liquid system. Dimethyl sulfoxide is used as the molecular probe to estimate the [OHdis] in an air plasma-liquid system, and usually the estimation of [OHdis] is deduced by quantifying the OHdis-induced derivative, the formaldehyde (HCHO). The analysis indicates that the true concentration of the OHdis should be estimated from the sum of three terms: the formed HCHO, the existing OH scavengers, and the H2O2 formed from the OHdis. The results show that the measured [HCHO] needs to be corrected since the HCHO consumption is not negligible in the plasma-liquid system. We conclude from the results and the analysis that the molecular probe method generally underestimates the [OHdis] in the plasma-liquid system. If one wants to obtain the true concentration of the OHdis in the plasma-liquid system, one needs to know the consumption behavior of the OHdis-induced derivatives, the information of the OH scavengers (such as hydrated electron, atomic hydrogen besides the molecular probe), and also the knowledge of the H2O2 formed from the OHdis.

Optimal control theory with continuously distributed target states: An application to NaK

NASA Astrophysics Data System (ADS)

Kaiser, Andreas; May, Volkhard

2006-01-01

Laser pulse control of molecular dynamics is studied theoretically by using optimal control theory. The control theory is extended to target states which are distributed in time as well as in a space of parameters which are responsible for a change of individual molecular properties. This generalized treatment of a control task is first applied to wave packet formation in randomly oriented diatomic systems. Concentrating on an ensemble of NaK molecules which are not aligned the control yield decreases drastically when compared with an aligned ensemble. Second, we demonstrate for NaK the maximization of the probe pulse transient absorption in a pump-probe scheme with an optimized pump pulse. These computations suggest an overall optical control scheme, whereby a flexible technique is suggested to form particular wave packets in the excited state potential energy surface. In particular, it is shown that considerable wave packet localization at the turning points of the first-excited Σ-state potential energy surfaces of NaK may be achieved. The dependency of the control yield on the probe pulse parameters is also discussed.

In vivo detection of free radicals using molecular MRI and immuno-spin trapping in a mouse model for amyotrophic lateral sclerosis.

PubMed

Towner, Rheal A; Smith, Nataliya; Saunders, Debra; Lupu, Florea; Silasi-Mansat, Robert; West, Melinda; Ramirez, Dario C; Gomez-Mejiba, Sandra E; Bonini, Marcelo G; Mason, Ronald P; Ehrenshaft, Marilyn; Hensley, Kenneth

2013-10-01

Free radicals associated with oxidative stress play a major role in amyotrophic lateral sclerosis (ALS). By combining immuno-spin trapping and molecular magnetic resonance imaging, in vivo trapped radical adducts were detected in the spinal cords of SOD1(G93A)-transgenic (Tg) mice, a model for ALS. For this study, the nitrone spin trap DMPO (5,5-dimethyl-1-pyrroline N-oxide) was administered (ip) over 5 days before administration (iv) of an anti-DMPO probe (anti-DMPO antibody covalently bound to an albumin-gadolinium-diethylenetriamine pentaacetic acid-biotin MRI contrast agent) to trap free radicals. MRI was used to detect the presence of the anti-DMPO radical adducts by a significant sustained increase in MR signal intensities (p < 0.05) or anti-DMPO probe concentrations measured from T₁ relaxations (p < 0.01). The biotin moiety of the anti-DMPO probe was targeted with fluorescence-labeled streptavidin to locate the probe in excised tissues. Negative controls included either Tg ALS mice initially administered saline rather than DMPO followed by the anti-DMPO probe or non-Tg mice initially administered DMPO and then the anti-DMPO probe. The anti-DMPO probe was found to bind to neurons via colocalization fluorescence microscopy. DMPO adducts were also confirmed in diseased/nondiseased tissues from animals administered DMPO. Apparent diffusion coefficients from diffusion-weighted images of spinal cords from Tg mice were significantly elevated (p < 0.001) compared to wild-type controls. This is the first report regarding the detection of in vivo trapped radical adducts in an ALS model. This novel, noninvasive, in vivo diagnostic method can be applied to investigate the involvement of free radical mechanisms in ALS rodent models. Copyright © 2013 Elsevier Inc. All rights reserved.

Stand-off molecular composition analysis

NASA Astrophysics Data System (ADS)

Hughes, Gary B.; Lubin, Philip; Meinhold, Peter; O'Neill, Hugh; Brashears, Travis; Zhang, Qicheng; Griswold, Janelle; Riley, Jordan; Motta, Caio

2015-09-01

Molecular composition of distant stars is explored by observing absorption spectra. The star produces blackbody radiation that passes through the molecular cloud of vaporized material surrounding the star. Characteristic absorption lines are discernible with a spectrometer, and molecular composition is investigated by comparing spectral observations with known material profiles. Most objects in the solar system—asteroids, comets, planets, moons—are too cold to be interrogated in this manner. Molecular clouds around cold objects consist primarily of volatiles, so bulk composition cannot be probed. Additionally, low volatile density does not produce discernible absorption lines in the faint signal generated by low blackbody temperatures. This paper describes a system for probing the molecular composition of cold solar system targets from a distant vantage. The concept utilizes a directed energy beam to melt and vaporize a spot on a distant target, such as from a spacecraft orbiting the object. With sufficient flux (~10 MW/m2), the spot temperature rises rapidly (to ~2 500 K), and evaporation of all materials on the target surface occurs. The melted spot creates a high-temperature blackbody source, and ejected material creates a molecular plume in front of the spot. Bulk composition is investigated by using a spectrometer to view the heated spot through the ejected material. Spatial composition maps could be created by scanning the surface. Applying the beam to a single spot continuously produces a borehole, and shallow sub-surface composition profiling is also possible. Initial simulations of absorption profiles with laser heating show great promise for molecular composition analysis.

Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale.

PubMed

Aminov, Rustam I; Walker, Alan W; Duncan, Sylvia H; Harmsen, Hermie J M; Welling, Gjalt W; Flint, Harry J

2006-09-01

Phylogenetic analysis was used to compare 16S rRNA sequences from 19 cultured human gut strains of Roseburia and Eubacterium rectale with 356 related sequences derived from clone libraries. The cultured strains were found to represent five of the six phylotypes identified. A new oligonucleotide probe, Rrec584, and the previous group probe Rint623, when used in conjunction with a new helper oligonucleotide, each recognized an average of 7% of bacteria detected by the eubacterial probe Eub338 in feces from 10 healthy volunteers. Most of the diversity within this important group of butyrate-producing gut bacteria can apparently be retrieved through cultivation.

Molecular Diversity, Cultivation, and Improved Detection by Fluorescent In Situ Hybridization of a Dominant Group of Human Gut Bacteria Related to Roseburia spp. or Eubacterium rectale

PubMed Central

Aminov, Rustam I.; Walker, Alan W.; Duncan, Sylvia H.; Harmsen, Hermie J. M.; Welling, Gjalt W.; Flint, Harry J.

2006-01-01

Phylogenetic analysis was used to compare 16S rRNA sequences from 19 cultured human gut strains of Roseburia and Eubacterium rectale with 356 related sequences derived from clone libraries. The cultured strains were found to represent five of the six phylotypes identified. A new oligonucleotide probe, Rrec584, and the previous group probe Rint623, when used in conjunction with a new helper oligonucleotide, each recognized an average of 7% of bacteria detected by the eubacterial probe Eub338 in feces from 10 healthy volunteers. Most of the diversity within this important group of butyrate-producing gut bacteria can apparently be retrieved through cultivation. PMID:16957265

Exogenous Molecular Probes for Targeted Imaging in Cancer: Focus on Multi-modal Imaging

PubMed Central

Joshi, Bishnu P.; Wang, Thomas D.

2010-01-01

Cancer is one of the major causes of mortality and morbidity in our healthcare system. Molecular imaging is an emerging methodology for the early detection of cancer, guidance of therapy, and monitoring of response. The development of new instruments and exogenous molecular probes that can be labeled for multi-modality imaging is critical to this process. Today, molecular imaging is at a crossroad, and new targeted imaging agents are expected to broadly expand our ability to detect and manage cancer. This integrated imaging strategy will permit clinicians to not only localize lesions within the body but also to manage their therapy by visualizing the expression and activity of specific molecules. This information is expected to have a major impact on drug development and understanding of basic cancer biology. At this time, a number of molecular probes have been developed by conjugating various labels to affinity ligands for targeting in different imaging modalities. This review will describe the current status of exogenous molecular probes for optical, scintigraphic, MRI and ultrasound imaging platforms. Furthermore, we will also shed light on how these techniques can be used synergistically in multi-modal platforms and how these techniques are being employed in current research. PMID:22180839

X-ray Pump–Probe Investigation of Charge and Dissociation Dynamics in Methyl Iodine Molecule

DOE PAGES

Fang, Li; Xiong, Hui; Kukk, Edwin; ...

2017-05-19

Molecular dynamics is of fundamental interest in natural science research. The capability of investigating molecular dynamics is one of the various motivations for ultrafast optics. Here, we present our investigation of photoionization and nuclear dynamics in methyl iodine (CH 3I) molecule with an X-ray pump X-ray probe scheme. The pump–probe experiment was realized with a two-mirror X-ray split and delay apparatus. Time-of-flight mass spectra at various pump–probe delay times were recorded to obtain the time profile for the creation of high charge states via sequential ionization and for molecular dissociation. We observed high charge states of atomic iodine up tomore » 29+, and visualized the evolution of creating these high atomic ion charge states, including their population suppression and enhancement as the arrival time of the second X-ray pulse was varied. We also show the evolution of the kinetics of the high charge states upon the timing of their creation during the ionization-dissociation coupled dynamics. We demonstrate the implementation of X-ray pump–probe methodology for investigating X-ray induced molecular dynamics with femtosecond temporal resolution. The results indicate the footprints of ionization that lead to high charge states, probing the long-range potential curves of the high charge states.« less

Identification of HLA-DP polymorphism with DP alpha and DP beta probes and monoclonal antibodies: correlation with primed lymphocyte typing.

PubMed Central

Bodmer, J; Bodmer, W; Heyes, J; So, A; Tonks, S; Trowsdale, J; Young, J

1987-01-01

Thirty-four lymphoblastoid cell lines that had been previously typed for HLA-DP antigens by primed lymphocyte typing (PLT) were tested by Southern blotting and by ELISA. Using two DP beta probes and a DP alpha probe with a series of enzymes, it is possible to identify restriction fragment length polymorphism (RFLP) patterns characteristic of DPw1, -2, -3, -4, and possibly -5. ELISA typing results, based on two polymorphic DP antibodies DP11.1 and ILR1, were compared with PLT-defined and RFLP-defined types. Thus, using a range of probes and enzymes it is possible to identify DP polymorphism. The value of monoclonal antibodies for such studies is demonstrated, and the molecular data can, in some cases, pinpoint the amino acids responsible for the specificity of the monoclonal antibodies. Images PMID:2885841

Homing peptide guiding optical molecular imaging for the diagnosis of bladder cancer

NASA Astrophysics Data System (ADS)

Yang, Xiao-feng; Pang, Jian-zhi; Liu, Jie-hao; Zhao, Yang; Jia, Xing-you; Li, Jun; Liu, Reng-xin; Wang, Wei; Fan, Zhen-wei; Zhang, Zi-qiang; Yan, San-hua; Luo, Jun-qian; Zhang, Xiao-lei

2014-11-01

Background: The limitations of primary transurethral resection of bladder tumor (TURBt) have led the residual tumors rates as high as 75%. The intraoperative fluorescence imaging offers a great potential for improving TURBt have been confirmed. So we aim to distinguish the residual tumors and normal mucosa using fluorescence molecular imaging formed by conjugated molecule of the CSNRDARRC bladder cancer homing peptide with fluorescent dye. The conjugated molecule was abbreviated FIuo-ACP. In our study, we will research the image features of FIuo-ACP probe targeted bladder cancer for fluorescence molecular imaging diagnosis for bladder cancer in vivo and ex vivo. Methods: After the FIuo-ACP probe was synthetized, the binding sites, factors affecting binding rates, the specificity and the targeting of Fluo-ACP labeled with bladder cancer cells were studied respectively by laser scanning confocal microscope (LSCM), immunofluorescence and multispectral fluorescence ex vivo optical molecular imaging system. Results: The binding sites were located in nucleus and the binding rates were correlated linearly with the dose of probe and the grade of pathology. Moreover, the probe has a binding specificity with bladder cancer in vivo and ex vivo. Tumor cells being labeled by the Fluo-ACP, bright green spots were observed under LSCM. The tissue samples and tumor cells can be labeled and identified by fluorescence microscope. Optical molecular imaging of xenograft tumor tissues was exhibited as fluorescent spots under EMCCD. Conclusion: The CSNRDARRC peptides might be a useful bladder cancer targeting vector. The FIuo-ACP molecular probe was suitable for fluorescence molecular imaging diagnosis for bladder cancer in vivo and ex vivo.

pH-Induced Modulation of One- and Two-Photon Absorption Properties in a Naphthalene-Based Molecular Probe.

PubMed

Murugan, N Arul; Kongsted, Jacob; Ågren, Hans

2013-08-13

Presently, there is a great demand for small probe molecules that can be used for two-photon excitation microscopy (TPM)-based monitoring of intracellular and intraorganelle activity and pH. The candidate molecules should ideally possess a large two-photon absorption cross section with optical properties sensitive to pH changes. In the present work, we investigate the potential of a methoxy napthalene (MONAP) derivative for its suitability to serve as a pH sensor using TPM. Using an integrated approach rooted in hybrid quantum mechanics/molecular mechanics, the structures, dynamics, and the one- and two-photon properties of the probe in dimethylformamide solvent are studied. It is found that the protonated form is responsible for the optical property of MONAP at moderately low pH, for which the calculated pH-induced red shift is in good agreement with experiments. A 2-fold increase in the two-photon absorption cross section in the IR region of the spectrum is predicted for the moderately low pH form of the probe, suggesting that this can be a potential probe for pH monitoring of living cells. We also propose some design principles aimed at obtaining control of the absorption spectral range of the probe by structural tuning. Our work indicates that the integrated approach employed is capable of capturing the pH-induced changes in structure and optical properties of organic molecular probes and that such in silico tools can be used to draw structure-property relationships to design novel molecular probes suitable for a specific application.

Mapping Rotational Wavepacket Dynamics with Chirped Probe Pulses

NASA Astrophysics Data System (ADS)

Romanov, Dmitri; Odhner, Johanan; Levis, Robert

2014-05-01

We develop an analytical model description of the strong-field pump-probe polarization spectroscopy of rotational transients in molecular gases in a situation when the probe pulse is considerably chirped: the frequency modulation over the pulse duration is comparable with the carrier frequency. In this scenario, a femtosecond pump laser pulse prepares a rotational wavepacket in a gas-phase sample at room temperature. The rotational revivals of the wavepacket are then mapped onto a chirped broadband probe pulse derived from a laser filament. The slow-varying envelope approximation being inapplicable, an alternative approach is proposed which is capable of incorporating the substantial chirp and the related temporal dispersion of refractive indices. Analytical expressions are obtained for the probe signal modulation over the interaction region and for the resulting heterodyned transient birefringence spectra. Dependencies of the outputs on the probe pulse parameters reveal the trade-offs and the ways to optimize the temporal-spectral imaging. The results are in good agreement with the experiments on snapshot imaging of rotational revival patterns in nitrogen gas. We gratefully acknowledge financial support through AFOSR MURI Grant No. FA9550-10-1-0561.

Local collective motion analysis for multi-probe dynamic imaging and microrheology

NASA Astrophysics Data System (ADS)

Khan, Manas; Mason, Thomas G.

2016-08-01

Dynamical artifacts, such as mechanical drift, advection, and hydrodynamic flow, can adversely affect multi-probe dynamic imaging and passive particle-tracking microrheology experiments. Alternatively, active driving by molecular motors can cause interesting non-Brownian motion of probes in local regions. Existing drift-correction techniques, which require large ensembles of probes or fast temporal sampling, are inadequate for handling complex spatio-temporal drifts and non-Brownian motion of localized domains containing relatively few probes. Here, we report an analytical method based on local collective motion (LCM) analysis of as few as two probes for detecting the presence of non-Brownian motion and for accurately eliminating it to reveal the underlying Brownian motion. By calculating an ensemble-average, time-dependent, LCM mean square displacement (MSD) of two or more localized probes and comparing this MSD to constituent single-probe MSDs, we can identify temporal regimes during which either thermal or athermal motion dominates. Single-probe motion, when referenced relative to the moving frame attached to the multi-probe LCM trajectory, provides a true Brownian MSD after scaling by an appropriate correction factor that depends on the number of probes used in LCM analysis. We show that LCM analysis can be used to correct many different dynamical artifacts, including spatially varying drifts, gradient flows, cell motion, time-dependent drift, and temporally varying oscillatory advection, thereby offering a significant improvement over existing approaches.

Toward real-time quantification of fluorescence molecular probes using target/background ratio for guiding biopsy and endoscopic therapy of esophageal neoplasia.

PubMed

Jiang, Yang; Gong, Yuanzheng; Rubenstein, Joel H; Wang, Thomas D; Seibel, Eric J

2017-04-01

Multimodal endoscopy using fluorescence molecular probes is a promising method of surveying the entire esophagus to detect cancer progression. Using the fluorescence ratio of a target compared to a surrounding background, a quantitative value is diagnostic for progression from Barrett's esophagus to high-grade dysplasia (HGD) and esophageal adenocarcinoma (EAC). However, current quantification of fluorescent images is done only after the endoscopic procedure. We developed a Chan-Vese-based algorithm to segment fluorescence targets, and subsequent morphological operations to generate background, thus calculating target/background (T/B) ratios, potentially to provide real-time guidance for biopsy and endoscopic therapy. With an initial processing speed of 2 fps and by calculating the T/B ratio for each frame, our method provides quasireal-time quantification of the molecular probe labeling to the endoscopist. Furthermore, an automatic computer-aided diagnosis algorithm can be applied to the recorded endoscopic video, and the overall T/B ratio is calculated for each patient. The receiver operating characteristic curve was employed to determine the threshold for classification of HGD/EAC using leave-one-out cross-validation. With 92% sensitivity and 75% specificity to classify HGD/EAC, our automatic algorithm shows promising results for a surveillance procedure to help manage esophageal cancer and other cancers inspected by endoscopy.

Deciphering Cryptic Binding Sites on Proteins by Mixed-Solvent Molecular Dynamics.

PubMed

Kimura, S Roy; Hu, Hai Peng; Ruvinsky, Anatoly M; Sherman, Woody; Favia, Angelo D

2017-06-26

In recent years, molecular dynamics simulations of proteins in explicit mixed solvents have been applied to various problems in protein biophysics and drug discovery, including protein folding, protein surface characterization, fragment screening, allostery, and druggability assessment. In this study, we perform a systematic study on how mixtures of organic solvent probes in water can reveal cryptic ligand binding pockets that are not evident in crystal structures of apo proteins. We examine a diverse set of eight PDB proteins that show pocket opening induced by ligand binding and investigate whether solvent MD simulations on the apo structures can induce the binding site observed in the holo structures. The cosolvent simulations were found to induce conformational changes on the protein surface, which were characterized and compared with the holo structures. Analyses of the biological systems, choice of probes and concentrations, druggability of the resulting induced pockets, and application to drug discovery are discussed here.

Lighting Up the Force: Investigating Mechanisms of Mechanotransduction Using Fluorescent Tension Probes

PubMed Central

Jurchenko, Carol

2015-01-01

The ability of cells to sense the physical nature of their surroundings is critical to the survival of multicellular organisms. Cellular response to physical cues from adjacent cells and the extracellular matrix leads to a dynamic cycle in which cells respond by remodeling their local microenvironment, fine-tuning cell stiffness, polarity, and shape. Mechanical regulation is important in cellular development, normal morphogenesis, and wound healing. The mechanisms by which these finely balanced mechanotransduction events occur, however, are not well understood. In large part, this is due to the limited availability of tools to study molecular mechanotransduction events in live cells. Several classes of molecular tension probes have been recently developed which are rapidly transforming the study of mechanotransduction. Molecular tension probes are primarily based on fluorescence resonance energy transfer (FRET) and report on piconewton scale tension events in live cells. In this minireview, we describe the two main classes of tension probes, genetically encoded tension sensors and immobilized tension sensors, and discuss the advantages and limitations of each type. We discuss future opportunities to address major biological questions and outline the challenges facing the next generation of molecular tension probes. PMID:26031334

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fang, Li; Xiong, Hui; Kukk, Edwin

Molecular dynamics is of fundamental interest in natural science research. The capability of investigating molecular dynamics is one of the various motivations for ultrafast optics. Here, we present our investigation of photoionization and nuclear dynamics in methyl iodine (CH 3I) molecule with an X-ray pump X-ray probe scheme. The pump–probe experiment was realized with a two-mirror X-ray split and delay apparatus. Time-of-flight mass spectra at various pump–probe delay times were recorded to obtain the time profile for the creation of high charge states via sequential ionization and for molecular dissociation. We observed high charge states of atomic iodine up tomore » 29+, and visualized the evolution of creating these high atomic ion charge states, including their population suppression and enhancement as the arrival time of the second X-ray pulse was varied. We also show the evolution of the kinetics of the high charge states upon the timing of their creation during the ionization-dissociation coupled dynamics. We demonstrate the implementation of X-ray pump–probe methodology for investigating X-ray induced molecular dynamics with femtosecond temporal resolution. The results indicate the footprints of ionization that lead to high charge states, probing the long-range potential curves of the high charge states.« less

Distinguishing between relaxation pathways by combining dissociative ionization pump probe spectroscopy and ab initio calculations: a case study of cytosine.

PubMed

Kotur, Marija; Weinacht, Thomas C; Zhou, Congyi; Kistler, Kurt A; Matsika, Spiridoula

2011-05-14

We present a general method for tracking molecular relaxation along different pathways from an excited state down to the ground state. We follow the excited state dynamics of cytosine pumped near the S(0)-S(1) resonance using ultrafast laser pulses in the deep ultraviolet and probed with strong field near infrared pulses which ionize and dissociate the molecules. The fragment ions are detected via time of flight mass spectroscopy as a function of pump probe delay and probe pulse intensity. Our measurements reveal that different molecular fragments show different timescales, indicating that there are multiple relaxation pathways down to the ground state. We interpret our measurements with the help of ab initio electronic structure calculations of both the neutral molecule and the molecular cation for different conformations en route to relaxation back down to the ground state. Our measurements and calculations show passage through two seams of conical intersections between ground and excited states and demonstrate the ability of dissociative ionization pump probe measurements in conjunction with ab initio electronic structure calculations to track molecular relaxation through multiple pathways.

A robust molecular probe for Ångstrom-scale analytics in liquids

PubMed Central

Nirmalraj, Peter; Thompson, Damien; Dimitrakopoulos, Christos; Gotsmann, Bernd; Dumcenco, Dumitru; Kis, Andras; Riel, Heike

2016-01-01

Traditionally, nanomaterial profiling using a single-molecule-terminated scanning probe is performed at the vacuum–solid interface often at a few Kelvin, but is not a notion immediately associated with liquid–solid interface at room temperature. Here, using a scanning tunnelling probe functionalized with a single C60 molecule stabilized in a high-density liquid, we resolve low-dimensional surface defects, atomic interfaces and capture Ångstrom-level bond-length variations in single-layer graphene and MoS2. Atom-by-atom controllable imaging contrast is demonstrated at room temperature and the electronic structure of the C60–metal probe complex within the encompassing liquid molecules is clarified using density functional theory. Our findings demonstrates that operating a robust single-molecular probe is not restricted to ultra-high vacuum and cryogenic settings. Hence the scope of high-precision analytics can be extended towards resolving sub-molecular features of organic elements and gauging ambient compatibility of emerging layered materials with atomic-scale sensitivity under experimentally less stringent conditions. PMID:27516157

Molecular Imaging Probes for Positron Emission Tomography and Optical Imaging of Sentinel Lymph Node and Tumor

NASA Astrophysics Data System (ADS)

Qin, Zhengtao

Molecular imaging is visualizations and measurements of in vivo biological processes at the molecular or cellular level using specific imaging probes. As an emerging technology, biocompatible macromolecular or nanoparticle based targeted imaging probes have gained increasing popularities. Those complexes consist of a carrier, an imaging reporter, and a targeting ligand. The active targeting ability dramatically increases the specificity. And the multivalency effect may further reduce the dose while providing a decent signal. In this thesis, sentinel lymph node (SLN) mapping and cancer imaging are two research topics. The focus is to develop molecular imaging probes with high specificity and sensitivity, for Positron Emission Tomography (PET) and optical imaging. The objective of this thesis is to explore dextran radiopharmaceuticals and porous silicon nanoparticles based molecular imaging agents. Dextran polymers are excellent carriers to deliver imaging reporters or therapeutic agents due to its well established safety profile and oligosaccharide conjugation chemistry. There is also a wide selection of dextran polymers with different lengths. On the other hand, Silicon nanoparticles represent another class of biodegradable materials for imaging and drug delivery. The success in fluorescence lifetime imaging and enhancements of the immune activation potency was briefly discussed. Chapter 1 begins with an overview on current molecular imaging techniques and imaging probes. Chapter 2 presents a near-IR dye conjugated probe, IRDye 800CW-tilmanocept. Fluorophore density was optimized to generate the maximum brightness. It was labeled with 68Ga and 99mTc and in vivo SLN mapping was successfully performed in different animals, such as mice, rabbits, dogs and pigs. With 99mTc labeled IRDye 800CW-tilmanocept, chapter 3 introduces a two-day imaging protocol with a hand-held imager. Chapter 4 proposed a method to dual radiolabel the IRDye 800CW-tilmanocept with both 68Ga and 99mTc. Chapter 5 introduces a 68Ga metal chelating bioorthogonal tetrazine dextran probe for multistep imaging of a colon cancer. Chapter 6 presents the synthesis and in vivo evaluation of a Hepatocellular Carcinoma targeting PET probe 68Ga-Insulin-Dextran. Chapter 7 discusses a novel method to prepare silicon nanoparticles with great yield and size control. The last chapter 8 concludes all probes developed in this thesis and their clinical relevance.

Intravital imaging of mouse colonic adenoma using MMP-based molecular probes with multi-channel fluorescence endoscopy.

PubMed

Oh, Gyungseok; Yoo, Su Woong; Jung, Yebin; Ryu, Yeon-Mi; Park, Youngrong; Kim, Sang-Yeob; Kim, Ki Hean; Kim, Sungjee; Myung, Seung-Jae; Chung, Euiheon

2014-05-01

Intravital imaging has provided molecular, cellular and anatomical insight into the study of tumor. Early detection and treatment of gastrointestinal (GI) diseases can be enhanced with specific molecular markers and endoscopic imaging modalities. We present a wide-field multi-channel fluorescence endoscope to screen GI tract for colon cancer using multiple molecular probes targeting matrix metalloproteinases (MMP) conjugated with quantum dots (QD) in AOM/DSS mouse model. MMP9 and MMP14 antibody (Ab)-QD conjugates demonstrate specific binding to colonic adenoma. The average target-to-background (T/B) ratios are 2.10 ± 0.28 and 1.78 ± 0.18 for MMP14 Ab-QD and MMP9 Ab-QD, respectively. The overlap between the two molecular probes is 67.7 ± 8.4%. The presence of false negative indicates that even more number of targeting could increase the sensitivity of overall detection given heterogeneous molecular expression in tumors. Our approach indicates potential for the screening of small or flat lesions that are precancerous.

Ionic calcium determination in skim milk with molecular probes and front-face fluorescence spectroscopy: simple linear regression.

PubMed

Gangidi, R R; Metzger, L E

2006-11-01

The purpose of this study was to determine if the ionic calcium content of skim milk could be determined using molecular probes and front-face fluorescence spectroscopy. Current methods for determining ionic calcium are not sensitive, overestimate ionic calcium, or require complex procedures. Molecular probes designed specifically for measuring ionic calcium could potentially be used to determine the ionic calcium content of skim milk. The goal of the current study was to develop foundation methods for future studies to determine ionic calcium directly in skim milk and other dairy products with molecular probes and fluorescence spectroscopy. In this study, the effect of pH on calcium-sensitive fluorescent probe (Rhod-5N and Fluo-5N) performance using various concentrations of skim milk was determined. The pH of diluted skim milk (1.9 to 8.9% skim milk), was adjusted to either 6.2 or 7.0, after which the samples were analyzed with fluorescent probes (1 microM) and front-face fluorescence spectroscopy. The ionic calcium content of each sample was also determined using a calcium ion-selective electrode. The results demonstrated that the ionic calcium content of each sample was highly correlated (R2 > 0.989) with the fluorescence intensities of the probe-calcium adduct using simple linear regression. Higher than suggested ionic calcium contents of 1,207 and 1,973 microM were determined with the probes (Fluo-5N and Rhod-5N) in diluted skim milk with pH 7.0 and 6.2, respectively. The fluorescence intensity of the probe-calcium adduct decreased with a decrease in pH for the same ionic calcium concentration. This study demonstrates that Fluo-5N and Rhod-5N can be used to determine the ionic-calcium content of diluted milk with front-face fluorescence spectroscopy. Furthermore, these probes may also have the potential to determine the ionic calcium content of undiluted skim milk.

In Silico Analyses of Substrate Interactions with Human Serum Paraoxonase 1

DTIC Science & Technology

2008-01-01

substrate interactions of HuPON1 remains elusive. In this study, we apply homology modeling, docking, and molecular dynamic (MD) simulations to probe the...mod- eling; docking; molecular dynamics simulations ; binding free energy decomposition. 486 PROTEINS Published 2008 WILEY-LISS, INC. yThis article is a...apply homology modeling, docking, and molecular dynamic (MD) simulations to probe the binding interactions of HuPON1 with representative substrates. The

Next-Generation Molecular Histology Using Highly Multiplexed Ion Beam Imaging (MIBI) of Breast Cancer Tissue Specimens for Enhanced Clinical Guidance

DTIC Science & Technology

2017-07-01

panels of MIBI multiplexed in situ detection reagents, and compare the quantitative data to the conventional clinically derived “one at a time” and...Measure standard curves for each analyte against western blots using cell lines and tumor samples. Compare quantitation dynamic ranges to...GSTM1, CD68, BAG1, ER, PGR, BCL2, SCUBE2, ACTB, GAPDH, RPLPO, GUS, TFRC) IIa. Compare hybridization results for mass tagged probe designs from both

Development and comparison of a rapid isothermal nucleic acid amplification test for typing of herpes simplex virus types 1 and 2 on a portable fluorescence detector.

PubMed

Tong, Yanhong; McCarthy, Kaitlin; Kong, Huimin; Lemieux, Bertrand

2012-11-01

We have developed a rapid and simple molecular test, the IsoGlow HSV Typing assay, for the detection and typing of herpes simplex virus (type 1 and 2) from genital or oral lesions. Clinical samples suspended in viral transport mediums are simply diluted and then added to a helicase-dependent amplification master mix. The amplification and detection were performed on a portable fluorescence detector called the FireFly instrument. Detection of amplification products is based on end-point analysis using cycling probe technology. An internal control nucleic acid was included in the amplification master mix to monitor the presence of amplification inhibitors in the samples. Because the device has only two fluorescence detection channels, two strategies were developed and compared to detect the internal control template: internal control detected by melting curve analysis using a dual-labeled probe, versus internal control detection using end-point fluorescence release by a CPT probe at a lower temperature. Both have a total turnaround time of about 1 hour. Clinical performance relative to herpes viral culture was evaluated using 176 clinical specimens. Both formats of the IsoGlow HSV typing assay had sensitivities comparable to that of the Food and Drug Administration-cleared IsoAmp HSV (BioHelix Corp., Beverly MA) test and specificity for the two types of HSV comparable to that of ELVIS HSV (Diagnostic Hybrids, Athens, OH). Copyright © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Molecular Imaging and Precision Medicine in Prostate Cancer.

PubMed

Ceci, Francesco; Fiorentino, Michelangelo; Castellucci, Paolo; Fanti, Stefano

2017-01-01

The aim of the present review is to discuss about the role of new probes for molecular imaging in the evaluation of prostate cancer (PCa). This review focuses particularly on the role of new promising radiotracers for the molecular imaging with PET/computed tomography in the detection of PCa recurrence. The role of these new imaging techniques to guide lesion-target therapies and the potential application of these molecular probes as theranostics agents is discussed. Finally, the molecular mechanisms underlying resistance to castration in PCa and the maintenance of active androgen receptor are discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

An ultrasensitive SiO2-encapsulated alloyed CdZnSeS quantum dot-molecular beacon nanobiosensor for norovirus.

PubMed

Adegoke, Oluwasesan; Seo, Min-Woong; Kato, Tatsuya; Kawahito, Shoji; Park, Enoch Y

2016-12-15

Ultrasensitive, rapid and selective diagnostic probes are urgently needed to overcome the limitations of traditional probes for norovirus (NV). Here, we report the detection of NV genogroup II via nucleic acid hybridization technology using a quantum dot (QD)-conjugated molecular beacon (MB) probe. To boost the sensitivity of the MB assay system, an ultrasensitive QD fluorophore with unique optical properties was synthesized, characterized and exploited as a fluorescence signal generator. Alloyed thioglycolic (TGA)-capped CdZnSeS QDs with a high photoluminescence (PL) quantum yield (QY) value of 92% were synthesized, and a modified silanization method was employed to encapsulate the thiol-capped QDs in a silica layer. The resulting highly luminescent alloyed SiO2-coated CdZnSeS QDs had a remarkable PL QY value of 98%. Transmission electron microscopy and dynamic light scattering confirmed the monodispersity of the alloyed nanocrystals, and zeta potential analysis confirmed their colloidal stability. Powder X-ray diffraction and PL lifetime measurements confirmed the surface modification of the QDs. The alloyed TGA-capped and SiO2-coated CdZnSeS QD-conjugated MB bioprobes detected extremely low concentrations of NV RNA. Ultrasensitive detection of low concentrations of NV RNA with a limit of detection (LOD) of 8.2copies/mL in human serum and a LOD of 9.3 copies/mL in buffer was achieved using the SiO2-coated CdZnSeS QD-MB probes, an increase in sensitivity of 3-fold compared with the detection limit for NV RNA using TGA-capped CdZnSeS QD-MBs. The additional merits of our detection system are rapidity, specificity and improved sensitivity over conventional molecular test probes. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Comparison of Cherenkov excited fluorescence and phosphorescence molecular sensing from tissue with external beam irradiation.

PubMed

Lin, Huiyun; Zhang, Rongxiao; Gunn, Jason R; Esipova, Tatiana V; Vinogradov, Sergei; Gladstone, David J; Jarvis, Lesley A; Pogue, Brian W

2016-05-21

Ionizing radiation delivered by a medical linear accelerator (LINAC) generates Cherenkov emission within the treated tissue. A fraction of this light, in the 600-900 nm wavelength region, propagates through centimeters of tissue and can be used to excite optical probes in vivo, enabling molecular sensing of tissue analytes. The success of isolating the emission signal from this Cherenkov excitation background is dependent on key factors such as: (i) the Stokes shift of the probe spectra; (ii) the excited state lifetime; (iii) the probe concentration; (iv) the depth below the tissue surface; and (v) the radiation dose used. Previous studies have exclusively focused on imaging phosphorescent dyes, rather than fluorescent dyes. However there are only a few biologically important phosphorescent dyes and yet in comparison there are thousands of biologically relevant fluorescent dyes. So in this study the focus was a study of efficacy of Cherenkov-excited luminescence using fluorescent commercial near-infrared probes, IRDye 680RD, IRDye 700DX, and IRDye 800CW, and comparing them to the well characterized phosphorescent probe Oxyphor PtG4, an oxygen sensitive dye. Each probe was excited by Cherenkov light from a 6 MV external radiation beam, and measured in continuous wave or time-gated modes. The detection was performed by spectrally resolving the luminescence signals, and measuring them with spectrometer-based separation on an ICCD detector. The results demonstrate that IRDye 700DX and PtG4 allowed for the maximal signal to noise ratio. In the case of the phosphorescent probe, PtG4, with emission decays on the microsecond (μs) time scale, time-gated acquisition was possible, and it allowed for higher efficacy in terms of the probe concentration and detection depth. Phantoms containing the probe at 5 mm depth could be detected at concentrations down to the nanoMolar range, and at depths into the tissue simulating phantom near 3 cm. In vivo studies showed that 5 nmol of dye was readily detected with radiation doses less than 5 cGy. Since concentration, radiation dose and depth each contribute to the level of the detected signal, it may be possible to improve any of these parameters at expense of the others. This paradigm of nanoMolar sensitivity for optical reporters in vivo introduces the concept of molecular sensing of tumors during therapy or diagnostically with biologically relevant concentrations of fluorescent reporters.

Comparison of Cherenkov excited fluorescence and phosphorescence molecular sensing from tissue with external beam irradiation

NASA Astrophysics Data System (ADS)

Lin, Huiyun; Zhang, Rongxiao; Gunn, Jason R.; Esipova, Tatiana V.; Vinogradov, Sergei; Gladstone, David J.; Jarvis, Lesley A.; Pogue, Brian W.

2016-05-01

Ionizing radiation delivered by a medical linear accelerator (LINAC) generates Cherenkov emission within the treated tissue. A fraction of this light, in the 600-900 nm wavelength region, propagates through centimeters of tissue and can be used to excite optical probes in vivo, enabling molecular sensing of tissue analytes. The success of isolating the emission signal from this Cherenkov excitation background is dependent on key factors such as: (i) the Stokes shift of the probe spectra; (ii) the excited state lifetime; (iii) the probe concentration; (iv) the depth below the tissue surface; and (v) the radiation dose used. Previous studies have exclusively focused on imaging phosphorescent dyes, rather than fluorescent dyes. However there are only a few biologically important phosphorescent dyes and yet in comparison there are thousands of biologically relevant fluorescent dyes. So in this study the focus was a study of efficacy of Cherenkov-excited luminescence using fluorescent commercial near-infrared probes, IRDye 680RD, IRDye 700DX, and IRDye 800CW, and comparing them to the well characterized phosphorescent probe Oxyphor PtG4, an oxygen sensitive dye. Each probe was excited by Cherenkov light from a 6 MV external radiation beam, and measured in continuous wave or time-gated modes. The detection was performed by spectrally resolving the luminescence signals, and measuring them with spectrometer-based separation on an ICCD detector. The results demonstrate that IRDye 700DX and PtG4 allowed for the maximal signal to noise ratio. In the case of the phosphorescent probe, PtG4, with emission decays on the microsecond (μs) time scale, time-gated acquisition was possible, and it allowed for higher efficacy in terms of the probe concentration and detection depth. Phantoms containing the probe at 5 mm depth could be detected at concentrations down to the nanoMolar range, and at depths into the tissue simulating phantom near 3 cm. In vivo studies showed that 5 nmol of dye was readily detected with radiation doses less than 5 cGy. Since concentration, radiation dose and depth each contribute to the level of the detected signal, it may be possible to improve any of these parameters at expense of the others. This paradigm of nanoMolar sensitivity for optical reporters in vivo introduces the concept of molecular sensing of tumors during therapy or diagnostically with biologically relevant concentrations of fluorescent reporters.

Creating and virtually screening databases of fluorescently-labelled compounds for the discovery of target-specific molecular probes

NASA Astrophysics Data System (ADS)

Kamstra, Rhiannon L.; Dadgar, Saedeh; Wigg, John; Chowdhury, Morshed A.; Phenix, Christopher P.; Floriano, Wely B.

2014-11-01

Our group has recently demonstrated that virtual screening is a useful technique for the identification of target-specific molecular probes. In this paper, we discuss some of our proof-of-concept results involving two biologically relevant target proteins, and report the development of a computational script to generate large databases of fluorescence-labelled compounds for computer-assisted molecular design. The virtual screening of a small library of 1,153 fluorescently-labelled compounds against two targets, and the experimental testing of selected hits reveal that this approach is efficient at identifying molecular probes, and that the screening of a labelled library is preferred over the screening of base compounds followed by conjugation of confirmed hits. The automated script for library generation explores the known reactivity of commercially available dyes, such as NHS-esters, to create large virtual databases of fluorescence-tagged small molecules that can be easily synthesized in a laboratory. A database of 14,862 compounds, each tagged with the ATTO680 fluorophore was generated with the automated script reported here. This library is available for downloading and it is suitable for virtual ligand screening aiming at the identification of target-specific fluorescent molecular probes.

Molecular Probing of the HPV-16 E6 Protein Alpha Helix Binding Groove with Small Molecule Inhibitors

PubMed Central

Rietz, Anne; Petrov, Dino P.; Bartolowits, Matthew; DeSmet, Marsha; Davisson, V. Jo; Androphy, Elliot J.

2016-01-01

The human papillomavirus (HPV) HPV E6 protein has emerged as a central oncoprotein in HPV-associated cancers in which sustained expression is required for tumor progression. A majority of the E6 protein interactions within the human proteome use an alpha-helix groove interface for binding. The UBE3A/E6AP HECT domain ubiquitin ligase binds E6 at this helix-groove interface. This enables formation of a trimeric complex with p53, resulting in destruction of this tumor suppressor. While recent x-ray crystal structures are useful, examples of small molecule probes that can modulate protein interactions at this interface are limited. To develop insights useful for potential structure-based design of ligands for HPV E6, a series of 2,6-disubstituted benzopyranones were prepared and tested as competitive antagonists of E6-E6AP helix-groove interactions. These small molecule probes were used in both binding and functional assays to evaluate recognition features of the E6 protein. Evidence for an ionic functional group interaction within the helix groove was implicated by the structure-activity among the highest affinity ligands. The molecular topographies of these protein-ligand interactions were evaluated by comparing the binding and activities of single amino acid E6 mutants with the results of molecular dynamic simulations. A group of arginine residues that form a rim-cap over the E6 helix groove offer compensatory roles in binding and recognition of the small molecule probes. The flexibility and impact on the overall helix-groove shape dictated by these residues offer new insights for structure-based targeting of HPV E6. PMID:26915086

Evaluation of two molecular techniques for rapid detection of the main dermatophytic agents of tinea capitis.

PubMed

Deng, S; Zhou, Z; de Hoog, G S; Wang, X; Abliz, P; Sun, J; Najafzadeh, M J; Pan, W; Lei, W; Zhu, S; Hasimu, H; Zhang, P; Guo, Y; Deng, D; Liao, W

2015-12-01

Tinea capitis is very common in Western China, with the most widespread aetiological agent being Trichophyton violaceum, while Microsporum canis is prevalent in the remainder of China. Conventional diagnostics and internal transcribed spacer (ITS) sequencing analyses have proven relatively limited due to the close phylogenetic relationship of anthropophilic dermatophytes. Therefore, alternative molecular tools with sufficient specificity, reproducibility and sensitivity are necessary. To evaluate two molecular techniques [multiplex ligation-dependent probe amplification (MLPA) and rolling circle amplification (RCA)] for rapid detection of the aetiological agents of tinea capitis, T. violaceum and M. canis. Probes of RCA and MLPA were designed with target sequences in the rDNA ITS gene region. Strains tested consist of 31 T. violaceum, 22 M. canis and 24 reference strains of species that are taxonomically close to the target species. The specificity and reproducibility of RCA and MLPA in detection of T. violaceum and M. canis were both 100% in both species. Sensitivity testing showed that RCA was positive at concentrations down to 1·68 × 10(6) copies of DNA in the TvioRCA probe, and 2·7 × 10(8) copies of DNA in McRCA. MLPA yielded positive results at concentrations of DNA down to 1·68 × 10(1) copies in the TvioMLPA probe and 2·7 × 10(2) in McMLPA. The two techniques were sufficiently specific and sensitive for discriminating the target DNA of T. violaceum and M. canis from that of closely related dermatophytes. RCA and MLPA are advantageous in their reliability and ease of operation compared with standard polymerase chain reaction and conventional methods. © 2015 British Association of Dermatologists.

Nanoscale patterning controls inorganic-membrane interface structure

NASA Astrophysics Data System (ADS)

Almquist, Benjamin D.; Verma, Piyush; Cai, Wei; Melosh, Nicholas A.

2011-02-01

The ability to non-destructively integrate inorganic structures into or through biological membranes is essential to realizing full bio-inorganic integration, including arrayed on-chip patch-clamps, drug delivery, and biosensors. Here we explore the role of nanoscale patterning on the strength of biomembrane-inorganic interfaces. AFM measurements show that inorganic probes functionalized with hydrophobic bands with thicknesses complimentary to the hydrophobic lipid bilayer core exhibit strong attachment in the bilayer. As hydrophobic band thickness increases to 2-3 times the bilayer core the interfacial strength decreases, comparable to homogeneously hydrophobic probes. Analytical calculations and molecular dynamics simulations predict a transition between a `fused' interface and a `T-junction' that matches the experimental results, showing lipid disorder and defect formation for thicker bands. These results show that matching biological length scales leads to more intimate bio-inorganic junctions, enabling rational design of non-destructive membrane interfaces.The ability to non-destructively integrate inorganic structures into or through biological membranes is essential to realizing full bio-inorganic integration, including arrayed on-chip patch-clamps, drug delivery, and biosensors. Here we explore the role of nanoscale patterning on the strength of biomembrane-inorganic interfaces. AFM measurements show that inorganic probes functionalized with hydrophobic bands with thicknesses complimentary to the hydrophobic lipid bilayer core exhibit strong attachment in the bilayer. As hydrophobic band thickness increases to 2-3 times the bilayer core the interfacial strength decreases, comparable to homogeneously hydrophobic probes. Analytical calculations and molecular dynamics simulations predict a transition between a `fused' interface and a `T-junction' that matches the experimental results, showing lipid disorder and defect formation for thicker bands. These results show that matching biological length scales leads to more intimate bio-inorganic junctions, enabling rational design of non-destructive membrane interfaces. Electronic supplementary information (ESI) available: Breakthrough rate as a function of force plots for 5 nm, 10 nm and ∞-probes.. See DOI: 10.1039/c0nr00486c

Fluorescent probes for real-time measurement of nitric oxide in living cells.

PubMed

Li, Huili; Wan, Ajun

2015-11-07

Nitric oxide (NO) is an important signaling molecule in biology. Both NO excess and insufficiency have been implicated in numerous physiological and pathological conditions. In order to study the diverse biological roles of NO in cells and tissues, many techniques have been developed for assaying NO. Recently, new generations of fluorescent probes have become indispensible tools for the study of NO biology because of their sensitivity, selectivity, spatiotemporal resolution, and experimental feasibility. Rational application of these probes in the study requires the understanding of the molecular mechanism that the probes are involved in. In this review, we will present an arsenal of fluorescent probes used to detect NO in living cells and animal tissues. We will also discuss the molecular mechanisms, actualities and prospects of fluorescent probes in detecting NO in cell biology.

Development of Thinopyrum ponticum-specific molecular markers and FISH probes based on SLAF-seq technology.

PubMed

Liu, Liqin; Luo, Qiaoling; Teng, Wan; Li, Bin; Li, Hongwei; Li, Yiwen; Li, Zhensheng; Zheng, Qi

2018-05-01

Based on SLAF-seq, 67 Thinopyrum ponticum-specific markers and eight Th. ponticum-specific FISH probes were developed, and these markers and probes could be used for detection of alien chromatin in a wheat background. Decaploid Thinopyrum ponticum (2n = 10x = 70) is a valuable gene reservoir for wheat improvement. Identification of Th. ponticum introgression would facilitate its transfer into diverse wheat genetic backgrounds and its practical utilization in wheat improvement. Based on specific-locus-amplified fragment sequencing (SLAF-seq) technology, 67 new Th. ponticum-specific molecular markers and eight Th. ponticum-specific fluorescence in situ hybridization (FISH) probes have been developed from a tiny wheat-Th. ponticum translocation line. These newly developed molecular markers allowed the detection of Th. ponticum DNA in a variety of materials specifically and steadily at high throughput. According to the hybridization signal pattern, the eight Th. ponticum-specific probes could be divided into two groups. The first group including five dispersed repetitive sequence probes could identify Th. ponticum chromatin more sensitively and accurately than genomic in situ hybridization (GISH). Whereas the second group having three tandem repetitive sequence probes enabled the discrimination of Th. ponticum chromosomes together with another clone pAs1 in wheat-Th. ponticum partial amphiploid Xiaoyan 68.

Multiplex detection of microRNAs by combining molecular beacon probes with T7 exonuclease-assisted cyclic amplification reaction.

PubMed

Liu, Yacui; Zhang, Jiangyan; Tian, Jingxiao; Fan, Xiaofei; Geng, Hao; Cheng, Yongqiang

2017-01-01

A simple, highly sensitive, and specific assay was developed for the homogeneous and multiplex detection of microRNAs (miRNAs) by combining molecular beacon (MB) probes and T7 exonuclease-assisted cyclic amplification. An MB probe with five base pairs in the stem region without special modification can effectively prevent the digestion by T7 exonuclease. Only in the presence of target miRNA is the MB probe hybridized with the target miRNA, and then digested by T7 exonuclease in the 5' to 3' direction. At the same time, the target miRNA is released and subsequently initiates the nuclease-assisted cyclic digestion process, generating enhanced fluorescence signal significantly. The results show that the combination of T7 exonuclease-assisted cyclic amplification reaction and MB probe possesses higher sensitivity for miRNA detection. Moreover, multiplex detection of miRNAs was successfully achieved by designing two MB probes labeled with FAM and Cy3, respectively. As a result, the method opens a new pathway for the sensitive and multiplex detection of miRNAs as well as clinical diagnosis. Graphical Abstract A simple, highly sensitive, and specific assay was developed for the detection of microRNAs by combining molecular beacon probes with T7 exonuclease-assisted cyclic amplification reaction.

Molecular Velcro constructed from polymer loop brushes showing enhanced adhesion force

NASA Astrophysics Data System (ADS)

Zhou, Tian; Han, Biao; Han, Lin; Li, Christopher; Department of Materials Science; Engineering Team; School of Biomedical Engineering, Science; Health Systems Team

2015-03-01

Molecular Velcro is commonly seen in biological systems as the formation of strong physical entanglement at molecular scale could induce strong adhesion, which is crucial to many biological processes. To mimic this structure, we designed, and fabricated polymer loop brushes using polymer single crystals with desired surface functionality and controlled chain folding. Compared with reported loop brushes fabricated using triblock copolymers, the present loop bushes have precise loop sizes, loop grafting density, and well controlled tethering locations on the solid surface. Atomic force microscopy-based force spectroscopy measurements using a polymer chain coated probe reveal that the adhesion force are significantly enhanced on the loop brush surface as compared with its single-strand counterpart. This study directly shows the effect of polymer brush conformation on their properties, and suggests a promising strategy for advanced polymer surface design.

Metal nanoinks as chemically stable surface enhanced scattering (SERS) probes for the analysis of blue BIC ballpoint pens.

PubMed

Alyami, A; Saviello, D; McAuliffe, M A P; Mirabile, A; Lewis, L; Iacopino, D

2017-06-07

Metal nanoinks constituted by Ag nanoparticles and Au nanorods were employed as probes for the Surface Enhanced Raman Scattering (SERS) analysis of a blue BIC ballpoint pen. The dye components of the pen ink were first separated by thin layer chromatography (TLC) and subsequently analysed by SERS at illumination wavelengths of 514 nm and 785 nm. Compared to normal Raman conditions, enhanced spectra were obtained for all separated spots, allowing easy identification of phthalocyanine Blue 38 and triarylene crystal violet in the ink mixture. A combination of effects such as molecular resonance, electromagnetic and chemical effects were the contributing factors to the generation of spectra enhanced compared to normal Raman conditions. Enhancement factors (EFs) between 5 × 10 3 and 3 × 10 6 were obtained, depending on the combination of SERS probes and laser illumination used. In contrast to previous conflicting reports, the metal nanoinks were chemically stable, allowing the collection of reproducible spectra for days after deposition on TLC plates. In addition and in advance to previously reported SERS probes, no need for additional aggregating agents or correction of electrostatic charge was necessary to induce the generation of enhanced SERS spectra.

X-ray circular dichroism signals: a unique probe of local molecular chirality

DOE PAGES

Zhang, Yu; Rouxel, Jeremy R.; Autschbach, Jochen; ...

2017-06-26

Core-resonant circular dichroism (CD) signals are induced by molecular chirality and vanish for achiral molecules and racemic mixtures. The highly localized nature of core excitations makes them ideal probes of local chirality within molecules. Simulations of the circular dichroism spectra of several molecular families illustrate how these signals vary with the electronic coupling to substitution groups, the distance between the X-ray chromophore and the chiral center, geometry, and chemical structure. As a result, clear insight into the molecular structure is obtained through analysis of the X-ray CD spectra.

X-ray circular dichroism signals: a unique probe of local molecular chirality

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yu; Rouxel, Jeremy R.; Autschbach, Jochen

Core-resonant circular dichroism (CD) signals are induced by molecular chirality and vanish for achiral molecules and racemic mixtures. The highly localized nature of core excitations makes them ideal probes of local chirality within molecules. Simulations of the circular dichroism spectra of several molecular families illustrate how these signals vary with the electronic coupling to substitution groups, the distance between the X-ray chromophore and the chiral center, geometry, and chemical structure. As a result, clear insight into the molecular structure is obtained through analysis of the X-ray CD spectra.

CTL-Tumor Cell Interaction: The Generation of Molecular Probes of Monitoring the HLA-A*0201-HER-2/neu Peptide Complex

DTIC Science & Technology

2005-03-01

anti- HLA -A2, -A24, -A28 mAb CR11-351 (13,14); anti- HLA -A2, -A28 mAb KS-1 (14); anti- HLA -B7, - B27 , -Bw42, -Bw54, -Bw55, -Bw56, -Bw67, -Bw73 mAb KS-4 (15...AD Award Number: W81XWH-04-1-0372 TITLE: CTL-Tumor Cell Interaction: The Generation of Molecular Probes of Monitoring the HLA -A*0201-HER-2/neu...AND SUBTITLE 5. FUNDING NUMBERS CTL-Tumor Cell Interaction: The Generation of Molecular W81XWH-04-1-0372 Probes of Monitoring the HLA -A*0201-HER-2/neu

Resonance Raman Probes for Organelle-Specific Labeling in Live Cells

NASA Astrophysics Data System (ADS)

Kuzmin, Andrey N.; Pliss, Artem; Lim, Chang-Keun; Heo, Jeongyun; Kim, Sehoon; Rzhevskii, Alexander; Gu, Bobo; Yong, Ken-Tye; Wen, Shangchun; Prasad, Paras N.

2016-06-01

Raman microspectroscopy provides for high-resolution non-invasive molecular analysis of biological samples and has a breakthrough potential for dissection of cellular molecular composition at a single organelle level. However, the potential of Raman microspectroscopy can be fully realized only when novel types of molecular probes distinguishable in the Raman spectroscopy modality are developed for labeling of specific cellular domains to guide spectrochemical spatial imaging. Here we report on the design of a next generation Raman probe, based on BlackBerry Quencher 650 compound, which provides unprecedentedly high signal intensity through the Resonance Raman (RR) enhancement mechanism. Remarkably, RR enhancement occurs with low-toxic red light, which is close to maximum transparency in the biological optical window. The utility of proposed RR probes was validated for targeting lysosomes in live cultured cells, which enabled identification and subsequent monitoring of dynamic changes in this organelle by Raman imaging.

In Vivo Biomarkers for Targeting Colorectal Neoplasms

PubMed Central

Hsiung, Pei-Lin; Wang, Thomas

2011-01-01

Summary Colorectal carcinoma continues to be a leading cause of cancer morbidity and mortality despite widespread adoption of screening methods. Targeted detection and therapy using recent advances in our knowledge of in vivo cancer biomarkers promise to significantly improve methods for early detection, risk stratification, and therapeutic intervention. The behavior of molecular targets in transformed tissues is being comprehensively assessed using new techniques of gene expression profiling and high throughput analyses. The identification of promising targets is stimulating the development of novel molecular probes, including significant progress in the field of activatable and peptide probes. These probes are being evaluated in small animal models of colorectal neoplasia and recently in the clinic. Furthermore, innovations in optical imaging instrumentation are resulting in the scaling down of size for endoscope compatibility. Advances in target identification, probe development, and novel instruments are progressing rapidly, and the integration of these technologies has a promising future in molecular medicine. PMID:19126961

Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample

NASA Technical Reports Server (NTRS)

Bune, Adris; Kaukler, William; Rose, M. Franklin (Technical Monitor)

2001-01-01

Molecular dynamic (MD) simulations is conducted in order to estimate forces of probe-substrate interaction in the Atomic Force Microscope (AFM). First a review of available molecular dynamic techniques is given. Implementation of MD simulation is based on an object-oriented code developed at the University of Delft. Modeling of the sample material - succinonitrile (SCN) - is based on the Lennard-Jones potentials. For the polystyrene probe an atomic interaction potential is used. Due to object-oriented structure of the code modification of an atomic interaction potential is straight forward. Calculation of melting temperature is used for validation of the code and of the interaction potentials. Various fitting parameters of the probe-substrate interaction potentials are considered, as potentials fitted to certain properties and temperature ranges may not be reliable for the others. This research provides theoretical foundation for an interpretation of actual measurements of an interaction forces using AFM.

Fluorescent hybridization probes for nucleic acid detection.

PubMed

Guo, Jia; Ju, Jingyue; Turro, Nicholas J

2012-04-01

Due to their high sensitivity and selectivity, minimum interference with living biological systems, and ease of design and synthesis, fluorescent hybridization probes have been widely used to detect nucleic acids both in vivo and in vitro. Molecular beacons (MBs) and binary probes (BPs) are two very important hybridization probes that are designed based on well-established photophysical principles. These probes have shown particular applicability in a variety of studies, such as mRNA tracking, single nucleotide polymorphism (SNP) detection, polymerase chain reaction (PCR) monitoring, and microorganism identification. Molecular beacons are hairpin oligonucleotide probes that present distinctive fluorescent signatures in the presence and absence of their target. Binary probes consist of two fluorescently labeled oligonucleotide strands that can hybridize to adjacent regions of their target and generate distinctive fluorescence signals. These probes have been extensively studied and modified for different applications by modulating their structures or using various combinations of fluorophores, excimer-forming molecules, and metal complexes. This review describes the applicability and advantages of various hybridization probes that utilize novel and creative design to enhance their target detection sensitivity and specificity.

A rational approach to elucidate human monoamine oxidase molecular selectivity.

PubMed

Mangiatordi, Giuseppe Felice; Alberga, Domenico; Pisani, Leonardo; Gadaleta, Domenico; Trisciuzzi, Daniela; Farina, Roberta; Carotti, Andrea; Lattanzi, Gianluca; Catto, Marco; Nicolotti, Orazio

2017-04-01

Designing highly selective human monoamine oxidase (hMAO) inhibitors is a challenging goal on the road to a more effective treatment of depression and anxiety (inhibition of hMAO-A isoform) as well as neurodegenerative diseases (inhibition of hMAO-B isoform). To uncover the molecular rationale of hMAOs selectivity, two recently prepared 2H-chromene-2-ones, namely compounds 1 and 2, were herein chosen as molecular probes being highly selective toward hMAO-A and hMAO-B, respectively. We performed molecular dynamics (MD) studies on four different complexes, cross-simulating one at a time the two hMAO-isoforms (dimer embedded in a lipid bilayer) with the two considered probes. Our comparative analysis on the obtained 100ns trajectories discloses a stable H-bond interaction between 1 and Gln215 as crucial for ligand selectivity toward hMAO-A whereas a water-mediated interaction might explain the observed hMAO-B selectivity of compound 2. Such hypotheses are further supported by binding free energy calculations carried out applying the molecular mechanics generalized Born surface area (MM-GBSA) method and allowing us to evaluate the contribution of each residue to the observed isoform selectivity. Taken as whole, this study represents the first attempt to explain at molecular level hMAO isoform selectivity and a valuable yardstick for better addressing the design of new and highly selective MAO inhibitors. Copyright © 2017 Elsevier B.V. All rights reserved.

Rapid detection of Listeria monocytogenes in foods, by a combination of PCR and DNA probe.

PubMed

Ingianni, A; Floris, M; Palomba, P; Madeddu, M A; Quartuccio, M; Pompei, R

2001-10-01

Listeria monocytogenes is a frequent contaminant of water and foods. Its rapid detection is needed before some foods can be prepared for marketing. In this work L. monocytogenes has been searched for in foods, by a combination of polymerase chain reaction (PCR) and a DNA probe. Both PCR and the probe were prepared for recognizing a specific region of the internalin gene, which is responsible for the production of one of the most important pathogenic factors of Listeria. The combined use of PCR and the DNA probe was used for the detection of L. monocytogenes in over 180 environmental and food samples. Several detection methods were compared in this study, namely conventional culture methods; direct PCR; PCR after an enrichment step; a DNA probe alone; a DNA probe after enrichment and another commercially available gene-probe. Finally PCR and the DNA probe were used in series on all the samples collected. When the DNA probe was associated with the PCR, specific and accurate detection of listeria in the samples could be obtained in about a working-day. The present molecular method showed some advantages in terms of rapidity and specificity in comparison to the other aforementioned tests. In addition, it resulted as being easy to handle, even for non-specialized personnel in small diagnostic microbiology laboratories. Copyright 2001 Academic Press.

Competitive Reporter Monitored Amplification (CMA) - Quantification of Molecular Targets by Real Time Monitoring of Competitive Reporter Hybridization

PubMed Central

Ullrich, Thomas; Ermantraut, Eugen; Schulz, Torsten; Steinmetzer, Katrin

2012-01-01

Background State of the art molecular diagnostic tests are based on the sensitive detection and quantification of nucleic acids. However, currently established diagnostic tests are characterized by elaborate and expensive technical solutions hindering the development of simple, affordable and compact point-of-care molecular tests. Methodology and Principal Findings The described competitive reporter monitored amplification allows the simultaneous amplification and quantification of multiple nucleic acid targets by polymerase chain reaction. Target quantification is accomplished by real-time detection of amplified nucleic acids utilizing a capture probe array and specific reporter probes. The reporter probes are fluorescently labeled oligonucleotides that are complementary to the respective capture probes on the array and to the respective sites of the target nucleic acids in solution. Capture probes and amplified target compete for reporter probes. Increasing amplicon concentration leads to decreased fluorescence signal at the respective capture probe position on the array which is measured after each cycle of amplification. In order to observe reporter probe hybridization in real-time without any additional washing steps, we have developed a mechanical fluorescence background displacement technique. Conclusions and Significance The system presented in this paper enables simultaneous detection and quantification of multiple targets. Moreover, the presented fluorescence background displacement technique provides a generic solution for real time monitoring of binding events of fluorescently labelled ligands to surface immobilized probes. With the model assay for the detection of human immunodeficiency virus type 1 and 2 (HIV 1/2), we have been able to observe the amplification kinetics of five targets simultaneously and accommodate two additional hybridization controls with a simple instrument set-up. The ability to accommodate multiple controls and targets into a single assay and to perform the assay on simple and robust instrumentation is a prerequisite for the development of novel molecular point of care tests. PMID:22539973

Carbon nanotubes as in vivo bacterial probes.

PubMed

Bardhan, Neelkanth M; Ghosh, Debadyuti; Belcher, Angela M

2014-09-17

With the rise in antibiotic-resistant infections, non-invasive sensing of infectious diseases is increasingly important. Optical imaging, although safer and simpler, is less developed than other modalities such as radioimaging, due to low availability of target-specific molecular probes. Here we report carbon nanotubes (SWNTs) as bacterial probes for fluorescence imaging of pathogenic infections. We demonstrate that SWNTs functionalized using M13 bacteriophage (M13-SWNT) can distinguish between F'-positive and F'-negative bacterial strains. Moreover, through one-step modification, we attach an anti-bacterial antibody on M13-SWNT, making it easily tunable for sensing specific F'-negative bacteria. We illustrate detection of Staphylococcus aureus intramuscular infections, with ~3.4 × enhancement in fluorescence intensity over background. SWNT imaging presents lower signal spread ~0.08 × and higher signal amplification ~1.4 × , compared with conventional dyes. We show the probe offers greater ~5.7 × enhancement in imaging of S. aureus infective endocarditis. These biologically functionalized, aqueous-dispersed, actively targeted, modularly tunable SWNT probes offer new avenues for exploration of deeply buried infections.

Carbon nanotubes as in vivo bacterial probes

NASA Astrophysics Data System (ADS)

Bardhan, Neelkanth M.; Ghosh, Debadyuti; Belcher, Angela M.

2014-09-01

With the rise in antibiotic-resistant infections, non-invasive sensing of infectious diseases is increasingly important. Optical imaging, although safer and simpler, is less developed than other modalities such as radioimaging, due to low availability of target-specific molecular probes. Here we report carbon nanotubes (SWNTs) as bacterial probes for fluorescence imaging of pathogenic infections. We demonstrate that SWNTs functionalized using M13 bacteriophage (M13-SWNT) can distinguish between F‧-positive and F‧-negative bacterial strains. Moreover, through one-step modification, we attach an anti-bacterial antibody on M13-SWNT, making it easily tunable for sensing specific F‧-negative bacteria. We illustrate detection of Staphylococcus aureus intramuscular infections, with ~3.4 × enhancement in fluorescence intensity over background. SWNT imaging presents lower signal spread ~0.08 × and higher signal amplification ~1.4 × , compared with conventional dyes. We show the probe offers greater ~5.7 × enhancement in imaging of S. aureus infective endocarditis. These biologically functionalized, aqueous-dispersed, actively targeted, modularly tunable SWNT probes offer new avenues for exploration of deeply buried infections.

Carbon Nanotubes as in vivo Bacterial Probes

PubMed Central

Bardhan, Neelkanth M.; Ghosh, Debadyuti; Belcher, Angela M.

2014-01-01

With the rise in antibiotic-resistant infections, noninvasive sensing of infectious diseases is increasingly important. Optical imaging, while safer and simpler, is less developed than other modalities like radioimaging; due to low availability of target-specific molecular probes. Here, we report carbon nanotubes (SWNTs) as bacterial probes for fluorescence imaging of pathogenic infections. We demonstrate that SWNTs functionalized using M13 bacteriophage (M13-SWNT) can distinguish between F'-positive and F'-negative bacterial strains. Moreover, through one-step modification, we attach an anti-bacterial antibody on M13-SWNT, making it easily tunable for sensing specific F’-negative bacteria. We illustrate detection of Staphylococcus aureus intramuscular infections, with ~3.4× enhancement in fluorescence intensity over background. SWNT imaging presents lower signal spread ~0.08×, and higher signal amplification ~1.4×, compared to conventional dyes. We show the probe offers greater ~5.7× enhancement in imaging of S. aureus infective endocarditis. These biologically-functionalized, aqueous-dispersed, actively-targeted, modularly-tunable SWNT probes offer new avenues for exploration of deeply-buried infections. PMID:25230005

Charge transport in molecular junctions: From tunneling to hopping with the probe technique

NASA Astrophysics Data System (ADS)

Kilgour, Michael; Segal, Dvira

2015-07-01

We demonstrate that a simple phenomenological approach can be used to simulate electronic conduction in molecular wires under thermal effects induced by the surrounding environment. This "Landauer-Büttiker's probe technique" can properly replicate different transport mechanisms, phase coherent nonresonant tunneling, ballistic behavior, and hopping conduction. Specifically, our simulations with the probe method recover the following central characteristics of charge transfer in molecular wires: (i) the electrical conductance of short wires falls off exponentially with molecular length, a manifestation of the tunneling (superexchange) mechanism. Hopping dynamics overtakes superexchange in long wires demonstrating an ohmic-like behavior. (ii) In off-resonance situations, weak dephasing effects facilitate charge transfer, but under large dephasing, the electrical conductance is suppressed. (iii) At high enough temperatures, kBT/ɛB > 1/25, with ɛB as the molecular-barrier height, the current is enhanced by a thermal activation (Arrhenius) factor. However, this enhancement takes place for both coherent and incoherent electrons and it does not readily indicate on the underlying mechanism. (iv) At finite-bias, dephasing effects may impede conduction in resonant situations. We further show that memory (non-Markovian) effects can be implemented within the Landauer-Büttiker's probe technique to model the interaction of electrons with a structured environment. Finally, we examine experimental results of electron transfer in conjugated molecular wires and show that our computational approach can reasonably reproduce reported values to provide mechanistic information.

Continuous sensing of tumor-targeted molecular probes with a vertical cavity surface emitting laser-based biosensor

NASA Astrophysics Data System (ADS)

Parashurama, Natesh; O'Sullivan, Thomas D.; De La Zerda, Adam; El Kalassi, Pascale; Cho, Seongjae; Liu, Hongguang; Teed, Robert; Levy, Hart; Rosenberg, Jarrett; Cheng, Zhen; Levi, Ofer; Harris, James S.; Gambhir, Sanjiv S.

2012-11-01

Molecular optical imaging is a widespread technique for interrogating molecular events in living subjects. However, current approaches preclude long-term, continuous measurements in awake, mobile subjects, a strategy crucial in several medical conditions. Consequently, we designed a novel, lightweight miniature biosensor for in vivo continuous optical sensing. The biosensor contains an enclosed vertical-cavity surface-emitting semiconductor laser and an adjacent pair of near-infrared optically filtered detectors. We employed two sensors (dual sensing) to simultaneously interrogate normal and diseased tumor sites. Having established the sensors are precise with phantom and in vivo studies, we performed dual, continuous sensing in tumor (human glioblastoma cells) bearing mice using the targeted molecular probe cRGD-Cy5.5, which targets αVβ3 cell surface integrins in both tumor neovasculature and tumor. The sensors capture the dynamic time-activity curve of the targeted molecular probe. The average tumor to background ratio after signal calibration for cRGD-Cy5.5 injection is approximately 2.43±0.95 at 1 h and 3.64±1.38 at 2 h (N=5 mice), consistent with data obtained with a cooled charge coupled device camera. We conclude that our novel, portable, precise biosensor can be used to evaluate both kinetics and steady state levels of molecular probes in various disease applications.

Continuous sensing of tumor-targeted molecular probes with a vertical cavity surface emitting laser-based biosensor

PubMed Central

Parashurama, Natesh; O’Sullivan, Thomas D.; De La Zerda, Adam; El Kalassi, Pascale; Cho, Seongjae; Liu, Hongguang; Teed, Robert; Levy, Hart; Rosenberg, Jarrett; Cheng, Zhen; Levi, Ofer; Harris, James S.

2012-01-01

Abstract. Molecular optical imaging is a widespread technique for interrogating molecular events in living subjects. However, current approaches preclude long-term, continuous measurements in awake, mobile subjects, a strategy crucial in several medical conditions. Consequently, we designed a novel, lightweight miniature biosensor for in vivo continuous optical sensing. The biosensor contains an enclosed vertical-cavity surface-emitting semiconductor laser and an adjacent pair of near-infrared optically filtered detectors. We employed two sensors (dual sensing) to simultaneously interrogate normal and diseased tumor sites. Having established the sensors are precise with phantom and in vivo studies, we performed dual, continuous sensing in tumor (human glioblastoma cells) bearing mice using the targeted molecular probe cRGD-Cy5.5, which targets αVβ3 cell surface integrins in both tumor neovasculature and tumor. The sensors capture the dynamic time-activity curve of the targeted molecular probe. The average tumor to background ratio after signal calibration for cRGD-Cy5.5 injection is approximately 2.43±0.95 at 1 h and 3.64±1.38 at 2 h (N=5 mice), consistent with data obtained with a cooled charge coupled device camera. We conclude that our novel, portable, precise biosensor can be used to evaluate both kinetics and steady state levels of molecular probes in various disease applications. PMID:23123976

In situ nanoplasmonic probing of enzymatic activity of monolayer-confined glucose oxidase on colloidal nanoparticles.

PubMed

He, Haili; Xu, Xiaolong; Wu, Haoxi; Zhai, Yujuan; Jin, Yongdong

2013-05-07

In situ probing protein-particle interactions and activities of proteins on colloidal nanoparticle (NP) surfaces is a long-standing key challenge in understanding the nanobio interfaces and virtually important for a variety of biological and biomedical applications. The interactions of NPs with proteins, for instance, are known to form NP bioconjugates or protein coronas; protein surface immobilization and molecular layer-by-layer deposition techniques are widely used, but a clear understanding of the confinement effect on protein activity by molecular coating, at the monolayer level, remains poorly understood. We explore here a novel approach, using colloidal plasmonic nanocomplexes coated with glucose oxidase (GOx) as self-sensing nanoprobes for in situ optical probing of surface-confined enzymatic activity, which is at least 1-2 orders of magnitude more sensitive than standard colorimetric assays for detecting GOx activity. We found that enzymatic activity of monolayer-confined GOx on colloidal NPs was significantly enhanced as compared with free GOx (also proved by conformational changes from circular dichroism studies), with a low apparent Michaelis-Menten constant Km of ~0.115 mM and high turnover kcat/Km of ~8394 M(-1)·s(-1); compared with the "anchored-type" suspending GOx, the outmost polyelectrolyte monolayer-protected "sandwiched-type" GOx exhibits significantly improved enzymatic activities toward higher temperatures and wider pH range. This finding is of fundamental important and instructive for safe use of such nanomaterials for bioapplications.

Probing molecular dynamics in solution with x-ray valence-to-core spectroscopy

NASA Astrophysics Data System (ADS)

Doumy, Gilles; March, Anne Marie; Tu, Ming-Feng; Al Haddad, Andre; Southworth, Stephen; Young, Linda; Walko, Donald; Bostedt, Christoph

2017-04-01

Hard X-ray spectroscopies are powerful tools for probing the electronic and geometric structure of molecules in complex or disordered systems and have been particularly useful for studying molecules in the solution phase. They are element specific, sensitive to the electronic structure and the local arrangements of surrounding atoms of the element being selectively probed. When combined in a pump-probe scheme with ultrafast lasers, X-ray spectroscopies can be used to track the evolution of structural changes that occur after photoexcitation. Efficient use of hard x-ray radiation coming from high brilliance synchrotrons and upcoming high repetition rate X-ray Free Electron Lasers requires MHz repetition rate lasers and data acquisition systems. High information content Valence-to-Core x-ray emission is directly sensitive to the molecular orbitals involved in photochemistry. We report on recent progress towards fully enabling this photon-hungry technique for the study of time-resolved molecular dynamics, including efficient detection and use of polychromatic x-ray micro-probe at the Advanced Photon Source. Work was supported by the U.S. Department of Energy, Office of Science, Chemical Sciences, Geosciences, and Biosciences Division.

Advanced electric-field scanning probe lithography on molecular resist using active cantilever

NASA Astrophysics Data System (ADS)

Kaestner, Marcus; Aydogan, Cemal; Lipowicz, Hubert-Seweryn; Ivanov, Tzvetan; Lenk, Steve; Ahmad, Ahmad; Angelov, Tihomir; Reum, Alexander; Ishchuk, Valentyn; Atanasov, Ivaylo; Krivoshapkina, Yana; Hofer, Manuel; Holz, Mathias; Rangelow, Ivo W.

2015-03-01

The routine "on demand" fabrication of features smaller than 10 nm opens up new possibilities for the realization of many novel nanoelectronic, NEMS, optical and bio-nanotechnology-based devices. Based on the thermally actuated, piezoresistive cantilever technology we have developed a first prototype of a scanning probe lithography (SPL) platform able to image, inspect, align and pattern features down to single digit nano regime. The direct, mask-less patterning of molecular resists using active scanning probes represents a promising path circumventing the problems in today's radiation-based lithography. Here, we present examples of practical applications of the previously published electric field based, current-controlled scanning probe lithography on molecular glass resist calixarene by using the developed tabletop SPL system. We demonstrate the application of a step-and-repeat scanning probe lithography scheme including optical as well as AFM based alignment and navigation. In addition, sequential read-write cycle patterning combining positive and negative tone lithography is shown. We are presenting patterning over larger areas (80 x 80 μm) and feature the practical applicability of the lithographic processes.

Genetically Encoded Molecular Tension Probe for Tracing Protein-Protein Interactions in Mammalian Cells.

PubMed

Kim, Sung Bae; Nishihara, Ryo; Citterio, Daniel; Suzuki, Koji

2016-02-17

Optical imaging of protein-protein interactions (PPIs) facilitates comprehensive elucidation of intracellular molecular events. We demonstrate an optical measure for visualizing molecular tension triggered by any PPI in mammalian cells. Twenty-three kinds of candidate designs were fabricated, in which a full-length artificial luciferase (ALuc) was sandwiched between two model proteins of interest, e.g., FKBP and FRB. One of the designs greatly enhanced the bioluminescence in response to varying concentrations of rapamycin. It is confirmed with negative controls that the elevated bioluminescence is solely motivated from the molecular tension. The probe design was further modified toward eliminating the C-terminal end of ALuc and was found to improve signal-to-background ratios, named "a combinational probe". The utilities were elucidated with detailed substrate selectivity, bioluminescence imaging of live cells, and different PPI models. This study expands capabilities of luciferases as a tool for analyses of molecular dynamics and cell signaling in living subjects.

Molecular Dynamics in Mixed Solvents Reveals Protein-Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions.

PubMed

Arcon, Juan Pablo; Defelipe, Lucas A; Modenutti, Carlos P; López, Elias D; Alvarez-Garcia, Daniel; Barril, Xavier; Turjanski, Adrián G; Martí, Marcelo A

2017-04-24

One of the most important biological processes at the molecular level is the formation of protein-ligand complexes. Therefore, determining their structure and underlying key interactions is of paramount relevance and has direct applications in drug development. Because of its low cost relative to its experimental sibling, molecular dynamics (MD) simulations in the presence of different solvent probes mimicking specific types of interactions have been increasingly used to analyze protein binding sites and reveal protein-ligand interaction hot spots. However, a systematic comparison of different probes and their real predictive power from a quantitative and thermodynamic point of view is still missing. In the present work, we have performed MD simulations of 18 different proteins in pure water as well as water mixtures of ethanol, acetamide, acetonitrile and methylammonium acetate, leading to a total of 5.4 μs simulation time. For each system, we determined the corresponding solvent sites, defined as space regions adjacent to the protein surface where the probability of finding a probe atom is higher than that in the bulk solvent. Finally, we compared the identified solvent sites with 121 different protein-ligand complexes and used them to perform molecular docking and ligand binding free energy estimates. Our results show that combining solely water and ethanol sites allows sampling over 70% of all possible protein-ligand interactions, especially those that coincide with ligand-based pharmacophoric points. Most important, we also show how the solvent sites can be used to significantly improve ligand docking in terms of both accuracy and precision, and that accurate predictions of ligand binding free energies, along with relative ranking of ligand affinity, can be performed.

High prevalence of Salmonella spp. in wastewater reused for irrigation assessed by molecular methods.

PubMed

Santiago, Paula; Jiménez-Belenguer, Ana; García-Hernández, Jorge; Estellés, Rosa Montes; Hernández Pérez, Manuel; Castillo López, M Angeles; Ferrús, María Antonia; Moreno, Yolanda

2018-01-01

Salmonella spp. is one of the most important causal agents of food-borne illness in developed countries and its presence in irrigation water poses a risk to public health. Its detection in environmental samples is not easy when culture methods are used, and molecular techniques such as PCR or ribosomal rRNA probe hybridization (Fluorescent in situ Hybridization, FISH) are outstanding alternatives. The aim of this work was to determine the environmental risk due to the presence of Salmonella spp. in wastewater by culture, PCR and FISH. A new specific rDNA probe for Salmonella was designed and its efficiency was compared with the rest of methods Serotype and antibiotic resistance of isolated strains were determined. Forty-five wastewater samples (collected from two secondary wastewater treatment plants) were analysed. Salmonella strains were isolated in 24 wastewater samples (53%), two of them after disinfection treatment. Twenty-three Salmonella strains exhibited resistance to one or more antimicrobial agent. Analysis of wastewater samples yielded PCR positive results for Salmonella in 28 out of the 45 wastewater samples (62%). FISH analysis allowed for the detection of Salmonella in 27 (60%) samples. By using molecular methods, Salmonella was detected in four samples after disinfection treatment. These results show the prevalence of Salmonella in reclaimed wastewater even after U.V. disinfection, what is a matter of public health concern, the high rates of resistance to antibiotics and the adequacy of molecular methods for its rapid detection. FISH method, with SA23 probe developed and assayed in this work provides a tool for detecting Salmonella in water within few hours, with a high rate of effectiveness. Copyright © 2017 Elsevier GmbH. All rights reserved.

Multifunctional gadolinium-based dendritic macromolecules as liver targeting imaging probes.

PubMed

Luo, Kui; Liu, Gang; He, Bin; Wu, Yao; Gong, Qingyong; Song, Bin; Ai, Hua; Gu, Zhongwei

2011-04-01

The quest for highly efficient and safe contrast agents has become the key factor for successful application of magnetic resonance imaging (MRI). The gadolinium (Gd) based dendritic macromolecules, with precise and tunable nanoscopic sizes, are excellent candidates as multivalent MRI probes. In this paper, a novel series of Gd-based multifunctional peptide dendritic probes (generation 2, 3, and 4) possessing highly controlled structures and single molecular weight were designed and prepared as liver MRI probes. These macromolecular Gd-ligand agents exhibited up to 3-fold increase in T(1) relaxivity comparing to Gd-DTPA complexes. No obvious in vitro cytotoxicity was observed from the measured concentrations. These dendritic probes were further functionalized with multiple galactosyl moieties and led to much higher cell uptake in vitro as demonstrated in T(1)-weighted scans. During in vivo animal studies, the probes provided better signal intensity (SI) enhancement in mouse liver, especially at 60 min post-injection, with the most efficient enhancement from the galactosyl moiety decorated third generation dendrimer. The imaging results were verified with analysis of Gd content in liver tissues. The design strategy of multifunctional Gd-ligand peptide dendritic macromolecules in this study may be used for developing other sensitive MRI probes with targeting capability. Copyright © 2011 Elsevier Ltd. All rights reserved.

Electron paramagnetic resonance studies of slowly tumbling vanadyl spin probes in nematic liquid crystals

NASA Technical Reports Server (NTRS)

Bruno, G. V.; Harrington, J. K.; Eastman, M. P.

1978-01-01

The purposes of this vanadyl spin probe study are threefold: (1) to establish when the breakdown of motionally narrowed formulas occurs; (2) to analyze the experimental vanadyl EPR line shapes by the stochastic Lioville method as developed by Polnaszek et al. (1973) for slow tumbling in an anisotropic liquid; and (3) to compare the vanadyl probe study results with those of Polnaszek and Freed (1975). Spectral EPR line shapes are simulated for experimental spectra of vanadyl acetylacetonate (VOAA) in nematic liquid crystal butyl p-(p-ethoxyphenoxycarbonyl) phenyl carbonate (BEPC) and Phase V of EM laboratories. It is shown that the use of typical vanadyl complexes as spin probes for nematic liquid crystals simplifies the theoretical analysis and the subsequent interpretation. Guidelines for the breakdown of motionally narrowed formulas are established. Both the slow tumbling aspects and the effects of non-Brownian rotation should be resolved in order to extract quantitative information about molecular ordering and rotational mobility.

Progress in molecular imaging in endoscopy and endomicroscopy for cancer imaging

PubMed Central

Khondee, Supang; Wang, Thomas D.

2014-01-01

Imaging is an essential tool for effective cancer management. Endoscopes are important medical instruments for performing in vivo imaging in hollow organs. Early detection of cancer can be achieved with surveillance using endoscopy, and has been shown to reduce mortality and to improve outcomes. Recently, great advancements have been made in endoscopic instruments, including new developments in optical designs, light sources, optical fibers, miniature scanners, and multimodal systems, allowing for improved resolution, greater tissue penetration, and multispectral imaging. In addition, progress has been made in the development of highly-specific optical probes, allowing for improved specificity for molecular targets. Integration of these new endoscopic instruments with molecular probes provides a unique opportunity for significantly improving patient outcomes and has potential to further improve early detection, image guided therapy, targeted therapy, and personalized medicine. This work summarizes current and evolving endoscopic technologies, and provides an overview of various promising optical molecular probes. PMID:23502247

A ratiometric fluorescent molecular probe for visualization of mitochondrial temperature in living cells.

PubMed

Homma, Mitsumasa; Takei, Yoshiaki; Murata, Atsushi; Inoue, Takafumi; Takeoka, Shinji

2015-04-11

Mitochondrial thermodynamics is the key to understand cellular activities related to homeostasis and energy balance. Here, we report the first ratiometric fluorescent molecular probe (Mito-RTP) that is selectively localized in the mitochondria and visualize the temperature. We confirmed that Mito-RTP could work as a ratiometric thermometer in a cuvette and living cells.

Activatable clinical fluorophore-quencher antibody pairs as dual molecular probes for the enhanced specificity of image-guided surgery

NASA Astrophysics Data System (ADS)

Obaid, Girgis; Spring, Bryan Q.; Bano, Shazia; Hasan, Tayyaba

2017-12-01

The emergence of fluorescently labeled therapeutic antibodies has given rise to molecular probes for image-guided surgery. However, the extraneous interstitial presence of an unbound and nonspecifically accumulated probe gives rise to false-positive detection of tumor tissue and margins. Thus, the concept of tumor-cell activation of smart probes provides a potentially superior mechanism of delineating tumor margins as well as small tumor deposits. The combination of molecular targeting with intracellular activation circumvents the presence of extracellular, nonspecific signals of targeted probe accumulation. Here, we present a demonstration of the clinical antibodies cetuximab (cet, anti-EGFR mAb) and trastuzumab (trast, anti-HER-2 mAb) conjugated to Alexa Fluor molecules and IRDye QC-1 quencher optimized at the ratio of 1∶2∶6 to provide the greatest degree of proteolytic fluorescence activation, synonymous with intracellular lysosomal degradation. The cet-AF-Q-C1 conjugate (1∶2∶6) provides up to 9.8-fold proteolytic fluorescence activation. By preparing a spectrally distinct, irrelevant sham IgG-AF-QC-1 conjugate, a dual-activatable probe approach is shown to enhance the specificity of imaging within an orthotopic AsPC-1 pancreatic cancer xenograft model. The dual-activatable approach warrants expedited clinical translation to improve the specificity of image-guided surgery by spectrally decomposing specific from nonspecific probe accumulation, binding, and internalization.

Picosecond Transient Photoconductivity in Functionalized Pentacene Molecular Crystals Probed by Terahertz Pulse Spectroscopy

NASA Astrophysics Data System (ADS)

Hegmann, F. A.; Tykwinski, R. R.; Lui, K. P.; Bullock, J. E.; Anthony, J. E.

2002-11-01

We have measured transient photoconductivity in functionalized pentacene molecular crystals using ultrafast optical pump-terahertz probe techniques. The single crystal samples were excited using 800nm, 100fs pulses, and the change in transmission of time-delayed, subpicosecond terahertz pulses was used to probe the photoconducting state over a temperature range from 10 to 300K. A subpicosecond rise in photoconductivity is observed, suggesting that mobile carriers are a primary photoexcitation. At times longer than 4ps, a power-law decay is observed consistent with dispersive transport.

Molecular cytogenetics using fluorescence in situ hybridization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gray, J.W.; Kuo, Wen-Lin; Lucas, J.

1990-12-07

Fluorescence in situ hybridization (FISH) with chromosome-specific probes enables several new areas of cytogenetic investigation by allowing visual determination of the presence and normality of specific genetic sequences in single metaphase or interphase cells. in this approach, termed molecular cytogenetics, the genetic loci to be analyzed are made microscopically visible in single cells using in situ hybridization with nucleic acid probes specific to these loci. To accomplish this, the DNA in the target cells is made single stranded by thermal denaturation and incubated with single-stranded, chemically modified probe under conditions where the probe will anneal only with DNA sequences tomore » which it has high DNA sequence homology. The bound probe is then made visible by treatment with a fluorescent reagent such as fluorescein that binds to the chemical modification carried by the probe. The DNA to which the probe does not bind is made visible by staining with a dye such as propidium iodide that fluoresces at a wavelength different from that of the reagent used for probe visualization. We show in this report that probes are now available that make this technique useful for biological dosimetry, prenatal diagnosis and cancer biology. 31 refs., 3 figs.« less

Report on the Current Inventory of the Toolbox for Plant Cell Wall Analysis: Proteinaceous and Small Molecular Probes

PubMed Central

Rydahl, Maja G.; Hansen, Aleksander R.; Kračun, Stjepan K.; Mravec, Jozef

2018-01-01

Plant cell walls are highly complex structures composed of diverse classes of polysaccharides, proteoglycans, and polyphenolics, which have numerous roles throughout the life of a plant. Significant research efforts aim to understand the biology of this cellular organelle and to facilitate cell-wall-based industrial applications. To accomplish this, researchers need to be provided with a variety of sensitive and specific detection methods for separate cell wall components, and their various molecular characteristics in vitro as well as in situ. Cell wall component-directed molecular detection probes (in short: cell wall probes, CWPs) are an essential asset to the plant glycobiology toolbox. To date, a relatively large set of CWPs has been produced—mainly consisting of monoclonal antibodies, carbohydrate-binding modules, synthetic antibodies produced by phage display, and small molecular probes. In this review, we summarize the state-of-the-art knowledge about these CWPs; their classification and their advantages and disadvantages in different applications. In particular, we elaborate on the recent advances in non-conventional approaches to the generation of novel CWPs, and identify the remaining gaps in terms of target recognition. This report also highlights the addition of new “compartments” to the probing toolbox, which is filled with novel chemical biology tools, such as metabolic labeling reagents and oligosaccharide conjugates. In the end, we also forecast future developments in this dynamic field. PMID:29774041

Probing energetics of Abeta fibril elongation by molecular dynamics simulations.

PubMed

Takeda, Takako; Klimov, Dmitri K

2009-06-03

Using replica exchange molecular dynamics simulations and an all-atom implicit solvent model, we probed the energetics of Abeta(10-40) fibril growth. The analysis of the interactions between incoming Abeta peptides and the fibril led us to two conclusions. First, considerable variations in fibril binding propensities are observed along the Abeta sequence. The peptides in the fibril and those binding to its edge interact primarily through their N-termini. Therefore, the mutations affecting the Abeta positions 10-23 are expected to have the largest impact on fibril elongation compared with those occurring in the C-terminus and turn. Second, we performed weak perturbations of the binding free energy landscape by scanning partial deletions of side-chain interactions at various Abeta sequence positions. The results imply that strong side-chain interactions--in particular, hydrophobic contacts--impede fibril growth by favoring disordered docking of incoming peptides. Therefore, fibril elongation may be promoted by moderate reduction of Abeta hydrophobicity. The comparison with available experimental data is presented.

Tracking reaction dynamics in solution by pump-probe X-ray absorption spectroscopy and X-ray liquidography (solution scattering).

PubMed

Kim, Jeongho; Kim, Kyung Hwan; Oang, Key Young; Lee, Jae Hyuk; Hong, Kiryong; Cho, Hana; Huse, Nils; Schoenlein, Robert W; Kim, Tae Kyu; Ihee, Hyotcherl

2016-03-07

Characterization of transient molecular structures formed during chemical and biological processes is essential for understanding their mechanisms and functions. Over the last decade, time-resolved X-ray liquidography (TRXL) and time-resolved X-ray absorption spectroscopy (TRXAS) have emerged as powerful techniques for molecular and electronic structural analysis of photoinduced reactions in the solution phase. Both techniques make use of a pump-probe scheme that consists of (1) an optical pump pulse to initiate a photoinduced process and (2) an X-ray probe pulse to monitor changes in the molecular structure as a function of time delay between pump and probe pulses. TRXL is sensitive to changes in the global molecular structure and therefore can be used to elucidate structural changes of reacting solute molecules as well as the collective response of solvent molecules. On the other hand, TRXAS can be used to probe changes in both local geometrical and electronic structures of specific X-ray-absorbing atoms due to the element-specific nature of core-level transitions. These techniques are complementary to each other and a combination of the two methods will enhance the capability of accurately obtaining structural changes induced by photoexcitation. Here we review the principles of TRXL and TRXAS and present recent application examples of the two methods for studying chemical and biological processes in solution. Furthermore, we briefly discuss the prospect of using X-ray free electron lasers for the two techniques, which will allow us to keep track of structural dynamics on femtosecond time scales in various solution-phase molecular reactions.

Design and verification of a pangenome microarray oligonucleotide probe set for Dehalococcoides spp.

PubMed

Hug, Laura A; Salehi, Maryam; Nuin, Paulo; Tillier, Elisabeth R; Edwards, Elizabeth A

2011-08-01

Dehalococcoides spp. are an industrially relevant group of Chloroflexi bacteria capable of reductively dechlorinating contaminants in groundwater environments. Existing Dehalococcoides genomes revealed a high level of sequence identity within this group, including 98 to 100% 16S rRNA sequence identity between strains with diverse substrate specificities. Common molecular techniques for identification of microbial populations are often not applicable for distinguishing Dehalococcoides strains. Here we describe an oligonucleotide microarray probe set designed based on clustered Dehalococcoides genes from five different sources (strain DET195, CBDB1, BAV1, and VS genomes and the KB-1 metagenome). This "pangenome" probe set provides coverage of core Dehalococcoides genes as well as strain-specific genes while optimizing the potential for hybridization to closely related, previously unknown Dehalococcoides strains. The pangenome probe set was compared to probe sets designed independently for each of the five Dehalococcoides strains. The pangenome probe set demonstrated better predictability and higher detection of Dehalococcoides genes than strain-specific probe sets on nontarget strains with <99% average nucleotide identity. An in silico analysis of the expected probe hybridization against the recently released Dehalococcoides strain GT genome and additional KB-1 metagenome sequence data indicated that the pangenome probe set performs more robustly than the combined strain-specific probe sets in the detection of genes not included in the original design. The pangenome probe set represents a highly specific, universal tool for the detection and characterization of Dehalococcoides from contaminated sites. It has the potential to become a common platform for Dehalococcoides-focused research, allowing meaningful comparisons between microarray experiments regardless of the strain examined.

Effect of Molecular Crowding on the Response of an Electrochemical DNA Sensor

PubMed Central

Ricci, Francesco; Lai, Rebecca Y.; Heeger, Alan J.; Plaxco, Kevin W.; Sumner, James J.

2009-01-01

E-DNA sensors, the electrochemical equivalent of molecular beacons, appear to be a promising means of detecting oligonucleotides. E-DNA sensors are comprised of a redox-modified (here, methylene blue or ferrocene) DNA stem-loop covalently attached to an interrogating electrode. Because E-DNA signaling arises due to binding-induced changes in the conformation of the stem-loop probe, it is likely sensitive to the nature of the molecular packing on the electrode surface. Here we detail the effects of probe density, target length, and other aspects of molecular crowding on the signaling properties, specificity, and response time of a model E-DNA sensor. We find that the highest signal suppression is obtained at the highest probe densities investigated, and that greater suppression is observed with longer and bulkier targets. In contrast, sensor equilibration time slows monotonically with increasing probe density, and the specificity of hybridization is not significantly affected. In addition to providing insight into the optimization of electrochemical DNA sensors, these results suggest that E-DNA signaling arises due to hybridization-linked changes in the rate, and thus efficiency, with which the redox moiety collides with the electrode and transfers electrons. PMID:17488132

Selection of turning-on fluorogenic probe as protein-specific detector obtained via the 10BASEd-T

NASA Astrophysics Data System (ADS)

Uematsu, Shuta; Midorikawa, Taiki; Ito, Yuji; Taki, Masumi

2017-01-01

In order to obtain a molecular probe for specific protein detection, we have synthesized fluorogenic probe library of vast diversity on bacteriophage T7 via the gp10 based-thioetherification (10BASEd-T). A remarkable turning- on probe which is excitable by widely applicable visible light was selected from the library.

A Single Molecular Beacon Probe Is Sufficient for the Analysis of Multiple Nucleic Acid Sequences

PubMed Central

Gerasimova, Yulia V.; Hayson, Aaron; Ballantyne, Jack; Kolpashchikov, Dmitry M.

2010-01-01

Molecular beacon (MB) probes are dual-labeled hairpin-shaped oligodeoxyribonucleotides that are extensively used for real-time detection of specific RNA/DNA analytes. In the MB probe, the loop fragment is complementary to the analyte: therefore, a unique probe is required for the analysis of each new analyte sequence. The conjugation of an oligonucleotide with two dyes and subsequent purification procedures add to the cost of MB probes, thus reducing their application in multiplex formats. Here we demonstrate how one MB probe can be used for the analysis of an arbitrary nucleic acid. The approach takes advantage of two oligonucleotide adaptor strands, each of which contains a fragment complementary to the analyte and a fragment complementary to an MB probe. The presence of the analyte leads to association of MB probe and the two DNA strands in quadripartite complex. The MB probe fluorescently reports the formation of this complex. In this design, the MB does not bind the analyte directly; therefore, the MB sequence is independent of the analyte. In this study one universal MB probe was used to genotype three human polymorphic sites. This approach promises to reduce the cost of multiplex real-time assays and improve the accuracy of single-nucleotide polymorphism genotyping. PMID:20665615

Institute for Molecular Medicine Research Program

DOE Office of Scientific and Technical Information (OSTI.GOV)

Phelps, Michael E

2012-12-14

The objectives of the project are the development of new Positron Emission Tomography (PET) imaging instrumentation, chemistry technology platforms and new molecular imaging probes to examine the transformations from normal cellular and biological processes to those of disease in pre-clinical animal models. These technology platforms and imaging probes provide the means to: 1. Study the biology of disease using pre-clinical mouse models and cells. 2. Develop molecular imaging probes for imaging assays of proteins in pre-clinical models. 3. Develop imaging assays in pre-clinical models to provide to other scientists the means to guide and improve the processes for discovering newmore » drugs. 4. Develop imaging assays in pre-clinical models for others to use in judging the impact of drugs on the biology of disease.« less

Molecular inversion probe assay.

PubMed

Absalan, Farnaz; Ronaghi, Mostafa

2007-01-01

We have described molecular inversion probe technologies for large-scale genetic analyses. This technique provides a comprehensive and powerful tool for the analysis of genetic variation and enables affordable, large-scale studies that will help uncover the genetic basis of complex disease and explain the individual variation in response to therapeutics. Major applications of the molecular inversion probes (MIP) technologies include targeted genotyping from focused regions to whole-genome studies, and allele quantification of genomic rearrangements. The MIP technology (used in the HapMap project) provides an efficient, scalable, and affordable way to score polymorphisms in case/control populations for genetic studies. The MIP technology provides the highest commercially available multiplexing levels and assay conversion rates for targeted genotyping. This enables more informative, genome-wide studies with either the functional (direct detection) approach or the indirect detection approach.

Lateral Membrane Diffusion Modulated by a Minimal Actin Cortex

PubMed Central

Heinemann, Fabian; Vogel, Sven K.; Schwille, Petra

2013-01-01

Diffusion of lipids and proteins within the cell membrane is essential for numerous membrane-dependent processes including signaling and molecular interactions. It is assumed that the membrane-associated cytoskeleton modulates lateral diffusion. Here, we use a minimal actin cortex to directly study proposed effects of an actin meshwork on the diffusion in a well-defined system. The lateral diffusion of a lipid and a protein probe at varying densities of membrane-bound actin was characterized by fluorescence correlation spectroscopy (FCS). A clear correlation of actin density and reduction in mobility was observed for both the lipid and the protein probe. At high actin densities, the effect on the protein probe was ∼3.5-fold stronger compared to the lipid. Moreover, addition of myosin filaments, which contract the actin mesh, allowed switching between fast and slow diffusion in the minimal system. Spot variation FCS was in accordance with a model of fast microscopic diffusion and slower macroscopic diffusion. Complementing Monte Carlo simulations support the analysis of the experimental FCS data. Our results suggest a stronger interaction of the actin mesh with the larger protein probe compared to the lipid. This might point toward a mechanism where cortical actin controls membrane diffusion in a strong size-dependent manner. PMID:23561523

Mass Transport of Macromolecules within an In Vitro Model of Supragingival Plaque

PubMed Central

Thurnheer, Thomas; Gmür, Rudolf; Shapiro, Stuart; Guggenheim, Bernhard

2003-01-01

The aim of this study was to examine the diffusion of macromolecules through an in vitro biofilm model of supragingival plaque. Polyspecies biofilms containing Actinomyces naeslundii, Fusobacterium nucleatum, Streptococcus oralis, Streptococcus sobrinus, Veillonella dispar, and Candida albicans were formed on sintered hydroxyapatite disks and then incubated at room temperature for defined periods with fluorescent markers with molecular weights ranging from 3,000 to 900,000. Subsequent examination by confocal laser scanning microscopy revealed that the mean square penetration depths for all tested macromolecules except immunoglobulin M increased linearly with time, diffusion coefficients being linearly proportional to the cube roots of the molecular weights of the probes (range, 10,000 to 240,000). Compared to diffusion in bulk water, diffusion in the biofilms was markedly slower. The rate of diffusion for each probe appeared to be constant and not a function of biofilm depth. Analysis of diffusion phenomena through the biofilms suggested tortuosity as the most probable explanation for retarded diffusion. Selective binding of probes to receptors present in the biofilms could not explain the observed extent of retardation of diffusion. These results are relevant to oral health, as selective attenuated diffusion of fermentable carbohydrates and acids produced within dental plaque is thought to be essential for the development of carious lesions. PMID:12620862

Pathological and Molecular Characterization of Xanthomonas campestris Strains Causing Diseases of Cassava (Manihot esculenta)

PubMed Central

Verdier, Valérie; Boher, Bernard; Maraite, Henri; Geiger, Jean-Paul

1994-01-01

Fifty-one strains representing Xanthomonas campestris pv. manihotis and cassavae and different pathovars occurring on plants of the family Euphorbiaceae were characterized by ribotyping with a 16S+23S rRNA probe of Escherichia coli and by restriction fragment length polymorphism analysis with a plasmid probe from X. campestris pv. manihotis. Pathogenicity tests were performed on cassava (Manihot esculenta). Histological comparative studies were conducted on strains of two pathovars of X. campestris (vascular and mesophyllic) that attack cassava. Our results indicated that X. campestris pv. manihotis and cassavae have different modes of action in the host and supplemented the taxonomic data on restriction fragment length polymorphism that clearly separate the two pathovars. The plasmid probe could detect multiple restriction fragment length polymorphisms among strains of the pathovar studied. Ribotyping provides a useful tool for rapid identification of X. campestris pathovars on cassava. Images PMID:16349463

Acoustic dynamics of supercooled indomethacin probed by Brillouin light scattering.

PubMed

De Panfilis, S; Pogna, E A A; Virga, A; Scopigno, T

2014-07-21

Acoustics dynamics of the molecular glass-former indomethacin (IMC) have been investigated by Brillouin light scattering (BLS) at GHz frequencies. Elastic response of the system has been tracked from the melting temperature down to the glass transition through the supercooled liquid. Both the structural arrest and the vibrational dynamics are described by modeling the experimentally determined dynamic structure factor within the framework of the Langevin equation, through a simplified choice of memory function which allows one to determine sound velocity and the acoustic attenuation coefficient as a function of temperature. The density fluctuation spectra in the glassy phase, as probed by BLS, are compared with time-domain results from photoacoustics experiments. The arising scenario is discussed in the context of current literature reporting inelastic X-ray scattering and BLS in platelet geometry. The link between the probed elastic properties and the non-ergodicity factor of the glass phase is finally scrutinized.

Identification of liver cancer-specific aptamers using whole live cells.

PubMed

Shangguan, Dihua; Meng, Ling; Cao, Zehui Charles; Xiao, Zeyu; Fang, Xiaohong; Li, Ying; Cardona, Diana; Witek, Rafal P; Liu, Chen; Tan, Weihong

2008-02-01

Liver cancer is the third most deadly cancers in the world. Unfortunately, there is no effective treatment. One of the major problems is that most cancers are diagnosed in the later stage, when surgical resection is not feasible. Thus, accurate early diagnosis would significantly improve the clinical outcome of liver cancer. Currently, there are no effective molecular probes to recognize biomarkers that are specific for liver cancer. The objective of our current study is to identify liver cancer cell-specific molecular probes that could be used for liver cancer recognition and diagnosis. We applied a newly developed cell-SELEX (Systematic Evolution of Ligands by EXponential enrichment) method for the generation of molecular probes for specific recognition of liver cancer cells. The cell-SELEX uses whole live cells as targets to select aptamers (designed DNA/RNA) for cell recognition. In generating aptamers for liver cancer recognition, two liver cell lines were used: a liver cancer cell line BNL 1ME A.7R.1 (MEAR) and a noncancer cell line, BNL CL.2 (BNL). Both cell lines were originally derived from Balb/cJ mice. Through multiple rounds of selection using BNL as a control, we have identified a panel of aptamers that specifically recognize the cancer cell line MEAR with Kd in the nanomolar range. We have also demonstrated that some of the selective aptamers could specifically bind liver cancer cells in a mouse model. There are two major new results (compared with our reported cell-SELEX methodology) in addition to the generation of aptamers specifically for liver cancer. The first one is that our current study demonstrates that cell-based aptamer selection can select specific aptamers for multiple cell lines, even for two cell lines with minor differences (MEAR cell is derived from BNL by chemical inducement); and the second result is that cell-SELEX can be used for adhesive cells and thus open the door for solid tumor selection and investigation. The newly generated cancer-specific aptamers hold great promise as molecular probes for cancer early diagnosis and basic mechanism studies.

Fluorescent probes for lipid rafts: from model membranes to living cells.

PubMed

Klymchenko, Andrey S; Kreder, Rémy

2014-01-16

Membrane microdomains (rafts) remain one of the controversial issues in biophysics. Fluorescent molecular probes, which make these lipid nanostructures visible through optical techniques, are one of the tools currently used to study lipid rafts. The most common are lipophilic fluorescent probes that partition specifically into liquid ordered or liquid disordered phase. Their partition depends on the lipid composition of a given phase, which complicates their use in cellular membranes. A second class of probes is based on environment-sensitive dyes, which partition into both phases, but stain them by different fluorescence color, intensity, or lifetime. These probes can directly address the properties of each separate phase, but their cellular applications are still limited. The present review focuses on summarizing the current state in the field of developing and applying fluorescent molecular probes to study lipid rafts. We highlight an urgent need to develop new probes, specifically adapted for cell plasma membranes and compatible with modern fluorescence microscopy techniques to push the understanding of membrane microdomains forward. Copyright © 2014 Elsevier Ltd. All rights reserved.

Complementary optical and nuclear imaging of caspase-3 activity using combined activatable and radio-labeled multimodality molecular probe.

PubMed

Lee, Hyeran; Akers, Walter J; Cheney, Philip P; Edwards, W Barry; Liang, Kexian; Culver, Joseph P; Achilefu, Samuel

2009-01-01

Based on the capability of modulating fluorescence intensity by specific molecular events, we report a new multimodal optical-nuclear molecular probe with complementary reporting strategies. The molecular probe (LS498) consists of tetraazacyclododecanetetraacetic acid (DOTA) for chelating a radionuclide, a near-infrared fluorescent dye, and an efficient quencher dye. The two dyes are separated by a cleavable peptide substrate for caspase-3, a diagnostic enzyme that is upregulated in dying cells. LS498 is radiolabeled with (64)Cu, a radionuclide used in positron emission tomography. In the native form, LS498 fluorescence is quenched until caspase-3 cleavage of the peptide substrate. Enzyme kinetics assay shows that LS498 is readily cleaved by caspase-3, with excellent enzyme kinetic parameters k(cat) and K(M) of 0.55+/-0.01 s(-1) and 1.12+/-0.06 microM, respectively. In mice, the initial fluorescence of LS498 is ten-fold less than control. Using radiolabeled (64)Cu-LS498 in a controlled and localized in-vivo model of caspase-3 activation, a time-dependent five-fold NIR fluorescence enhancement is observed, but radioactivity remains identical in caspase-3 positive and negative controls. These results demonstrate the feasibility of using radionuclide imaging for localizing and quantifying the distribution of molecular probes and optical imaging for reporting the functional status of diagnostic enzymes.

Complementary optical and nuclear imaging of caspase-3 activity using combined activatable and radio-labeled multimodality molecular probe

NASA Astrophysics Data System (ADS)

Lee, Hyeran; Akers, Walter J.; Cheney, Philip P.; Edwards, W. Barry; Liang, Kexian; Culver, Joseph P.; Achilefu, Samuel

2009-07-01

Based on the capability of modulating fluorescence intensity by specific molecular events, we report a new multimodal optical-nuclear molecular probe with complementary reporting strategies. The molecular probe (LS498) consists of tetraazacyclododecanetetraacetic acid (DOTA) for chelating a radionuclide, a near-infrared fluorescent dye, and an efficient quencher dye. The two dyes are separated by a cleavable peptide substrate for caspase-3, a diagnostic enzyme that is upregulated in dying cells. LS498 is radiolabeled with 64Cu, a radionuclide used in positron emission tomography. In the native form, LS498 fluorescence is quenched until caspase-3 cleavage of the peptide substrate. Enzyme kinetics assay shows that LS498 is readily cleaved by caspase-3, with excellent enzyme kinetic parameters kcat and KM of 0.55+/-0.01 s-1 and 1.12+/-0.06 μM, respectively. In mice, the initial fluorescence of LS498 is ten-fold less than control. Using radiolabeled 64Cu-LS498 in a controlled and localized in-vivo model of caspase-3 activation, a time-dependent five-fold NIR fluorescence enhancement is observed, but radioactivity remains identical in caspase-3 positive and negative controls. These results demonstrate the feasibility of using radionuclide imaging for localizing and quantifying the distribution of molecular probes and optical imaging for reporting the functional status of diagnostic enzymes.

Molecular magnetic resonance imaging of atherosclerotic vessel wall disease.

PubMed

Nörenberg, Dominik; Ebersberger, Hans U; Diederichs, Gerd; Hamm, Bernd; Botnar, René M; Makowski, Marcus R

2016-03-01

Molecular imaging aims to improve the identification and characterization of pathological processes in vivo by visualizing the underlying biological mechanisms. Molecular imaging techniques are increasingly used to assess vascular inflammation, remodeling, cell migration, angioneogenesis and apoptosis. In cardiovascular diseases, molecular magnetic resonance imaging (MRI) offers new insights into the in vivo biology of pathological vessel wall processes of the coronary and carotid arteries and the aorta. This includes detection of early vascular changes preceding plaque development, visualization of unstable plaques and assessment of response to therapy. The current review focuses on recent developments in the field of molecular MRI to characterise different stages of atherosclerotic vessel wall disease. A variety of molecular MR-probes have been developed to improve the non-invasive detection and characterization of atherosclerotic plaques. Specifically targeted molecular probes allow for the visualization of key biological steps in the cascade leading to the development of arterial vessel wall lesions. Early detection of processes which lead to the development of atherosclerosis and the identification of vulnerable atherosclerotic plaques may enable the early assessment of response to therapy, improve therapy planning, foster the prevention of cardiovascular events and may open the door for the development of patient-specific treatment strategies. Targeted MR-probes allow the characterization of atherosclerosis on a molecular level. Molecular MRI can identify in vivo markers for the differentiation of stable and unstable plaques. Visualization of early molecular changes has the potential to improve patient-individualized risk-assessment.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakayama, T.; Kubo, O.; Shingaya, Y.

the research of advanced materials based on nanoscience and nanotechnology, it is often desirable to measure nanoscale local electrical conductivity at a designated position of a given sample. For this purpose, multiple-probe scanning probe microscopes (MP-SPMs), in which two, three or four scanning tunneling microscope (STM) or atomic force microscope (AFM) probes are operated independently, have been developed. Each probe in an MP-SPM is used not only for observing high-resolution STM or AFM images but also for forming an electrical contact enabling nanoscale local electrical conductivity measurement. The world's first double-probe STM (DP-STM) developed by the authors, which was subsequentlymore » modified to a triple-probe STM (TP-STM), has been used to measure the conductivities of one-dimensional metal nanowires and carbon nanotubes and also two-dimensional molecular films. A quadruple-probe STM (QP-STM) has also been developed and used to measure the conductivity of two-dimensional molecular films without the ambiguity of contact resistance between the probe and sample. Moreover, a quadruple-probe AFM (QP-AFM) with four conductive tuning-fork-type self-detection force sensing probes has been developed to measure the conductivity of a nanostructure on an insulating substrate. A general-purpose computer software to control four probes at the same time has also been developed and used in the operation of the QP-AFM. These developments and applications of MP-SPMs are reviewed in this paper.« less

A small molecular pH-dependent fluorescent probe for cancer cell imaging in living cell.

PubMed

Ma, Junbao; Li, Wenqi; Li, Juanjuan; Shi, Rongguang; Yin, Gui; Wang, Ruiyong

2018-05-15

A novel pH-dependent two-photon fluorescent molecular probe ABMP has been prepared based on the fluorophore of 2, 4, 6-trisubstituted pyridine. The probe has an absorption wavelength at 354 nm and corresponding emission wavelength at 475 nm with the working pH range from 2.20 to 7.00, especially owning a good liner response from pH = 2.40 to pH = 4.00. ABMP also has excellent reversibility, photostability and selectivity which promotes its ability in analytical application. The probe can be excited with a two-photon fluorescence microscopy and the fluorescence cell imaging indicated that the probe can distinguish Hela cancer cells out of normal cells with a two-photon fluorescence microscopy which suggested its potential application in tumor cell detection. Copyright © 2018 Elsevier B.V. All rights reserved.

Hall-Effect Measurements Probing the Degree of Charge-Carrier Delocalization in Solution-Processed Crystalline Molecular Semiconductors

NASA Astrophysics Data System (ADS)

Chang, Jui-Fen; Sakanoue, Tomo; Olivier, Yoann; Uemura, Takafumi; Dufourg-Madec, Marie-Beatrice; Yeates, Stephen G.; Cornil, Jérôme; Takeya, Jun; Troisi, Alessandro; Sirringhaus, Henning

2011-08-01

Intramolecular structure and intermolecular packing in crystalline molecular semiconductors should have profound effects on the charge-carrier wave function, but simple drift mobility measurements are not very sensitive to this. Here we show that differences in the Hall resistance of two soluble pentacene derivatives can be explained with different degrees of carrier delocalization being limited by thermal lattice fluctuations. A combination of Hall measurements, optical spectroscopy, and theoretical simulations provides a powerful probe of structure-property relationships at a molecular level.

Molecular Elucidation of Disease Biomarkers at the Interface of Chemistry and Biology.

PubMed

Zhang, Liqin; Wan, Shuo; Jiang, Ying; Wang, Yanyue; Fu, Ting; Liu, Qiaoling; Cao, Zhijuan; Qiu, Liping; Tan, Weihong

2017-02-22

Disease-related biomarkers are objectively measurable molecular signatures of physiological status that can serve as disease indicators or drug targets in clinical diagnosis and therapy, thus acting as a tool in support of personalized medicine. For example, the prostate-specific antigen (PSA) biomarker is now widely used to screen patients for prostate cancer. However, few such biomarkers are currently available, and the process of biomarker identification and validation is prolonged and complicated by inefficient methods of discovery and few reliable analytical platforms. Therefore, in this Perspective, we look at the advanced chemistry of aptamer molecules and their significant role as molecular probes in biomarker studies. As a special class of functional nucleic acids evolved from an iterative technology termed Systematic Evolution of Ligands by Exponential Enrichment (SELEX), these single-stranded oligonucleotides can recognize their respective targets with selectivity and affinity comparable to those of protein antibodies. Because of their fast turnaround time and exceptional chemical properties, aptamer probes can serve as novel molecular tools for biomarker investigations, particularly in assisting identification of new disease-related biomarkers. More importantly, aptamers are able to recognize biomarkers from complex biological environments such as blood serum and cell surfaces, which can provide direct evidence for further clinical applications. This Perspective highlights several major advancements of aptamer-based biomarker discovery strategies and their potential contribution to the practice of precision medicine.

Probing and Improving Student's Understanding of Protein a-Helix Structure Using Targeted Assessment and Classroom Interventions in Collaboration with a Faculty Community of Practice

ERIC Educational Resources Information Center

Loertscher, Jennifer; Villafañe, Sachel M.; Lewis, Jennifer E.; Minderhout, Vicky

2014-01-01

The increasing availability of concept inventories and other assessment tools in the molecular life sciences provides instructors with myriad avenues to probe student understanding. For example, although molecular visualization is central to the study of biochemistry, a growing body of evidence suggests that students have substantial limitations…

The structure of [MnIII6 CrIII]3+ single-molecule magnets deposited in submono-layers and monolayers on surfaces studied by means of molecular resolved atomic force microscopy (AFM) and Kelvin Probe Force Microscopy in UHV

NASA Astrophysics Data System (ADS)

Heinzmann, U.; Gryzia, A.; Volkmann, T.; Brechling, A.; Hoeke, V.; Glaser, T.

2014-04-01

Single molecule magnets (SMM) deposited in submonolayers and monolayers have been analyzed with respect to their structures by means of non-contact AFM (topographic as well as damping mode) and Kelvin Probe Force Microscopy with molecular resolution.

Optical/MRI Multimodality Molecular Imaging

NASA Astrophysics Data System (ADS)

Ma, Lixin; Smith, Charles; Yu, Ping

2007-03-01

Multimodality molecular imaging that combines anatomical and functional information has shown promise in development of tumor-targeted pharmaceuticals for cancer detection or therapy. We present a new multimodality imaging technique that combines fluorescence molecular tomography (FMT) and magnetic resonance imaging (MRI) for in vivo molecular imaging of preclinical tumor models. Unlike other optical/MRI systems, the new molecular imaging system uses parallel phase acquisition based on heterodyne principle. The system has a higher accuracy of phase measurements, reduced noise bandwidth, and an efficient modulation of the fluorescence diffuse density waves. Fluorescent Bombesin probes were developed for targeting breast cancer cells and prostate cancer cells. Tissue phantom and small animal experiments were performed for calibration of the imaging system and validation of the targeting probes.

Core Binding Site of a Thioflavin-T-Derived Imaging Probe on Amyloid β Fibrils Predicted by Computational Methods.

PubMed

Kawai, Ryoko; Araki, Mitsugu; Yoshimura, Masashi; Kamiya, Narutoshi; Ono, Masahiro; Saji, Hideo; Okuno, Yasushi

2018-05-16

Development of new diagnostic imaging probes for Alzheimer's disease, such as positron emission tomography (PET) and single photon emission computed tomography (SPECT) probes, has been strongly desired. In this study, we investigated the most accessible amyloid β (Aβ) binding site of [ 123 I]IMPY, a Thioflavin-T-derived SPECT probe, using experimental and computational methods. First, we performed a competitive inhibition assay with Orange-G, which recognizes the KLVFFA region in Aβ fibrils, suggesting that IMPY and Orange-G bind to different sites in Aβ fibrils. Next, we precisely predicted the IMPY binding site on a multiple-protofilament Aβ fibril model using computational approaches, consisting of molecular dynamics and docking simulations. We generated possible IMPY-binding structures using docking simulations to identify candidates for probe-binding sites. The binding free energy of IMPY with the Aβ fibril was calculated by a free energy simulation method, MP-CAFEE. These computational results suggest that IMPY preferentially binds to an interfacial pocket located between two protofilaments and is stabilized mainly through hydrophobic interactions. Finally, our computational approach was validated by comparing it with the experimental results. The present study demonstrates the possibility of computational approaches to screen new PET/SPECT probes for Aβ imaging.

Photoacoustic lifetime contrast between methylene blue monomers and self-quenched dimers as a model for dual-labeled activatable probes

NASA Astrophysics Data System (ADS)

Morgounova, Ekaterina; Shao, Qi; Hackel, Benjamin J.; Thomas, David D.; Ashkenazi, Shai

2013-05-01

Activatable photoacoustic probes efficiently combine the high spatial resolution and penetration depth of ultrasound with the high optical contrast and versatility of molecular imaging agents. Our approach is based on photoacoustic probing of the excited-state lifetime of methylene blue (MB), a fluorophore widely used in clinical therapeutic and diagnostic applications. Upon aggregation, static quenching between the bound molecules dramatically shortens their lifetime by three orders of magnitude. We present preliminary results demonstrating the ability of photoacoustic imaging to probe the lifetime contrast between monomers and dimers with high sensitivity in cylindrical phantoms. Gradual dimerization enhancement, driven by the addition of increasing concentrations of sodium sulfate to a MB solution, showed that lifetime-based photoacoustic probing decreases linearly with monomer concentration. Similarly, the addition of 4 mM sodium dodecyl sulfate, a concentration that amplifies MB aggregation and reduces the monomer concentration by more than 20-fold, led to a signal decrease of more than 20 dB compared to a solution free of surfactant. These results suggest that photoacoustic imaging can be used to selectively detect the presence of monomers. We conclude by discussing the implementation of the monomer-dimer contrast mechanism for the development of an enzyme-specific activatable probe.

Eliminating Size-Associated Diffusion Constraints for Rapid On-Surface Bioassays with Nanoparticle Probes.

PubMed

Li, Junwei; Zrazhevskiy, Pavel; Gao, Xiaohu

2016-02-24

Nanoparticle probes enable implementation of advanced on-surface assay formats, but impose often underappreciated size-associated constraints, in particular on assay kinetics and sensitivity. The present study highlights substantially slower diffusion-limited assay kinetics due to the rapid development of a nanoprobe depletion layer next to the surface, which static incubation and mixing of bulk solution employed in conventional assay setups often fail to disrupt. In contrast, cyclic solution draining and replenishing yields reaction-limited assay kinetics irrespective of the probe size. Using common surface bioassays, enzyme-linked immunosorbent assays and immunofluorescence, this study shows that this conceptually distinct approach effectively "erases" size-dependent diffusion constraints, providing a straightforward route to rapid on-surface bioassays employing bulky probes and procedures involving multiple labeling cycles, such as multicycle single-cell molecular profiling. For proof-of-concept, the study demonstrates that the assay time can be shortened from hours to minutes with the same probe concentration and, at a typical incubation time, comparable target labeling can be achieved with up to eight times lower nanoprobe concentration. The findings are expected to enable realization of novel assay formats and stimulate development of rapid on-surface bioassays with nanoparticle probes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Charge separation in photoredox reactions. Technical progress report, May 1, 1981-May 1, 1984. [N,N,N',N'-tetramethylbenzidine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kevan, L.

1984-05-01

The structural aspects controlling charge separation in molecular photoionization reactions in organized molecular assemblies involving micelles and vesicles are being studied by optical and electron magnetic resonance techniques including the time domain technique of electron spin echo modulation (ESEM). Photoionization of N,N,N',N'-tetramethylbenzidine (TMB) to give the cation radical has been carried out in both liquid and frozen micellar and vesicular solutions. Cation-water interactions have been detected by ESEM analysis and indicate that the cation is localized asymmetrically within these organized molecular assemblies. x-Doxylstearic acid spin probes have been used to determine that the neutral TMB molecule before photoionization is alsomore » localized asymmetrically within such organized molecular assemblies. Electron spin echo detection of laser photogenerated TMB cation in liquid micellar solutions gives a direct measurement of the phase memory magnetic relaxation time which gives additional structural information. The photoionization efficiency has been related to cation-water interactions measured by ESEM. The photoionization efficiency is also dependent on surface charge and is about twofold greater in cationic micelles and vesicles compared to anionic micelles and vesicles. TMB is in a less polar environment in vesicles compared to micelles consistent with ESEM results. The preferential adsorption of metal species at micellar surfaces has been detected by ESEM. Modifications in the micelle surface have been effected by added salts and varying counterions which have been related to cation-water interactions and to the TMB photoionization efficiency. Corresponding changes in the surface and internal micellar structure have been investigated by x-doxylstearic acid spin probes and specifically deuterated surfactants. The decay kinetics of TMB cations in micelles have been interpreted in terms of a time dependent rate constant.« less

High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

PubMed Central

Wang, Yuker; Carlton, Victoria EH; Karlin-Neumann, George; Sapolsky, Ronald; Zhang, Li; Moorhead, Martin; Wang, Zhigang C; Richardson, Andrea L; Warren, Robert; Walther, Axel; Bondy, Melissa; Sahin, Aysegul; Krahe, Ralf; Tuna, Musaffe; Thompson, Patricia A; Spellman, Paul T; Gray, Joe W; Mills, Gordon B; Faham, Malek

2009-01-01

Background A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small (~40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue. Results Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE. Conclusion MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples. PMID:19228381

Low-temperature electron-spin relaxation in the crystalline and glassy states of solid ethanol

NASA Astrophysics Data System (ADS)

Kveder, Marina; Merunka, Dalibor; Jokić, Milan; Rakvin, Boris

2008-03-01

X -band electron paramagnetic resonance spectroscopy was used to study the spectral properties of a nitroxide spin probe in ethanol glass and crystalline ethanol, at 5-11.5K . The different anisotropy of molecular packing in the two host matrices was evidenced by different rigid limit values for maximal hyperfine splitting in the signal of the spin probe. The significantly shorter phase memory time Tm for the spin probe dissolved in crystalline ethanol, as compared to ethanol glass, was discussed in terms of contribution from spectral diffusion. The effect of low-frequency dynamics was manifested in the temperature dependence of Tm and in the difference between the data measured at different spectral positions. This phenomenon was addressed within the framework of the slow-motional isotropic diffusion model [S. Lee and S. Z. Tang, Phys. Rev. B 31, 1308 (1985)] predicting the spin probe dynamics within the millisecond range, at very low temperatures. The shorter spin-lattice relaxation time of the spin probe in ethanol glass was interpreted in terms of enhanced energy exchange between the spin system and the lattice in the glass matrix due to boson peak excitations.

Label-Free Potentiometry for Detecting DNA Hybridization Using Peptide Nucleic Acid and DNA Probes

PubMed Central

Goda, Tatsuro; Singi, Ankit Balram; Maeda, Yasuhiro; Matsumoto, Akira; Torimura, Masaki; Aoki, Hiroshi; Miyahara, Yuji

2013-01-01

Peptide nucleic acid (PNA) has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM)-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer. The charge readout allows label-free, reagent-less, and multi-parallel detection of target oligonucleotides without any optical assistance. The differences in the probe lengths between 15- to 22-mer dramatically influenced on the sensitivity of the PNA and DNA sensors. Molecular type of the capturing probe did not affect the degree of potential shift. Theoretical model for charged rod-like duplex using the Gouy-Chapman equation indicates the dominant effect of electrostatic attractive forces between anionic DNA and underlying electrode at the electrolyte/electrode interface in the potentiometry. PMID:23435052

Quantifying Nucleic Acid Ensembles with X-ray Scattering Interferometry.

PubMed

Shi, Xuesong; Bonilla, Steve; Herschlag, Daniel; Harbury, Pehr

2015-01-01

The conformational ensemble of a macromolecule is the complete description of the macromolecule's solution structures and can reveal important aspects of macromolecular folding, recognition, and function. However, most experimental approaches determine an average or predominant structure, or follow transitions between states that each can only be described by an average structure. Ensembles have been extremely difficult to experimentally characterize. We present the unique advantages and capabilities of a new biophysical technique, X-ray scattering interferometry (XSI), for probing and quantifying structural ensembles. XSI measures the interference of scattered waves from two heavy metal probes attached site specifically to a macromolecule. A Fourier transform of the interference pattern gives the fractional abundance of different probe separations directly representing the multiple conformation states populated by the macromolecule. These probe-probe distance distributions can then be used to define the structural ensemble of the macromolecule. XSI provides accurate, calibrated distance in a model-independent fashion with angstrom scale sensitivity in distances. XSI data can be compared in a straightforward manner to atomic coordinates determined experimentally or predicted by molecular dynamics simulations. We describe the conceptual framework for XSI and provide a detailed protocol for carrying out an XSI experiment. © 2015 Elsevier Inc. All rights reserved.

Linear Schiff-base fluorescence probe with aggregation-induced emission characteristics for Al3+ detection and its application in live cell imaging.

PubMed

Wen, Xiaoye; Fan, Zhefeng

2016-11-16

A simple Schiff-base derivative with salicylaldehyde moieties as fluorescent probe 1 was reported by aggregation-induced emission (AIE) characterization for the detection of metal ions. Spectral analysis revealed that probe 1 was highly selective and sensitive to Al 3+ . The probe 1 was also subject to minimal interference from other common competitive metal ions. The detection limit of Al 3+ was 0.4 μM, which is considerably lower than the World Health Organization standard (7.41 μM), and the acceptable level of Al 3+ (1.85 μM) in drinking water. The Job's plot and the results of 1 H-NMR and FT-IR analyses indicated that the binding stoichiometry ratio of probe 1 to Al 3+ was 1:2. Probe 1 demonstrated a fluorescence-enhanced response upon binding with Al 3+ based on AIE characterization. This response was due to the restricted molecular rotation and increased rigidity of the molecular assembly. Probe 1 exhibited good biocompatibility, and Al 3+ was detected in live cells. Therefore, probe 1 is a promising fluorescence probe for Al 3+ detection in the environment. Copyright © 2016 Elsevier B.V. All rights reserved.

Validation of ALK/ROS1 Dual Break Apart FISH Probe probe in non-small-cell lung cancer.

PubMed

Lim, Sun Min; Chang, Hyun; Cha, Yoon Jin; Liang, Shile; Tai, Yan Chin; Li, Gu; Pestova, Ekaterina; Policht, Frank; Perez, Thomas; Soo, Ross A; Park, Won Young; Kim, Hye Ryun; Shim, Hyo Sup; Cho, Byoung Chul

2017-09-01

ALK and ROS1 gene rearrangements are distinct molecular subsets of non-small-cell lung cancer (NSCLC), and they are strong predictive biomarkers of response to ALK/ROS1 inhibitors, such as crizotinib. Thus, it is clinically important to develop an effective screening strategy to detect patients who will benefit from such treatment. In this study, we aimed to validate analytical performance of Vysis ALK/ROS1 Dual Break Apart Probe Kit (RUO) in NSCLC. Study population composed of three patient cohorts with histologically confirmed lung adenocarcinoma (patients with ALK rearrangement, patients with ROS1 rearrangement and patients with wild-type ALK and ROS1). Specimens consisted of 12 ALK-positive, 8 ROS1-positive and 21 ALK/ROS1-wild type formalin-fixed paraffin-embedded samples obtained from surgical resection or excisional biopsy. ALK rearrangement was previously assessed by Vysis ALK Break Apart FISH Probe Kit (Abbott Molecular, Abbot Park, IL, USA) and ROS1 rearrangement was previously assessed by ZytoLight ® SPEC ROS1 Break Apart Probe (ZytoVision, GmbH). All specimens were re-evaluated by Vysis ALK/ROS1 Dual Break Apart Probe Kit. FISH images were scanned on BioView AllegroPlus system and interpreted via BioView SoloWeb remotely. For a total of 41 patient samples, the concordance of the results by Vysis ALK/ROS1 Dual Break Apart Probe Kit was evaluated and compared to the known ALK and ROS1 rearrangement status of the specimen. Of the 12 ALK-positive cases, hybridization with Vysis ALK/ROS1 Dual Break Apart Probe Kit was successful in 10 cases (success rate 10/12, 83%) and of these 10 cases, all showed ALK rearrangement (100% concordance with the results of Vysis ALK Break Apart FISH Probe Kit). Two of the ALK+ cases were excluded due to weak ROS1 signals that could not be enumerated. Of the 8 ROS1-positive cases, 6 cases were successfully evaluated using Vysis ALK/ROS1 Dual Break Apart Probe Kit. The success rate was 75% (6/8), and of these 6 cases, all showed ROS1 rearrangement, giving a 100% concordance with ZytoLight ® SPEC ROS1 Break Apart Probe. Two of the cases were excluded due to weak ROS1 gold signal or high background. In the cohort of 21 wild-type cases, the success rate using Vysis ALK/ROS1 Dual Break Apart FISH Probe Kit was 85% (18/21) and the concordance with ALK and ROS1 probe kit was 100% (18/18). Vysis ALK/ROS1 Dual Break Apart Probe Kit (RUO) can detect ALK and ROS1 rearrangement simultaneously in NSCLC. Copyright © 2017 Elsevier B.V. All rights reserved.

Vibrational spectroscopic, molecular docking and quantum chemical studies on 6-aminonicotinamide

NASA Astrophysics Data System (ADS)

Mohamed Asath, R.; Premkumar, S.; Mathavan, T.; Milton Franklin Benial, A.

2017-04-01

The most stable molecular structure of 6-aminonicotinamide (ANA) molecule was predicted by conformational analysis and vibrational spectral analysis was carried out by experimental and theoretical methods. The calculated and experimentally observed vibrational frequencies were assigned and compared. The π→π* electronic transition of the molecule was predicted by theoretically calculated ultraviolet-visible spectra in gas and liquid phase and further validated experimentally using ethanol as a solvent. Frontier molecular orbitals analysis was carried out to probe the reactive nature of the ANA molecule and further the site selectivity to specific chemical reactions were effectively analyzed by Fukui function calculation. The molecular electrostatic potential surface was simulated to confirm the reactive sites of the molecule. The natural bond orbital analysis was also performed to understand the intra molecular interactions, which confirms the bioactivity of the ANA molecule. Neuroprotective nature of the ANA molecule was analyzed by molecular docking analysis and the ANA molecule was identified as a good inhibitor against Alzheimer's disease.

Detection of DNA damage by using hairpin molecular beacon probes and graphene oxide.

PubMed

Zhou, Jie; Lu, Qian; Tong, Ying; Wei, Wei; Liu, Songqin

2012-09-15

A hairpin molecular beacon tagged with carboxyfluorescein in combination with graphene oxide as a quencher reagent was used to detect the DNA damage by chemical reagents. The fluorescence of molecular beacon was quenched sharply by graphene oxide; while in the presence of its complementary DNA the quenching efficiency decreased because their hybridization prevented the strong adsorbability of molecular beacon on graphene oxide. If the complementary DNA was damaged by a chemical reagent and could not form intact duplex structure with molecular beacon, more molecular beacon would adsorb on graphene oxide increasing the quenching efficiency. Thus, damaged DNA could be detected based on different quenching efficiencies afforded by damaged and intact complementary DNA. The damage effects of chlorpyrifos-methyl and three metabolites of styrene such as mandelieaeids, phenylglyoxylieaeids and epoxystyrene on DNA were studied as models. The method for detection of DNA damage was reliable, rapid and simple compared to the biological methods. Copyright © 2012 Elsevier B.V. All rights reserved.

[Development of a Fluorescence Probe for Live Cell Imaging].

PubMed

Shibata, Aya

2017-01-01

 Probes that detect specific biological materials are indispensable tools for deepening our understanding of various cellular phenomena. In live cell imaging, the probe must emit fluorescence only when a specific substance is detected. In this paper, we introduce a new probe we developed for live cell imaging. Glutathione S-transferase (GST) activity is higher in tumor cells than in normal cells and is involved in the development of resistance to various anticancer drugs. We previously reported the development of a general strategy for the synthesis of probes for detection of GST enzymes, including fluorogenic, bioluminogenic, and 19 F-NMR probes. Arylsulfonyl groups were used as caging groups during probe design. The fluorogenic probes were successfully used to quantitate very low levels of GST activity in cell extracts and were also successfully applied to the imaging of microsomal MGST1 activity in living cells. The bioluminogenic and 19 F-NMR probes were able to detect GST activity in Escherichia coli cells. Oligonucleotide-templated reactions are powerful tools for nucleic acid sensing. This strategy exploits the target strand as a template for two functionalized probes and provides a simple molecular mechanism for multiple turnover reactions. We developed a nucleophilic aromatic substitution reaction-triggered fluorescent probe. The probe completed its reaction within 30 s of initiation and amplified the fluorescence signal from 0.5 pM target oligonucleotide by 1500 fold under isothermal conditions. Additionally, we applied the oligonucleotide-templated reaction for molecular releasing and peptide detection.

Thermal conductance at the interface between crystals using equilibrium and nonequilibrium molecular dynamics

NASA Astrophysics Data System (ADS)

Merabia, Samy; Termentzidis, Konstantinos

2012-09-01

In this article, we compare the results of nonequilibrium (NEMD) and equilibrium (EMD) molecular dynamics methods to compute the thermal conductance at the interface between solids. We propose to probe the thermal conductance using equilibrium simulations measuring the decay of the thermally induced energy fluctuations of each solid. We also show that NEMD and EMD give generally speaking inconsistent results for the thermal conductance: Green-Kubo simulations probe the Landauer conductance between two solids which assumes phonons on both sides of the interface to be at equilibrium. On the other hand, we show that NEMD give access to the out-of-equilibrium interfacial conductance consistent with the interfacial flux describing phonon transport in each solid. The difference may be large and reaches typically a factor 5 for interfaces between usual semiconductors. We analyze finite size effects for the two determinations of the interfacial thermal conductance, and show that the equilibrium simulations suffer from severe size effects as compared to NEMD. We also compare the predictions of the two above-mentioned methods—EMD and NEMD—regarding the interfacial conductance of a series of mass mismatched Lennard-Jones solids. We show that the Kapitza conductance obtained with EMD can be well described using the classical diffuse mismatch model (DMM). On the other hand, NEMD simulation results are consistent with an out-of-equilibrium generalization of the acoustic mismatch model (AMM). These considerations are important in rationalizing previous results obtained using molecular dynamics, and help in pinpointing the physical scattering mechanisms taking place at atomically perfect interfaces between solids, which is a prerequisite to understand interfacial heat transfer across real interfaces.

Ultrafast and nonlinear spectroscopy of brilliant green-based nanoGUMBOS with enhanced near-infrared emission

NASA Astrophysics Data System (ADS)

Karam, Tony E.; Siraj, Noureen; Zhang, Zhenyu; Ezzir, Abdulrahman F.; Warner, Isiah M.; Haber, Louis H.

2017-10-01

The synthesis, characterization, ultrafast dynamics, and nonlinear spectroscopy of 30 nm nanospheres of brilliant green-bis(pentafluoroethylsulfonyl)imide ([BG][BETI]) in water are reported. These thermally stable nanoparticles are derived from a group of uniform materials based on organic salts (nanoGUMBOS) that exhibit enhanced near-infrared emission compared with the molecular dye in water. The examination of ultrafast transient absorption spectroscopy results reveals that the overall excited-state relaxation lifetimes of [BG][BETI] nanoGUMBOS are longer than the brilliant green molecular dye in water due to steric hindrance of the torsional degrees of freedom of the phenyl rings around the central carbon. Furthermore, the second harmonic generation signal of [BG][BETI] nanoGUMBOS is enhanced by approximately 7 times and 23 times as compared with colloidal gold nanoparticles of the same size and the brilliant green molecular dye in water, respectively. A very clear third harmonic generation signal is observed from the [BG][BETI] nanoGUMBOS but not from either the molecular dye or the gold nanoparticles. Overall, these results show that [BG][BETI] nanoGUMBOS exhibit altered ultrafast and nonlinear spectroscopy that is beneficial for various applications including nonlinear imaging probes, biomedical imaging, and molecular sensing.

Impacts of Sampling and Handling Procedures on DNA- and RNA-based Microbial Characterization and Quantification of Groundwater and Saturated Soil

DTIC Science & Technology

2012-07-01

use of molecular biological techniques (MBTs) has allowed microbial ecologists and environmental engineers to determine microbial community...metabolic genes). The most common approaches used in bioremediation research are those based on the polymerase chain reaction (PCR) amplification of... bioremediation . Because of its sensitivity compared to direct hybridization/probing, PCR is increasingly used to analyze groundwater samples and soil samples

Inelastic effects in molecular transport junctions: The probe technique at high bias

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kilgour, Michael; Segal, Dvira, E-mail: dsegal@chem.utoronto.ca

2016-03-28

We extend the Landauer-Büttiker probe formalism for conductances to the high bias regime and study the effects of environmentally induced elastic and inelastic scattering on charge current in single molecule junctions, focusing on high-bias effects. The probe technique phenomenologically incorporates incoherent elastic and inelastic effects to the fully coherent case, mimicking a rich physical environment at trivial cost. We further identify environmentally induced mechanisms which generate an asymmetry in the current, manifested as a weak diode behavior. This rectifying behavior, found in two types of molecular junction models, is absent in the coherent-elastic limit and is only active in themore » case with incoherent-inelastic scattering. Our work illustrates that in the low bias-linear response regime, the commonly used “dephasing probe” (mimicking only elastic decoherence effects) operates nearly indistinguishably from a “voltage probe” (admitting inelastic-dissipative effects). However, these probes realize fundamentally distinct I-V characteristics at high biases, reflecting the central roles of dissipation and inelastic scattering processes on molecular electronic transport far-from-equilibrium.« less

Tandem Payne/Dakin Reaction: A New Strategy for Hydrogen Peroxide Detection and Molecular Imaging.

PubMed

Yang, Dan; Ye, Sen; Hu, Jun Jacob

2018-06-22

Hydrogen peroxide (H2O2) has been recognized as one of the most significant ROS (reactive oxygen species) in human health and disease. Due to the intrinsic attributes of H2O2 such as low reactivity under physiological pH, it is exceedingly challenging to develop small molecule fluorescent probes with high selectivity and sensitivity to visualize H2O2 in intricate biological milieux. To address this gap, we report a rationally designed tandem Payne/Dakin reaction that is specific to molecular recognition of H2O2, and demonstrate its application in developing novel biocompatible fluorescent probes. New H2O2 probes based on this unique chemical strategy can be facilely synthesized by a general coupling reaction, and the practical applicability of those probes has been confirmed by the visualization of endogenously produced H2O2 in living cells. In particular, starvation induced H2O2 production in mouse macrophages has been detected by our novel probe in both confocal imaging and flow cytometry. This tandem Payne/Dakin reaction provides a basis for developing more sophisticated molecular tools to interrogate H2O2 functions in biological phenomena. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Jeongho; Kim, Kyung Hwan; Oang, Key Young

Characterization of transient molecular structures formed during chemical and biological processes is essential for understanding their mechanisms and functions. Over the last decade, time-resolved X-ray liquidography (TRXL) and time-resolved X-ray absorption spectroscopy (TRXAS) have emerged as powerful techniques for molecular and electronic structural analysis of photoinduced reactions in the solution phase. Both techniques make use of a pump–probe scheme that consists of (1) an optical pump pulse to initiate a photoinduced process and (2) an X-ray probe pulse to monitor changes in the molecular structure as a function of time delay between pump and probe pulses. TRXL is sensitive tomore » changes in the global molecular structure and therefore can be used to elucidate structural changes of reacting solute molecules as well as the collective response of solvent molecules. On the other hand, TRXAS can be used to probe changes in both local geometrical and electronic structures of specific X-ray-absorbing atoms due to the element-specific nature of core-level transitions. These techniques are complementary to each other and a combination of the two methods will enhance the capability of accurately obtaining structural changes induced by photoexcitation. Here we review the principles of TRXL and TRXAS and present recent application examples of the two methods for studying chemical and biological processes in solution. Furthermore, we briefly discuss the prospect of using X-ray free electron lasers for the two techniques, which will allow us to keep track of structural dynamics on femtosecond time scales in various solution-phase molecular reactions.« less

Multimodal fluorescence molecular imaging for in vivo characterization of skin cancer using endogenous and exogenous fluorophores

NASA Astrophysics Data System (ADS)

Miller, Jessica P.; Habimana-Griffin, LeMoyne; Edwards, Tracy S.; Achilefu, Samuel

2017-06-01

Similarity of skin cancer with many benign skin pathologies requires reliable methods to detect and differentiate the different types of these lesions. Previous studies have explored the use of disparate optical techniques to identify and estimate the invasive nature of melanoma and basal cell carcinoma with varying outcomes. Here, we used a concerted approach that provides complementary information for rapid screening and characterization of tumors, focusing on squamous cell carcinoma (SCC) of the skin. Assessment of in vivo autofluorescence lifetime (FLT) imaging of endogenous fluorophores that are excitable at longer wavelengths (480 nm) than conventional NADH and FAD revealed a decrease in the short FLT component for SCC compared to normal skin, with mean values of 0.57±0.026 ns and 0.61±0.021 ns, respectively (p=0.004). Subsequent systemic administration of a near-infrared fluorescent molecular probe in SCC bearing mice, followed by the implementation of image processing methods on data acquired from two-dimensional and three-dimensional fluorescence molecular imaging, allowed us to estimate the tumor volume and depth, as well as quantify the fluorescent probe in the tumor. The result suggests the involvement of lipofuscin-like lipopigments and riboflavin in SCC metabolism and serves as a model for staging SCC.

Energy Donor Effect on the Sensing Performance for a Series of FRET-Based Two-Photon Fluorescent Hg2+ Probes.

PubMed

Zhang, Yujin; Hu, Wei

2017-01-25

Nonlinear optical properties of a series of newly-synthesized molecular fluorescent probes for Hg 2+ containing the same acceptor (rhodamine group) are analyzed by using time-dependent density functional theory in combination with analytical response theory. Special emphasis is placed on evolution of the probes' optical properties in the absence and presence of Hg 2+ . These compounds show drastic changes in their photoabsorption and photoemission properties when they react with Hg 2+ , indicating that they are excellent candidates for ratiometric and colorimetric fluorescent chemosensors. Most importantly, the energy donor moiety is found to play a dominant role in sensing performance of these probes. Two-photon absorption cross sections of the compounds are increased with the presence of Hg 2+ , which theoretically suggests the possibility of the probes to be two-photon fluorescent Hg 2+ sensors. Moreover, analysis of molecular orbitals is presented to explore responsive mechanism of the probes, where the fluorescence resonant energy transfer process is theoretically demonstrated. Our results elucidate the available experimental measurements. This work provides guidance for designing efficient two-photon fluorescent probes that are geared towards biological and chemical applications.

Magnetic Gold Nanoparticle-Labeled Heparanase Monoclonal Antibody and its Subsequent Application for Tumor Magnetic Resonance Imaging

NASA Astrophysics Data System (ADS)

Li, Ning; Jie, Meng-Meng; Yang, Min; Tang, Li; Chen, Si-Yuan; Sun, Xue-Mei; Tang, Bo; Yang, Shi-Ming

2018-04-01

Heparanase (HPA) is ubiquitously expressed in various metastatic malignant tumors; previous studies have demonstrated that HPA was a potential tumor-associated antigen (TAA) for tumor immunotherapy. We sought to evaluate the feasibility of HPA as a common TAA for magnetic resonance imaging (MRI) of tumor metastasis and its potential application in tumor molecular imaging. We prepared a targeted probe based on magnetic gold nanoparticles coupled with an anti-HPA antibody for the specific detection of HPA by MRI. The specificity of the targeted probe was validated in vitro by incubation of the probe with various tumor cells, and the probe was able to selectively detect HPA (+) cells. We found the probes displayed significantly reduced signal intensity in several tumor cells, and the signal intensity decreased significantly after the targeted probe was injected in tumor-bearing nude mice. In the study, we demonstrated that the HPA&GoldMag probe had excellent physical and chemical properties and immune activities and could specifically target many tumor cell tissues both in vitro and in vivo. This may provide an experimental base for molecular imaging of tumor highly expressing heparanase using HPA mAbs.

Probing Long-Range Configurations of Molecular Hydrogen

NASA Astrophysics Data System (ADS)

McCormack, Elizabeth

2011-05-01

Very long-range molecular configurations are of interest in a variety of contexts, for example, in the astro-chemistry of cold molecular clouds and in planetary atmospheres, including our own. Such states can be more than 10 times the size of the ground state and often possess energies above multiple ionization potentials and dissociation limits resulting in diverse and complex decay dynamics. Many of these configurations possess a double-well character arising from the interaction of molecular Rydberg states, repulsive doubly-excited states, and ionic states. The ion pair in hydrogen, an unusual molecular configuration consisting of one proton shrouded in a cloud of two electrons separated very far from the other proton, is notoriously difficult to create and study. We report results from on our investigation of such states using resonantly enhanced multi-photon ionization via the E,F v = 6, J = 0, 1, and 2 states to probe the H(n = 1) + H(n = 3) dissociation threshold energy region. Both molecular and atomic ion production were detected as a function of wavelength by using a time-of-flight mass spectrometer. Below threshold a series of highly excited vibrational levels of several long range states are observed. Above threshold broad resonances are observed with energies that agree well with the predictions of a mass-scaled Rydberg formula for bound states of the H+ H- ion pair. Measured linewidths, quantum defects, and rotational dependences are reported for ion pair principal quantum numbers in the range of n = 130 to 206. Our new results can be compared to recent experimental work using a different excitation scheme, which was the first spectroscopic observation of heavy Rydberg states in hydrogen, and new ab initio theoretical work. Supported by the National Science Foundation.

A Highly Sensitive Fluorogenic Probe for Imaging Glycoproteins and Mucine Activity in Live Cells in the Near-Infrared Region.

PubMed

Samaniego Lopez, Cecilia; Hebe Martínez, Jimena; Uhrig, María Laura; Coluccio Leskow, Federico; Spagnuolo, Carla Cecilia

2018-04-25

A novel fluorescent molecular probe is reported, which is able to detect glycoproteins, especially mucins, with high sensitivity and with a turn-on response along with a large Stokes shift (>130 nm), within the biologically active window. The probe contains an aminotricarbocyanine as the fluorescent reporter with a linked benzoboroxole as the recognition unit, which operates through a dynamic covalent reaction between the boronic hemiester residue of the receptor and cis-diols of the analyte. The superior selectivity of the probe is displayed by the labeling of mucins present in Calu-3 cells. The new benzoboroxole fluorescent derivative gathers together key properties to make it a highly rated molecular probe: specificity, excellent solubility in water, and off-on near infrared emission. This probe is expected to be an excellent tool for imaging intracellular mucin to evaluate mucus-related diseases as well as a sensing strategy towards glycosylated structures with a high potential for theranostics approaches in biological samples. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Advances of Molecular Imaging for Monitoring the Anatomical and Functional Architecture of the Olfactory System.

PubMed

Zhang, Xintong; Bi, Anyao; Gao, Quansheng; Zhang, Shuai; Huang, Kunzhu; Liu, Zhiguo; Gao, Tang; Zeng, Wenbin

2016-01-20

The olfactory system of organisms serves as a genetically and anatomically model for studying how sensory input can be translated into behavior output. Some neurologic diseases are considered to be related to olfactory disturbance, especially Alzheimer's disease, Parkinson's disease, multiple sclerosis, and so forth. However, it is still unclear how the olfactory system affects disease generation processes and olfaction delivery processes. Molecular imaging, a modern multidisciplinary technology, can provide valid tools for the early detection and characterization of diseases, evaluation of treatment, and study of biological processes in living subjects, since molecular imaging applies specific molecular probes as a novel approach to produce special data to study biological processes in cellular and subcellular levels. Recently, molecular imaging plays a key role in studying the activation of olfactory system, thus it could help to prevent or delay some diseases. Herein, we present a comprehensive review on the research progress of the imaging probes for visualizing olfactory system, which is classified on different imaging modalities, including PET, MRI, and optical imaging. Additionally, the probes' design, sensing mechanism, and biological application are discussed. Finally, we provide an outlook for future studies in this field.

Influence of Donor on the Sensing Performance of a Series of Through-Bond Energy Transfer-Based Two-photon Fluorescent Cu(2+) Probes.

PubMed

Zhang, Yu-Jin; Wang, Xin; Zhou, Yong; Wang, Chuan-Kui

2016-07-01

Optical properties of a series of molecular two-photon fluorescent Cu(2+) probes containing the same acceptor (rhodamine group) are analyzed using time-dependent density functional theory in combination with analytical response theory. Special emphasis is placed on evolution of the probes' optical properties in the presence of Cu(2+) . In this study, the compound with naphthalene as the donor is shown to be excellent ratiometric fluorescent chemosensor, whereas the compound with quinoline derivative as the donor shows off/on-typed colorimetric fluorescent response. For the compound with naphthalimide derivative as the donor, changing the connection between the donor and acceptor can efficiently prevent the fluorescent quenching of the probe both in the absence and presence of Cu(2+) . The donor moiety and the connection between donor and acceptor are thus found to play dominant roles on sensing performance of these probes. Moreover, distributions of molecular orbitals involved in the excitation and emission of the probes are analyzed to explore responsive mechanism of the probes. The through-bond energy transfer process is theoretically demonstrated. Our results are used to elucidate the available experimental measurements. This work is helpful to understand the relationships of structure with optical properties for the studied probes. © 2016 The American Society of Photobiology.

Target-protecting dumbbell molecular probe against exonucleases digestion for sensitive detection of ATP and streptavidin.

PubMed

Chen, Jinyang; Liu, Yucheng; Ji, Xinghu; He, Zhike

2016-09-15

In this work, a versatile dumbbell molecular (DM) probe was designed and employed in the sensitively homogeneous bioassay. In the presence of target molecule, the DM probe was protected from the digestion of exonucleases. Subsequently, the protected DM probe specifically bound to the intercalation dye and resulted in obvious fluorescence signal which was used to determine the target molecule in return. This design allows specific and versatile detection of diverse targets with easy operation and no sophisticated fluorescence labeling. Integrating the idea of target-protecting DM probe with adenosine triphosphate (ATP) involved ligation reaction, the DM probe with 5'-end phosphorylation was successfully constructed for ATP detection, and the limitation of detection was found to be 4.8 pM. Thanks to its excellent selectivity and sensitivity, this sensing strategy was used to detect ATP spiked in human serum as well as cellular ATP. Moreover, the proposed strategy was also applied in the visual detection of ATP in droplet-based microfluidic platform with satisfactory results. Similarly, combining the principle of target-protecting DM probe with streptavidin (SA)-biotin interaction, the DM probe with 3'-end biotinylation was developed for selective and sensitive SA determination, which demonstrated the robustness and versatility of this design. Copyright © 2016 Elsevier B.V. All rights reserved.

Conserved electrostatic fields at the Ras-effector interface measured through vibrational Stark effect spectroscopy explain the difference in tilt angle in the Ras binding domains of Raf and RalGDS.

PubMed

Walker, David M; Wang, Ruifei; Webb, Lauren J

2014-10-07

Vibrational Stark effect (VSE) spectroscopy was used to measure the electrostatic fields present at the interface of the human guanosine triphosphatase (GTPase) Ras docked with the Ras binding domain (RBD) of the protein kinase Raf. Nine amino acids located on the surface of Raf were selected for labeling with a nitrile vibrational probe. Eight of the probe locations were situated along the interface of Ras and Raf, and one probe was 2 nm away on the opposite side of Raf. Vibrational frequencies of the nine Raf nitrile probes were compared both in the monomeric, solvated protein and when docked with wild-type (WT) Ras to construct a comprehensive VSE map of the Ras-Raf interface. Molecular dynamics (MD) simulations employing an umbrella sampling strategy were used to generate a Boltzmann-weighted ensemble of nitrile positions in both the monomeric and docked complexes to determine the effect that docking has on probe location and orientation and to aid in the interpretation of VSE results. These results were compared to an identical study that was previously conducted on nine nitrile probes on the RBD of Ral guanidine dissociation stimulator (RalGDS) to make comparisons between the docked complexes formed when either of the two effectors bind to WT Ras. This comparison finds that there are three regions of conserved electrostatic fields that are formed upon docking of WT Ras with both downstream effectors. Conservation of this pattern in the docked complex then results in different binding orientations observed in otherwise structurally similar proteins. This work supports an electrostatic cause of the known binding tilt angle between the Ras-Raf and Ras-RalGDS complexes.

Evaluation of phototoxicity of dendritic porphyrin-based phosphorescent oxygen probes: an in vitro study†

PubMed Central

Lebedev, Artem Y.; Marchi, Enrico; Yuan, Min; Esipova, Tatiana V.; Bergamini, Giacomo; Wilson, David F.

2013-01-01

Biological oxygen measurements by phosphorescence quenching make use of exogenous phosphorescent probes, which are introduced directly into the medium of interest (e.g. blood or interstitial fluid) where they serve as molecular sensors for oxygen. The byproduct of the quenching reaction is singlet oxygen, a highly reactive species capable of damaging biological tissue. Consequently, potential probe phototoxicity is a concern for biological applications. Herein, we compared the ability of polyethyleneglycol (PEG)-coated Pd tetrabenzoporphyrin (PdTBP)-based dendritic nanoprobes of three successive generations to sensitize singlet oxygen. It was found that the size of the dendrimer has practically no effect on the singlet oxygen sensitization efficiency in spite of the strong attenuation of the triplet quenching rate with an increase in the dendrimer generation. This unexpected result is due to the fact that the lifetime of the PdTBP triplet state in the absence of oxygen increases with dendritic generation, thus compensating for the concomitant decrease in the rate of quenching. Nevertheless, in spite of their ability to sensitize singlet oxygen, the phosphorescent probes were found to be non-phototoxic when compared with the commonly used photodynamic drug Photofrin in a standard cell-survival assay. The lack of phototoxicity is presumably due to the inability of PEGylated probes to associate with cell surfaces and/or penetrate cellular membranes. In contrast, conventional photosensitizers bind to cell components and act by generating singlet oxygen inside or in the immediate vicinity of cellular organelles. Therefore, PEGylated dendritic probes are safe to use for tissue oxygen measurements as long as the light doses are less than or equal to those commonly employed in photodynamic therapy. PMID:21409208

Molecular Probes in Marine Ecology: Concepts, Techniques and Applications.

DTIC Science & Technology

1991-08-16

AD-A240 938 FINAL TECNCAL REPORT Title: Molecular Probes In Marine Ecology: Concepts, Techniques and Applications Office of Naval Research Program ...Contact: Leslie D. Garrick, Office of Sponsored Programs (508) 548-3705, ext. 218 Date: August 16, 1991 91-11818 DISCLAIMER NOTICE THIS DOCUMENT IS BEST...disguise, embi-aces the many questions and seeks workable solutions. The 1990 MBL marine ecology course, entered into its second year of a program in

Measuring the mechanical properties of molecular conformers

NASA Astrophysics Data System (ADS)

Jarvis, S. P.; Taylor, S.; Baran, J. D.; Champness, N. R.; Larsson, J. A.; Moriarty, P.

2015-09-01

Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules.

Development of a Submillimeter Multipass Spectrometer for the Study of Molecular Ions

NASA Astrophysics Data System (ADS)

Carroll, A.; Rocher, B.; Laas, J. C.; Deprince, B. A.; Hays, B.; Weaver, S. L. Widicus; Lang, S.

2012-06-01

We have developed a multipass spectrometer for the submillimeter spectral region that is being used to study molecular ions through gas phase spectroscopy. The optical configuration is based on the design of Perry and coworkers that was implemented in the optical regime. To our knowledge, this is the first implementation of this optical configuration at long wavelengths. The setup involves two nearly concentric spherical mirrors that focus the multiple beam passes into a small area, or ``waist'', in the middle of the sample chamber. A supersonic molecular beam is coupled to the setup so that the molecular beam crosses the optical path at the waist. Initial studies have focused on neutral test molecules to probe the physical properties of the molecular beam under various arrangements of the molecular source relative to the optical path. Current studies focus on coupling a plasma discharge source to the setup to enable the study of molecular ions. Here we present the design of this instrument, compare the spectrometer capabilities to a traditional single pass spectrometer, and discuss the results of initial spectroscopic studies.

Characterizing molecular probes for diffusion measurements in the brain

PubMed Central

Kaur, Gurjinder; Hrabetova, Sabina; Guilfoyle, David N.; Nicholson, Charles; Hrabe, Jan

2008-01-01

Brain diffusion properties are at present most commonly evaluated by magnetic resonance (MR) diffusion imaging. MR cannot easily distinguish between the extracellular and intracellular signal components, but the older technique of Real-Time Iontophoresis (RTI) detects exclusively extracellular diffusion. Interpretation of the MR results would therefore benefit from auxiliary RTI measurements. This requires a molecular probe detectable by both techniques. Our aim was to specify a minimum set of requirements that such a diffusion probe should fulfill and apply it to two candidate probes: the cation tetramethylammonium (TMA+), used routinely in the RTI experiments, and the anion hexafluoroantimonate (SbF6−). Desirable characteristics of a molecular diffusion probe include predictable diffusion properties, stability, minimum interaction with cellular physiology, very slow penetration into the cells, and sufficiently strong and selective MR and RTI signals. These properties were evaluated using preparations of rat neocortical slices under normal and ischemic conditions, as well as solutions and agarose gel. While both molecules can be detected by MR and RTI, neither proved an ideal candidate. TMA+ was very stable but it penetrated into the cells and accumulated there within tens of minutes. SbF6− did not enter the cells as readily but it was not stable, particularly in ischemic tissue and at higher temperatures. Its presence also resulted in a decreased extracellular volume. These probe properties help to interpret previously published MR data on TMA+ diffusion and might play a role in other diffusion experiments obtained with them. PMID:18466980

Multiprobe Spectroscopic Inverstigation of Molecular-level Behavior within Aqueous 1-Butyl-3-methylimidazolium Tetrafluoroborate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sarkar, Abhra; Ali, Maroof; Baker, Gary A

2009-01-01

In this work, an array of molecular-level solvent featuressincluding solute-solvent/solvent-solvent interactions, dipolarity, heterogeneity, dynamics, probe accessibility, and diffusionswere investigated across the entire composition of ambient mixtures containing the ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate, [bmim][BF4], and pH 7.0 phosphate buffer, based on results assembled for nine different molecular probes utilized in a range of spectroscopic modes. These studies uncovered interesting and unusual solvatochromic probe behavior within this benchmark mixture. Solvatochromic absorbance probessa watersoluble betaine dye (betaine dye 33), N,N-diethyl-4-nitroaniline, and 4-nitroanilineswere employed to determine ET (a blend of dipolarity/polarizability and hydrogen bond donor contributions) and the Kamlet-Taft indices * (dipolarity/polarizability), R (hydrogenmore » bond donor acidity), and (hydrogen bond acceptor basicity) characterizing the [bmim][BF4] + phosphate buffer system. These parameters each showed a marked deviation from ideality, suggesting selective solvation of the individual probe solutes by [bmim][BF4]. Similar conclusions were derived from the responses of the fluorescent polarity-sensitive probes pyrene and pyrene-1-carboxaldehyde. Importantly, the fluorescent microfluidity probe 1,3-bis(1-pyrenyl)propane senses a microviscosity within the mixture that significantly exceeds expectations derived from simple interpolation of the behavior in the neat solvents. On the basis of results from this probe, a correlation between microviscosity and bulk viscosity was established; pronounced solvent-solvent hydrogen-bonding interactions were implicit in this behavior. The greatest deviation from ideal additive behavior for the probes studied herein was consistently observed to occur in the buffer-rich regime. Nitromethane-based fluorescence quenching of pyrene within the [bmim][BF4] + phosphate buffer system showed unusual compliance with a sphere-of-action quenching model, a further manifestation of the microheterogeneity of the system. Fluorescence correlation spectroscopic results for both small (BODIPY FL) and macromolecular (Texas Red-10 kDa dextran conjugate) diffusional probes provide additional evidence in support of microphase segregation inherent to aqueous [bmim][BF4].« less

Experimental validation of a theoretical model of dual wavelength photoacoustic (PA) excitation in fluorophores

NASA Astrophysics Data System (ADS)

Märk, Julia; Theiss, Christoph; Schmitt, Franz-Josef; Laufer, Jan

2015-03-01

Fluorophores, such as exogenous dyes and genetically expressed proteins, exhibit radiative relaxation with long excited state lifetimes. This can be exploited for PA detection based on dual wavelength excitation using pump and probe wavelengths that coincide with the absorption and emission spectra, respectively. While the pump pulse raises the fluorophore to a long-lived excited state, simultaneous illumination with the probe pulse reduces the excited state lifetime due to stimulated emission (SE).This leads to a change in thermalized energy, and hence PA signal amplitude, compared to single wavelength illumination. By introducing a time delay between pump and probe pulses, the change in PA amplitude can be modulated. Since the effect is not observed in endogenous chromophores, it provides a contrast mechanism for the detection of fluorophores via PA difference imaging. In this study, a theoretical model of the PA signal generation in fluorophores was developed and experimentally validated. The model is based on a system of coupled rate equations, which describe the spatial and temporal changes in the population of the molecular energy levels of a fluorophore as a function of pump-probe energy and concentration. This allows the prediction of the thermalized energy distribution, and hence the time-resolved PA signal amplitude. The model was validated by comparing its predictions to PA signals measured in solutions of rhodamine 6G, a well-known laser dye, and Atto680, a NIR fluorophore.

A NASBA on microgel-tethered molecular-beacon microarray for real-time microbial molecular diagnostics.

PubMed

Ma, Y; Dai, X; Hong, T; Munk, G B; Libera, M

2016-12-19

Despite their many advantages and successes, molecular beacon (MB) hybridization probes have not been extensively used in microarray formats because of the complicating probe-substrate interactions that increase the background intensity. We have previously shown that tethering to surface-patterned microgels is an effective means for localizing MB probes to specific surface locations in a microarray format while simultaneously maintaining them in as water-like an environment as possible and minimizing probe-surface interactions. Here we extend this approach to include both real-time detection together with integrated NASBA amplification. We fabricate small (∼250 μm × 250 μm) simplex, duplex, and five-plex assays with microarray spots of controllable size (∼20 μm diameter), position, and shape to detect bacteria and fungi in a bloodstream-infection model. The targets, primers, and microgel-tethered probes can be combined in a single isothermal reaction chamber with no post-amplification labelling. We extract total RNA from clinical blood samples and differentiate between Gram-positive and Gram-negative bloodstream infection in a duplex assay to detect RNA- amplicons. The sensitivity based on our current protocols in a simplex assay to detect specific ribosomal RNA sequences within total RNA extracted from S. aureus and E. coli cultures corresponds to tens of bacteria per ml. We furthermore show that the platform can detect RNA- amplicons from synthetic target DNA with 1 fM sensitivity in sample volumes that contain about 12 000 DNA molecules. These experiments demonstrate an alternative approach that can enable rapid and real-time microarray-based molecular diagnostics.

Resonant antenna probes for tip-enhanced infrared near-field microscopy.

PubMed

Huth, Florian; Chuvilin, Andrey; Schnell, Martin; Amenabar, Iban; Krutokhvostov, Roman; Lopatin, Sergei; Hillenbrand, Rainer

2013-03-13

We report the development of infrared-resonant antenna probes for tip-enhanced optical microscopy. We employ focused-ion-beam machining to fabricate high-aspect ratio gold cones, which replace the standard tip of a commercial Si-based atomic force microscopy cantilever. Calculations show large field enhancements at the tip apex due to geometrical antenna resonances in the cones, which can be precisely tuned throughout a broad spectral range from visible to terahertz frequencies by adjusting the cone length. Spectroscopic analysis of these probes by electron energy loss spectroscopy, Fourier transform infrared spectroscopy, and Fourier transform infrared near-field spectroscopy corroborates their functionality as resonant antennas and verifies the broad tunability. By employing the novel probes in a scattering-type near-field microscope and imaging a single tobacco mosaic virus (TMV), we experimentally demonstrate high-performance mid-infrared nanoimaging of molecular absorption. Our probes offer excellent perspectives for optical nanoimaging and nanospectroscopy, pushing the detection and resolution limits in many applications, including nanoscale infrared mapping of organic, molecular, and biological materials, nanocomposites, or nanodevices.

Artemisinin activity-based probes identify multiple molecular targets within the asexual stage of the malaria parasites Plasmodium falciparum 3D7

PubMed Central

Ismail, Hanafy M.; Barton, Victoria; Phanchana, Matthew; Charoensutthivarakul, Sitthivut; Wong, Michael H. L.; Hemingway, Janet; Biagini, Giancarlo A.; O’Neill, Paul M.; Ward, Stephen A.

2016-01-01

The artemisinin (ART)-based antimalarials have contributed significantly to reducing global malaria deaths over the past decade, but we still do not know how they kill parasites. To gain greater insight into the potential mechanisms of ART drug action, we developed a suite of ART activity-based protein profiling probes to identify parasite protein drug targets in situ. Probes were designed to retain biological activity and alkylate the molecular target(s) of Plasmodium falciparum 3D7 parasites in situ. Proteins tagged with the ART probe can then be isolated using click chemistry before identification by liquid chromatography–MS/MS. Using these probes, we define an ART proteome that shows alkylated targets in the glycolytic, hemoglobin degradation, antioxidant defense, and protein synthesis pathways, processes essential for parasite survival. This work reveals the pleiotropic nature of the biological functions targeted by this important class of antimalarial drugs. PMID:26858419

Light, Molecules, Action: Using Ultrafast Uv-Visible and X-Ray Spectroscopy to Probe Excited State Dynamics in Photoactive Molecules

NASA Astrophysics Data System (ADS)

Sension, R. J.

2017-06-01

Light provides a versatile energy source capable of precise manipulation of material systems on size scales ranging from molecular to macroscopic. Photochemistry provides the means for transforming light energy from photon to process via movement of charge, a change in shape, a change in size, or the cleavage of a bond. Photochemistry produces action. In the work to be presented here ultrafast UV-Visible pump-probe, and pump-repump-probe methods have been used to probe the excited state dynamics of stilbene-based molecular motors, cyclohexadiene-based switches, and polyene-based photoacids. Both ultrafast UV-Visible and X-ray absorption spectroscopies have been applied to the study of cobalamin (vitamin B_{12}) based compounds. Optical measurements provide precise characterization of spectroscopic signatures of the intermediate species on the S_{1} surface, while time-resolved XANES spectra at the Co K-edge probe the structural changes that accompany these transformations.

Modular Synthesis of Biologically Active Phosphatidic Acid Probes Using Click Chemistry

PubMed Central

Smith, Matthew D.; Sudhahar, Christopher G.; Gong, Denghuang; Stahelin, Robert V.

2018-01-01

Phosphatidic acid (PA) is an important signaling lipid that plays roles in a range of biological processes including both physiological and pathophysiological events. PA is one of a number of signaling lipids that can act as site-specific ligands for protein receptors in binding events that enforce membrane-association and generally regulate both receptor function and subcellular localization. However, elucidation of the full scope of PA activities has proven problematic, primarily due to the lack of a consensus sequence among PA-binding receptors. Thus, experimental approaches, such as those employing lipid probes, are necessary for characterizing interactions at the molecular level. Herein, we describe an efficient modular approach to the synthesis of a range of PA probes that employs a late stage introduction of reporter groups. This strategy was exploited in the synthesis of PA probes bearing fluorescent and photoaffinity tags as well as a bifunctional probe containing both a photoaffinity moiety and an azide as a secondary handle for purification purposes. To discern the ability of these PA analogues to mimic the natural lipid in protein binding properties, each compound was incorporated into vesicles for binding studies using a known PA receptor, the C2 domain of PKCα. In these studies, each compound exhibited binding properties that were comparable to those of synthetic PA, indicating their viability as probes for effectively studying the activities of PA in cellular processes. PMID:19668861

Molecular photoacoustic imaging of breast cancer using an actively targeted conjugated polymer

PubMed Central

Balasundaram, Ghayathri; Ho, Chris Jun Hui; Li, Kai; Driessen, Wouter; Dinish, US; Wong, Chi Lok; Ntziachristos, Vasilis; Liu, Bin; Olivo, Malini

2015-01-01

Conjugated polymers (CPs) are upcoming optical contrast agents in view of their unique optical properties and versatile synthetic chemistry. Biofunctionalization of these polymer-based nanoparticles enables molecular imaging of biological processes. In this work, we propose the concept of using a biofunctionalized CP for noninvasive photoacoustic (PA) molecular imaging of breast cancer. In particular, after verifying the PA activity of a CP nanoparticle (CP dots) in phantoms and the targeting efficacy of a folate-functionalized version of the same (folate-CP dots) in vitro, we systemically administered the probe into a folate receptor-positive (FR+ve) MCF-7 breast cancer xenograft model to demonstrate the possible application of folate-CP dots for imaging FR+ve breast cancers in comparison to CP dots with no folate moieties. We observed a strong PA signal at the tumor site of folate-CP dots-administered mice as early as 1 hour after administration as a result of the active targeting of the folate-CP dots to the FR+ve tumor cells but a weak PA signal at the tumor site of CP-dots-administered mice as a result of the passive accumulation of the probe by enhanced permeability and retention effect. We also observed that folate-CP dots produced ~4-fold enhancement in the PA signal in the tumor, when compared to CP dots. These observations demonstrate the great potential of this active-targeting CP to be used as a contrast agent for molecular PA diagnostic imaging in various biomedical applications. PMID:25609951

Hyperspectral small animal fluorescence imaging: spectral selection imaging

NASA Astrophysics Data System (ADS)

Leavesley, Silas; Jiang, Yanan; Patsekin, Valery; Hall, Heidi; Vizard, Douglas; Robinson, J. Paul

2008-02-01

Molecular imaging is a rapidly growing area of research, fueled by needs in pharmaceutical drug-development for methods for high-throughput screening, pre-clinical and clinical screening for visualizing tumor growth and drug targeting, and a growing number of applications in the molecular biology fields. Small animal fluorescence imaging employs fluorescent probes to target molecular events in vivo, with a large number of molecular targeting probes readily available. The ease at which new targeting compounds can be developed, the short acquisition times, and the low cost (compared to microCT, MRI, or PET) makes fluorescence imaging attractive. However, small animal fluorescence imaging suffers from high optical scattering, absorption, and autofluorescence. Much of these problems can be overcome through multispectral imaging techniques, which collect images at different fluorescence emission wavelengths, followed by analysis, classification, and spectral deconvolution methods to isolate signals from fluorescence emission. We present an alternative to the current method, using hyperspectral excitation scanning (spectral selection imaging), a technique that allows excitation at any wavelength in the visible and near-infrared wavelength range. In many cases, excitation imaging may be more effective at identifying specific fluorescence signals because of the higher complexity of the fluorophore excitation spectrum. Because the excitation is filtered and not the emission, the resolution limit and image shift imposed by acousto-optic tunable filters have no effect on imager performance. We will discuss design of the imager, optimizing the imager for use in small animal fluorescence imaging, and application of spectral analysis and classification methods for identifying specific fluorescence signals.

77 FR 2738 - Center for Scientific Review; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-19

..., Review Group; Clinical Molecular Imaging and Probe Development. Date: February 2-3, 2012. Time: 7 p.m. to..., Bethesda, MD 20892, (301) 435-1777, [email protected] . Name of Committee: Molecular, Cellular and...: Molecular, Cellular and Developmental Neuroscience Integrated Review Group; Cellular and Molecular Biology...

The effect of hybridization-induced secondary structure alterations on RNA detection using backscattering interferometry

PubMed Central

Adams, Nicholas M.; Olmsted, Ian R.; Haselton, Frederick R.; Bornhop, Darryl J.; Wright, David W.

2013-01-01

Backscattering interferometry (BSI) has been used to successfully monitor molecular interactions without labeling and with high sensitivity. These properties suggest that this approach might be useful for detecting biomarkers of infection. In this report, we identify interactions and characteristics of nucleic acid probes that maximize BSI signal upon binding the respiratory syncytial virus nucleocapsid gene RNA biomarker. The number of base pairs formed upon the addition of oligonucleotide probes to a solution containing the viral RNA target correlated with the BSI signal magnitude. Using RNA folding software mfold, we found that the predicted number of unpaired nucleotides in the targeted regions of the RNA sequence generally correlated with BSI sensitivity. We also demonstrated that locked nucleic acid (LNA) probes improved sensitivity approximately 4-fold compared to DNA probes of the same sequence. We attribute this enhancement in BSI performance to the increased A-form character of the LNA:RNA hybrid. A limit of detection of 624 pM, corresponding to ∼105 target molecules, was achieved using nine distinct ∼23-mer DNA probes complementary to regions distributed along the RNA target. Our results indicate that BSI has promise as an effective tool for sensitive RNA detection and provides a road map for further improving detection limits. PMID:23519610

Molecular environmental geochemistry

NASA Astrophysics Data System (ADS)

O'Day, Peggy A.

1999-05-01

The chemistry, mobility, and bioavailability of contaminant species in the natural environment are controlled by reactions that occur in and among solid, aqueous, and gas phases. These reactions are varied and complex, involving changes in chemical form and mass transfer among inorganic, organic, and biochemical species. The field of molecular environmental geochemistry seeks to apply spectroscopic and microscopic probes to the mechanistic understanding of environmentally relevant chemical processes, particularly those involving contaminants and Earth materials. In general, empirical geochemical models have been shown to lack uniqueness and adequate predictive capability, even in relatively simple systems. Molecular geochemical tools, when coupled with macroscopic measurements, can provide the level of chemical detail required for the credible extrapolation of contaminant reactivity and bioavailability over ranges of temperature, pressure, and composition. This review focuses on recent advances in the understanding of molecular chemistry and reaction mechanisms at mineral surfaces and mineral-fluid interfaces spurred by the application of new spectroscopies and microscopies. These methods, such as synchrotron X-ray absorption and scattering techniques, vibrational and resonance spectroscopies, and scanning probe microscopies, provide direct chemical information that can elucidate molecular mechanisms, including element speciation, ligand coordination and oxidation state, structural arrangement and crystallinity on different scales, and physical morphology and topography of surfaces. Nonvacuum techniques that allow examination of reactions in situ (i.e., with water or fluids present) and in real time provide direct links between molecular structure and reactivity and measurements of kinetic rates or thermodynamic properties. Applications of these diverse probes to laboratory model systems have provided fundamental insight into inorganic and organic reactions at mineral surfaces and mineral-water interfaces. A review of recent studies employing molecular characterizations of soils, sediments, and biological samples from contaminated sites exemplifies the utility and benefits, as well as the challenge, of applying molecular probes to complicated natural materials. New techniques, technological advances, and the crossover of methods from other disciplines such as biochemistry and materials science promise better examination of environmental chemical processes in real time and at higher resolution, and will further the integration of molecular information into field-scale chemical and hydrologic models.

Karyotype Evolution in Birds: From Conventional Staining to Chromosome Painting

PubMed Central

Ferguson-Smith, Malcolm A.

2018-01-01

In the last few decades, there have been great efforts to reconstruct the phylogeny of Neoaves based mainly on DNA sequencing. Despite the importance of karyotype data in phylogenetic studies, especially with the advent of fluorescence in situ hybridization (FISH) techniques using different types of probes, the use of chromosomal data to clarify phylogenetic proposals is still minimal. Additionally, comparative chromosome painting in birds is restricted to a few orders, while in mammals, for example, virtually all orders have already been analyzed using this method. Most reports are based on comparisons using Gallus gallus probes, and only a small number of species have been analyzed with more informative sets of probes, such as those from Leucopternis albicollis and Gyps fulvus, which show ancestral macrochromosomes rearranged in alternative patterns. Despite this, it is appropriate to review the available cytogenetic information and possible phylogenetic conclusions. In this report, the authors gather both classical and molecular cytogenetic data and describe some interesting and unique characteristics of karyotype evolution in birds. PMID:29584697

Karyotype Evolution in Birds: From Conventional Staining to Chromosome Painting.

PubMed

Kretschmer, Rafael; Ferguson-Smith, Malcolm A; de Oliveira, Edivaldo Herculano Correa

2018-03-27

In the last few decades, there have been great efforts to reconstruct the phylogeny of Neoaves based mainly on DNA sequencing. Despite the importance of karyotype data in phylogenetic studies, especially with the advent of fluorescence in situ hybridization (FISH) techniques using different types of probes, the use of chromosomal data to clarify phylogenetic proposals is still minimal. Additionally, comparative chromosome painting in birds is restricted to a few orders, while in mammals, for example, virtually all orders have already been analyzed using this method. Most reports are based on comparisons using Gallus gallus probes, and only a small number of species have been analyzed with more informative sets of probes, such as those from Leucopternis albicollis and Gyps fulvus , which show ancestral macrochromosomes rearranged in alternative patterns. Despite this, it is appropriate to review the available cytogenetic information and possible phylogenetic conclusions. In this report, the authors gather both classical and molecular cytogenetic data and describe some interesting and unique characteristics of karyotype evolution in birds.

Electron Tunneling, a Quantum Probe for the Quantum World of Nanotechnology

ERIC Educational Resources Information Center

Hipps, K. W.; Scudiero, L.

2005-01-01

A quantum-mechanical probe is essential to study the quantum world, which is provided by electron tunneling. A spectroscopic mapping to image the electron-transport pathways on a sub-molecular scale is used.

A quantum spin-probe molecular microscope

NASA Astrophysics Data System (ADS)

Perunicic, V. S.; Hill, C. D.; Hall, L. T.; Hollenberg, L. C. L.

2016-10-01

Imaging the atomic structure of a single biomolecule is an important challenge in the physical biosciences. Whilst existing techniques all rely on averaging over large ensembles of molecules, the single-molecule realm remains unsolved. Here we present a protocol for 3D magnetic resonance imaging of a single molecule using a quantum spin probe acting simultaneously as the magnetic resonance sensor and source of magnetic field gradient. Signals corresponding to specific regions of the molecule's nuclear spin density are encoded on the quantum state of the probe, which is used to produce a 3D image of the molecular structure. Quantum simulations of the protocol applied to the rapamycin molecule (C51H79NO13) show that the hydrogen and carbon substructure can be imaged at the angstrom level using current spin-probe technology. With prospects for scaling to large molecules and/or fast dynamic conformation mapping using spin labels, this method provides a realistic pathway for single-molecule microscopy.

Imaging of radicals following injury or acute stress in peripheral nerves with activatable fluorescent probes.

PubMed

Zhou, Haiying; Yan, Ying; Ee, Xueping; Hunter, Daniel A; Akers, Walter J; Wood, Matthew D; Berezin, Mikhail Y

2016-12-01

Peripheral nerve injury evokes a complex cascade of chemical reactions including generation of molecular radicals. Conversely, the reactions within nerve induced by stress are difficult to directly detect or measure to establish causality. Monitoring these reactions in vivo would enable deeper understanding of the nature of the injury and healing processes. Here, we utilized near-infrared fluorescence molecular probes delivered via intra-neural injection technique to enable live, in vivo imaging of tissue response associated with nerve injury and stress. These initially quenched fluorescent probes featured specific sensitivity to hydroxyl radicals and become fluorescent upon encountering reactive oxygen species (ROS). Intraneurally delivered probes demonstrated rapid activation in injured rat sciatic nerve but minimal activation in normal, uninjured nerve. In addition, these probes reported activation within sciatic nerves of living rats after a stress caused by a pinprick stimulus to the abdomen. This imaging approach was more sensitive to detecting changes within nerves due to the induced stress than other techniques to evaluate cellular and molecular changes. Specifically, neither histological analysis of the sciatic nerves, nor the expression of pain and stress associated genes in dorsal root ganglia could provide statistically significant differences between the control and stressed groups. Overall, the results demonstrate a novel imaging approach to measure ROS in addition to the impact of ROS within nerve in live animals. Copyright © 2016 Elsevier Inc. All rights reserved.

Luminescent probes for optical in vivo imaging

NASA Astrophysics Data System (ADS)

Texier, Isabelle; Josserand, Veronique; Garanger, Elisabeth; Razkin, Jesus; Jin, Zhaohui; Dumy, Pascal; Favrot, Marie; Boturyn, Didier; Coll, Jean-Luc

2005-04-01

Going along with instrumental development for small animal fluorescence in vivo imaging, we are developing molecular fluorescent probes, especially for tumor targeting. Several criteria have to be taken into account for the optimization of the luminescent label. It should be adapted to the in vivo imaging optical conditions : red-shifted absorption and emission, limited overlap between absorption and emission for a good signal filtering, optimized luminescence quantum yield, limited photo-bleaching. Moreover, the whole probe should fulfill the biological requirements for in vivo labeling : adapted blood-time circulation, biological conditions compatibility, low toxicity. We here demonstrate the ability of the imaging fluorescence set-up developed in LETI to image the bio-distribution of molecular probes on short times after injection. Targeting with Cy5 labeled holo-transferrin of subcutaneous TS/Apc (angiogenic murine breast carcinoma model) or IGROV1 (human ovarian cancer) tumors was achieved. Differences in the kinetics of the protein uptake by the tumors were evidenced. IGROV1 internal metastatic nodes implanted in the peritoneal cavity could be detected in nude mice. However, targeted metastatic nodes in lung cancer could only be imaged after dissection of the mouse. These results validate our fluorescence imaging set-up and the use of Cy5 as a luminescent label. New fluorescent probes based on this dye and a molecular delivery template (the RAFT molecule) can thus be envisioned.

Synthesis and evaluation of new NIR-fluorescent probes for cathepsin B: ICT versus FRET as a turn-ON mode-of-action.

PubMed

Kisin-Finfer, Einat; Ferber, Shiran; Blau, Rachel; Satchi-Fainaro, Ronit; Shabat, Doron

2014-06-01

Recent years have seen tremendous progress in the design and study of molecular imaging geared towards biological and biomedical applications. The expression or activity of specific enzymes including proteases can be monitored by cutting edge molecular imaging techniques. Cathepsin B plays key roles in tumor progression via controlled degradation of extracellular matrix. Consequently, this protease has been attracting significant attention in cancer research, and many imaging probes targeting its activity have been developed. Here, we describe the design, synthesis and evaluation of two novel near infrared (NIR) fluorescent probes for detection of cathepsin B activity with different turn-ON mechanisms. One probe is based on an ICT activation mechanism of a donor-two-acceptor π-electron dye system, while the other is based on the FRET mechanism obtained by a fluorescent dye and a quencher. The two probes exhibit significant fluorescent turn-ON response upon cleavage by cathepsin B. The NIR fluorescence of the ICT probe in its OFF state was significantly lower than that of the FRET-based probe. This effect results in a higher signal-to-noise ratio and consequently increased sensitivity and better image contrast. Copyright © 2014 Elsevier Ltd. All rights reserved.

Biology of Symbioses between Marine Invertebrates and Intracellular Bacteria

DTIC Science & Technology

1989-01-05

number of gene probes for enzymes of CO2 (ribulose-1,5-bisphosphate carboxylase; RuBisCo ) and N2 (nitrogenase) fixation (see table 2). Using these probes... RuBisCo we could establish relationships and homologies for this enzyme among different symbionts. Table 1. Type and disposition of symblont DNA samples...st:;bution I Avail ?, I Table 2. Molecular probes available for this study. Prokaryote Type Plasrnid Probe Carbon Fixation ( RuBisCo ) Anabaena 7120

Molecular Dynamics Studies of Thermal Induced Chemistry in Tatb

NASA Astrophysics Data System (ADS)

Quenneville, J.; Germann, T. C.; Thompson, A. P.; Kober, E. M.

2007-12-01

A reactive force field (ReaxFF) is used with molecular dynamics to probe the chemistry induced by intense heating (`accelerated cook-off') of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). Large-system simulations are desired for TATB because of the high degree of carbon clustering expected in this material. Using small, 32-molecule simulations, we calculate the reaction rate as a function of temperature and compare the Arrhenius-predicted activation energy with experiment. Decomposition product evolution (mainly N2, H2O, CO2 and graphitic carbon clusters) is followed using a 576-molecule larger simulation, which also illustrates the effect of system size on both carbon clustering and reaction rate.

Wide interguild relationships among entomopathogenic and free-living nematodes in soil as measured by real time qPCR.

PubMed

Campos-Herrera, Raquel; El-Borai, Fahiem E; Duncan, Larry W

2012-10-01

Entomopathogenic nematodes (EPNs) are promising biological control agents of soil-dwelling insect pests of many crops. These nematodes are ubiquitous in both natural and agricultural areas. Their efficacy against arthropods is affected directly and indirectly by food webs and edaphic conditions. It has long been suggested that a greater understanding of EPN ecology is needed to achieve consistent biological control by these nematodes and the development of molecular tools is helping to overcome obstacles to the study of cryptic organisms and complex interactions. Here we extend the repertoire of molecular tools to characterize soil food webs by describing primers/probe set to quantify certain free-living, bactivorous nematodes (FLBNs) that interact with EPNs in soil. Three FLBN isolates were recovered from soil baited with insect larvae. Morphological and molecular characterization confirmed their identities as Acrobeloides maximum (RT-1-R15C and RT-2-R25A) and Rhabditis rainai (PT-R14B). Laboratory experiments demonstrated the ability of these FLBNs to interfere with the development of Steinernema diaprepesi, Steinernema riobrave and Heterorhabditis indica parasitizing the weevil Diaprepes abbreviatus (P<0.001), perhaps due to resource competition. A molecular probe was developed for the strongest competitor, A. maximum. We selected the highly conserved SSU rDNA sequence to design the primers/probe, because these sequences are more abundantly available for free-living nematodes than ITS sequences that can likely provide better taxonomic resolution. Our molecular probe can identify organisms that share ⩾98% similarity at this locus. The use of this molecular probe to characterize soil communities from samples of nematode DNA collected within a citrus orchard revealed positive correlations (P<0.01) between Acrobeloides-group nematodes and total numbers of EPNs (S. diaprepesi, H. indica and Heterorhabditis zealandica) as well as a complex of nematophagous fungi comprising Catenaria sp. and Monachrosporium gephyropagum that are natural enemies of EPNs. These relationships can be broadly interpreted as supporting Linford's hypothesis, i.e., decomposition of organic matter (here, insect cadavers) greatly increases bactivorous nematodes and their natural enemies. Copyright © 2012 Elsevier Inc. All rights reserved.

The behavior of Kevlar fibers under environmental-stress conditions

NASA Astrophysics Data System (ADS)

Perry, Mark Charles

There are a myriad of mechanisms by which polymers can degrade and fail. It is therefore important to understand the physical mechanics, chemistry, their interactions, and kinetics. This pursuit becomes more than just "academic" because these mechanisms might just change with service conditions (i.e. environment and loading). If one does not understand these processes from the molecular to macroscopic scale it would be exceedingly difficult to gain information from accelerated testing because the mechanisms just might change from one condition to another. The purpose of this study was to probe these processes on scales ranging from molecular to macroscopic in environmental stress conditions. This study reports the results of environmental-stress degradation of Kevlar 49 fibers. The environmental agent of focus was the ubiquitous air pollutant complex NOsb{x}. Other materials and environments were investigated to a lesser extent for purposes of comparison. Mechanical property (i.e., short-term strength, modulus, and creep lifetime) degradation was examined using single fiber, yarn, and epoxy coated yarn (composite) specimens under environmental-stress conditions. Optical and scanning electron microscopes were employed to examine and compare the appearance of fracture features resulting from the various testing conditions. Atomic force microscopy augmented these studies with detailed topographical mappings and measures of the fracture surface frictional and modulus properties. Molecular processes (i.e., chain scission and other mechanical-chemical reactions) were probed by measures of changes in viscosity average molecular weight and the infrared spectra. It was demonstrated that environmental-stress degradation effects do occur in the Kevlar-NOsb{x} gas system. Strength decay in environmentally exposed unloaded fibers was demonstrated and a synergistic response in creep reduced fiber lifetimes by three orders of magnitude at moderate loadings. That is to say, the combination of creep load and environment attack was greater than the sum of their individual contributions when measured separately. Microscopy showed a relatively unchanged taxonomy of fracture features over the range of environmental-stress testing conditions employed. Molecular scale probes failed to evidence occurrence of macroscopically homogeneous chain scission, but localized chain scission mechanisms could not be dismissed. The failure mechanism was dominated by fibrillation and plastic slippage on a morphological level. The mechanism of NOx enhanced degradation was postulated as a plasticizing effect in the interfibrillar lower molecular weight phase.

Refinement of glucagon-like peptide 1 docking to its intact receptor using mid-region photolabile probes and molecular modeling.

PubMed

Miller, Laurence J; Chen, Quan; Lam, Polo C-H; Pinon, Delia I; Sexton, Patrick M; Abagyan, Ruben; Dong, Maoqing

2011-05-06

The glucagon-like peptide 1 (GLP1) receptor is an important drug target within the B family of G protein-coupled receptors. Its natural agonist ligand, GLP1, has incretin-like actions and the receptor is a recognized target for management of type 2 diabetes mellitus. Despite recent solution of the structure of the amino terminus of the GLP1 receptor and several close family members, the molecular basis for GLP1 binding to and activation of the intact receptor remains unclear. We previously demonstrated molecular approximations between amino- and carboxyl-terminal residues of GLP1 and its receptor. In this work, we study spatial approximations with the mid-region of this peptide to gain insights into the orientation of the intact receptor and the ligand-receptor complex. We have prepared two new photolabile probes incorporating a p-benzoyl-l-phenylalanine into positions 16 and 20 of GLP1(7-36). Both probes bound to the GLP1 receptor specifically and with high affinity. These were each fully efficacious agonists, stimulating cAMP accumulation in receptor-bearing CHO cells in a concentration-dependent manner. Each probe specifically labeled a single receptor site. Protease cleavage and radiochemical sequencing identified receptor residue Leu(141) above transmembrane segment one as its site of labeling for the position 16 probe, whereas the position 20 probe labeled receptor residue Trp(297) within the second extracellular loop. Establishing ligand residue approximation with this loop region is unique among family members and may help to orient the receptor amino-terminal domain relative to its helical bundle region.

Probing Nucleobase Interactions and Predicting Mechanisms of Synthetic Interest Using Computational Chemistry, and Furthering the Development of BVI Education in Chemistry

ERIC Educational Resources Information Center

Harrison, Jason Gordon

2013-01-01

Quantum mechanical (QM) and molecular docking methods are used to probe systems of biological and synthetic interest. Probing interactions of nucleobases within proteins, and properly modeling said interactions toward novel nucleobase development, is extremely difficult, and of great utility in RNA interference (RNAi) therapeutics. The issues in…

A Crowdsourcing Evaluation of the NIH Chemical Probes

PubMed Central

Oprea, Tudor I.; Bologa, Cristian G.; Boyer, Scott; Curpan, Ramona F.; Glen, Robert C.; Hopkins, Andrew L.; Lipinski, Christopher A.; Marshall, Garland R.; Martin, Yvonne C.; Ostopovici-Halip, Liliana; Rishton, Gilbert; Ursu, Oleg; Vaz, Roy J.; Waller, Chris; Waldmann, Herbert; Sklar, Larry A.

2013-01-01

Between 2004 and 2008, the NIH molecular libraries and imaging initiative (MLI) pilot phase funded ten high-throughput Screening Centers, resulting in the deposition of 691 assays into PubChem and the nomination of 64 chemical probes. We crowdsourced the MLI output to 11 experts, who expressed medium or high levels of confidence in 48 of these 64 probes. PMID:19536101

Energy Donor Effect on the Sensing Performance for a Series of FRET-Based Two-Photon Fluorescent Hg2+ Probes

PubMed Central

Zhang, Yujin; Hu, Wei

2017-01-01

Nonlinear optical properties of a series of newly-synthesized molecular fluorescent probes for Hg2+ containing the same acceptor (rhodamine group) are analyzed by using time-dependent density functional theory in combination with analytical response theory. Special emphasis is placed on evolution of the probes’ optical properties in the absence and presence of Hg2+. These compounds show drastic changes in their photoabsorption and photoemission properties when they react with Hg2+, indicating that they are excellent candidates for ratiometric and colorimetric fluorescent chemosensors. Most importantly, the energy donor moiety is found to play a dominant role in sensing performance of these probes. Two-photon absorption cross sections of the compounds are increased with the presence of Hg2+, which theoretically suggests the possibility of the probes to be two-photon fluorescent Hg2+ sensors. Moreover, analysis of molecular orbitals is presented to explore responsive mechanism of the probes, where the fluorescence resonant energy transfer process is theoretically demonstrated. Our results elucidate the available experimental measurements. This work provides guidance for designing efficient two-photon fluorescent probes that are geared towards biological and chemical applications. PMID:28772466

Gd-EDDA/HYNIC-RGD as an MR molecular probe imaging integrin alphanubeta3 receptor-expressed tumor-MR molecular imaging of angiogenesis.

PubMed

Huo, Tianlong; Du, Xiangke; Zhang, Sen; Liu, Xia; Li, Xubing

2010-02-01

The aim of this study is to develop a novel MR probe containing arginine-glycine-aspartic acid (RGD) motif for imaging integrin alphanubeta3 receptor-expressed tumor. Commercially available HYNIC-RGD conjugated with co-ligand EDDA was labeled with Gd(3+), and the mixture was isolated and purified by solid phase extract (SPE) to get the entire probe Gd-EDDA/HYNIC-RGD. Human hepatocellular carcinoma (HHCC) cell line BEL-7402 was cultured and the cells harvested and suspended in serum-free Dulbecco's modified Eagle medium (DMEM) were subcutaneously inoculated into athymic nude mice for tumor growth. In vitro cell binding assay to integrin alphanubeta3 receptor and cell viability experiments were conducted. The in vivo imaging of the three arms of xenografts were performed by MR scan with a dedicated animal coil at time points of 0, 30, 60, 90min and 24-h post-intravenous injection (p.i.). Three arms of nude mice then were sacrificed for histological examination to confirm the imaging results. Gd-EDDA/HYNIC-RGD was successfully isolated by SPE and validity was verified on signal enhancement through in vitro and in vivo experiments. The nude mice model bearing HHCC was well established. There was approx. 30% signal enhancement on T1WI FSE images at 90min post-intravenous injection of the Gd-EDDA/HYNIC-RGD compared with baseline, and the signal to time curve is straightforward over time in the span of 0-90min p.i., while the control arms do not show this tendency. Gd-EDDA/HYNIC-RGD has the potential to serve as an MR probe detecting integrin alphanubeta3 receptor-expressed tumor. Copyright (c) 2008 Elsevier Ireland Ltd. All rights reserved.

Urinary p-cresol diagnosis using nanocomposite of ZnO/MoS2 and molecular imprinted polymer on optical fiber based lossy mode resonance sensor.

PubMed

Usha, Sruthi P; Gupta, Banshi D

2018-03-15

A lossy mode resonance (LMR) based sensor for urinary p-cresol testing on optical fiber substrate is developed. The sensor probe fabrication includes dip coating of nanocomposite layer of zinc oxide and molybdenum sulphide (ZnO/MoS 2 ) over unclad core of optical fiber as the transducer layer followed by the layer of molecular imprinted polymer (MIP) as the recognition medium. The addition of molybdenum sulphide in the transducer layer increases the absorption of light in the medium which enhances the LMR properties of zinc oxide thereby increasing the conductivity and hence the sensitivity of the sensor. The sensor probe is characterized for p-cresol concentration range from 0µM (reference sample) to 1000µM in artificially prepared urine. Optimizations of various probe fabrication parameters are carried to bring out the sensor's optimal performance with a sensitivity of 11.86nm/µM and 28nM as the limit of detection (LOD). A two-order improvement in LOD is obtained as compared to the recently reported p-cresol sensor. The proposed sensor possesses a response time of 15s which is 8 times better than that reported in the literature utilizing electrochemical method. Its response time is also better than the p-cresol sensor currently available in the market for the medical field. Thus, with a fast response, significant stability and repeatability, the proposed sensor holds practical implementation possibilities in the medical field. Further, the realization of sensor probe over optical fiber substrate adds remote sensing and online monitoring feasibilities. Copyright © 2017 Elsevier B.V. All rights reserved.

Chemical Probes for Molecular Imaging and Detection of Hydrogen Sulfide and Reactive Sulfur Species in Biological Systems

PubMed Central

2014-01-01

Hydrogen sulfide (H2S), a gaseous species produced by both bacteria and higher eukaryotic organisms, including mammalian vertebrates, has attracted attention in recent years for its contributions to human health and disease. H2S has been proposed as a cytoprotectant and gasotransmitter in many tissue types, including mediating vascular tone in blood vessels as well as neuromodulation in the brain. The molecular mechanisms dictating how H2S affects cellular signaling and other physiological events remain insufficiently understood. Furthermore, the involvement of H2S in metal-binding interactions and formation of related RSS such as sulfane sulfur may contribute to other distinct signaling pathways. Owing to its widespread biological roles and unique chemical properties, H2S is an appealing target for chemical biology approaches to elucidate its production, trafficking, and downstream function. In this context, reaction-based fluorescent probes offer a versatile set of screening tools to visualize H2S pools in living systems. Three main strategies used in molecular probe development for H2S detection include azide and nitro group reduction, nucleophilic attack, and CuS precipitation. Each of these approaches exploit the strong nucleophilicity and reducing potency of H2S to achieve selectivity over other biothiols. In addition, a variety of methods have been developed for the detection of other reactive sulfur species (RSS), including sulfite and bisulfite, as well as sulfane sulfur species and related modifications such as S-nitrosothiols. Access to this growing chemical toolbox of new molecular probes for H2S and related RSS sets the stage for applying these developing technologies to probe reactive sulfur biology in living systems. PMID:25474627

Molecular Cytogenetic Analysis of One African and Five Asian Macaque Species Reveals Identical Karyotypes as in Mandrill.

PubMed

Sangpakdee, Wiwat; Tanomtong, Alongkoad; Chaveerach, Arunrat; Pinthong, Krit; Trifonov, Vladimir; Loth, Kristina; Hensel, Christiana; Liehr, Thomas; Weise, Anja; Fan, Xiaobo

2018-04-01

The question how evolution and speciation work is one of the major interests of biology. Especially, genetic including karyotypic evolution within primates is of special interest due to the close phylogenetic position of Macaca and Homo sapiens and the role as in vivo models in medical research, neuroscience, behavior, pharmacology, reproduction and Acquired Immune Deficiency Syndrome (AIDS). Karyotypes of five macaque species from South East Asia and of one macaque species as well as mandrill from Africa were analyzed by high resolution molecular cytogenetics to obtain new insights into karyotypic evolution of old world monkeys. Molecular cytogenetics applying human probes and probe sets was applied in chromosomes of Macaca arctoides, M. fascicularis, M. nemestrina, M. assamensis, M. sylvanus, M. mulatta and Mandrillus sphinx. Established two- to multicolor-fluorescence in situ hybridization (FISH) approaches were applied. Locus-specific probes, whole and partial chromosome paint probes were hybridized. Especially the FISH-banding approach multicolor-banding (MCB) as well as probes oriented towards heterochromatin turned out to be highly efficient for interspecies comparison. Karyotypes of all seven studied species could be characterized in detail. Surprisingly, no evolutionary conserved differences were found among macaques, including mandrill. Between the seven here studied and phenotypically so different species we expected several via FISH detectable karyoypic and submicroscopic changes and were surprised to find none of them on a molecular cytogenetic level. Spatial separation, may explain the speciation and different evolution for some of them, like African M. sylvanus, Mandrillus sphinx and the South Asian macaques. However, for the partially or completely overlapping habitats of the five studied South Asian macaques the species separation process can also not be deduced to karyotypic separation.

Probing molecular orientations in thin films by x-ray photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Li, Y.; Li, P.; Lu, Z.-H.

2018-03-01

A great number of functional organic molecules in active thin-film layers of optoelectronic devices have highly asymmetric structures, such as plate-like, rod-like, etc. This makes molecular orientation an important aspect in thin-films as it can significantly affect both the optical and electrical performance of optoelectronic devices. With a combination of in-situ ultra violet photoelectron spectroscopy (UPS) and x-ray photoelectron spectroscopy (XPS) investigations for organic molecules having a broad range of structural properties, we discovered a rigid connection of core levels and frontier highest occupied molecular orbital levels at organic interfaces. This finding opens up opportunities of using X-ray photoemission spectroscopy as an alternative tool to UPS for providing an easy and unambiguous data interpretation in probing molecular orientations.

Quantum-chemical investigations of spectroscopic properties of a fluorescence probe

NASA Astrophysics Data System (ADS)

Titova, T. Yu.; Morozova, Yu. P.; Zharkova, O. M.; Artyukhov, V. Ya.; Korolev, B. V.

2012-09-01

The prodan molecule (6-propionyl-2-dimethylamino naphthalene) - fluorescence probe - is investigated by quantum-chemical methods of intermediate neglect of differential overlap (INDO) and molecular electrostatic potential (MEP). The dipole moments of the ground and excited states, the nature and position of energy levels, the centers of specific solvation, the rate constants of photoprocesses, and the fluorescence quantum yield are estimated. To elucidate the role of the dimethylamino group in the formation of bands and spectral characteristics, the molecule only with the propionyl group (pron) is investigated. The long-wavelength absorption bands of prodan and pron molecules are interpreted. The results obtained for the prodan molecule by the INDO method with original spectroscopic parameterization are compared with the literature data obtained by the DFT/CIS, ZINDO/S, and AM1/CISD methods.

A High Affinity Red Fluorescence and Colorimetric Probe for Amyloid β Aggregates

NASA Astrophysics Data System (ADS)

Rajasekhar, K.; Narayanaswamy, Nagarjun; Murugan, N. Arul; Kuang, Guanglin; Ågren, Hans; Govindaraju, T.

2016-04-01

A major challenge in the Alzheimer’s disease (AD) is its timely diagnosis. Amyloid β (Aβ) aggregates have been proposed as the most viable biomarker for the diagnosis of AD. Here, we demonstrate hemicyanine-based benzothiazole-coumarin (TC) as a potential probe for the detection of highly toxic Aβ42 aggregates through switch-on, enhanced (~30 fold) red fluorescence (Emax = 654 nm) and characteristic colorimetric (light red to purple) optical outputs. Interestingly, TC exhibits selectivity towards Aβ42 fibrils compared to other abnormal protein aggregates. TC probe show nanomolar binding affinity (Ka = 1.72 × 107 M-1) towards Aβ42 aggregates and also displace ThT bound to Aβ42 fibrils due to its high binding affinity. The Aβ42 fibril-specific red-shift in the absorption spectra of TC responsible for the observed colorimetric optical output has been attributed to micro-environment change around the probe from hydrophilic-like to hydrophobic-like nature. The binding site, binding energy and changes in optical properties observed for TC upon interaction with Aβ42 fibrils have been further validated by molecular docking and time dependent density functional theory studies.

Nanomaterials for in vivo imaging of mechanical forces and electrical fields

NASA Astrophysics Data System (ADS)

Mehlenbacher, Randy D.; Kolbl, Rea; Lay, Alice; Dionne, Jennifer A.

2018-02-01

Cellular signalling is governed in large part by mechanical forces and electromagnetic fields. Mechanical forces play a critical role in cell differentiation, tissue organization and diseases such as cancer and heart disease; electrical fields are essential for intercellular communication, muscle contraction, neural signalling and sensory perception. Therefore, quantifying a biological system's forces and fields is crucial for understanding physiology and disease pathology and for developing medical tools for repair and recovery. This Review highlights advances in sensing mechanical forces and electrical fields in vivo, focusing on optical probes. The emergence of biocompatible optical probes, such as genetically encoded voltage indicators, molecular rotors, fluorescent dyes, semiconducting nanoparticles, plasmonic nanoparticles and lanthanide-doped upconverting nanoparticles, offers exciting opportunities to push the limits of spatial and temporal resolution, stability, multi-modality and stimuli sensitivity in bioimaging. We further discuss the materials design principles behind these probes and compare them across various metrics to facilitate sensor selection. Finally, we examine which advances are necessary to fully unravel the role of mechanical forces and electrical fields in vivo, such as the ability to probe the vectorial nature of forces, the development of combined force and field sensors, and the design of efficient optical actuators.

Strong and Long Makes Short: Strong-Pump Strong-Probe Spectroscopy.

PubMed

Gelin, Maxim F; Egorova, Dassia; Domcke, Wolfgang

2011-01-20

We propose a new time-domain spectroscopic technique that is based on strong pump and probe pulses. The strong-pump strong-probe (SPSP) technique provides temporal resolution that is not limited by the durations of the pump and probe pulses. By numerically exact simulations of SPSP signals for a multilevel vibronic model, we show that the SPSP signals exhibit electronic and vibrational beatings on time scales which are significantly shorter than the pulse durations. This suggests the possible application of SPSP spectroscopy for the real-time investigation of molecular processes that cannot be temporally resolved by pump-probe spectroscopy with weak pump and probe pulses.

A Multiwavelength Study of the Nature of Diffuse Atomic and Molecular Gas

NASA Astrophysics Data System (ADS)

Federman, Steven

2015-10-01

Our proposed observations under the UV Initiative form a key component of a multiwavelength study of diffuse atomic and molecular clouds. The Herschel GOT C+ survey associated [C II] emission at 158 microns with emission from H I at 21 cm and CO at 2.6 mm, revealing the presence of warm neutral gas, cold neutral gas, CO-dark H2 gas, and molecular clouds. Ground-based measurements of Ca II, CH+, CH, and CN at visible wavelengths show absorption at the same velocities as the components seen in the GOT C+ survey. A main focus of our project is a detailed investigation of the nature of CO-dark H2 gas, interstellar material not associated with H I and CO emission. The presence of this additional material alters our view of molecular gas in galaxies and its connection to star formation rates. We propose ultraviolet observations of three targets with STIS that probe two of the pointings in the GOT C+ survey. Absorption from CO, at much greater sensitivies than is possible from surveying CO emission, will be sought. Analysis of CO, C I, and C2 absorption will yield the physical conditions (gas density and temperature) along the sight lines. The results will be compared with those inferred from CN chemistry based on the observations at visible wavelengths. Other probes seen at UV wavelengths, such as O I, Cu II, and Cl I, will provide a more complete picture of the environment seen in the atomic components of the GOT C+ survey. The outcome of the project will be the most detailed study of diffuse atomic and molecular gas from spectral measurements spanning nearly seven orders of magnitude in wavelength.

Protein crystals as scanned probes for recognition atomic force microscopy.

PubMed

Wickremasinghe, Nissanka S; Hafner, Jason H

2005-12-01

Lysozyme crystal growth has been localized at the tip of a conventional silicon nitride cantilever through seeded nucleation. After cross-linking with glutaraldehyde, lysozyme protein crystal tips image gold nanoparticles and grating standards with a resolution comparable to that of conventional tips. Force spectra between the lysozyme crystal tips and surfaces covered with antilysozyme reveal an adhesion force that drops significantly upon blocking with free lysozyme, thus confirming that lysozyme crystal tips can detect molecular recognition interactions.

Probing Structural Changes among Analogous Inhibitor-Bound Forms of HIV-1 Protease and a Drug-Resistant Mutant in Solution by Nuclear Magnetic Resonance.

PubMed

Khan, Shahid N; Persons, John D; Paulsen, Janet L; Guerrero, Michel; Schiffer, Celia A; Kurt-Yilmaz, Nese; Ishima, Rieko

2018-03-13

In the era of state-of-the-art inhibitor design and high-resolution structural studies, detection of significant but small protein structural differences in the inhibitor-bound forms is critical to further developing the inhibitor. Here, we probed differences in HIV-1 protease (PR) conformation among darunavir and four analogous inhibitor-bound forms and compared them with a drug-resistant mutant using nuclear magnetic resonance chemical shifts. Changes in amide chemical shifts of wild-type (WT) PR among these inhibitor-bound forms, ΔCSP, were subtle but detectable and extended >10 Å from the inhibitor-binding site, asymmetrically between the two subunits of PR. Molecular dynamics simulations revealed differential local hydrogen bonding as the molecular basis of this remote asymmetric change. Inhibitor-bound forms of the drug-resistant mutant also showed a similar long-range ΔCSP pattern. Differences in ΔCSP values of the WT and the mutant (ΔΔCSPs) were observed at the inhibitor-binding site and in the surrounding region. Comparing chemical shift changes among highly analogous inhibitors and ΔΔCSPs effectively eliminated local environmental effects stemming from different chemical groups and enabled exploitation of these sensitive parameters to detect subtle protein conformational changes and to elucidate asymmetric and remote conformational effects upon inhibitor interaction.

Molecularly "engineered" anode adsorbates for probing OLED interfacial structure-charge injection/luminance relationships: large, structure-dependent effects.

PubMed

Huang, Qinglan; Evmenenko, Guennadi; Dutta, Pulak; Marks, Tobin J

2003-12-03

Molecule-scale structure effects at organic light-emitting diodes (OLED) anode-organic transport layer interfaces are probed via a self-assembly approach. A series of ITO anode-linked silyltriarylamine molecules differing in aryl group and linker density are synthesized for this purpose and used to probe the relationship between nanoscale interfacial chemical structure, charge injection and electroluminescence properties. Dramatic variations in hole injection magnitude and OLED performance can be correlated with the molecular structures and electrochemically derived heterogeneous electron-transfer rates of such triarylamine fragments, placed precisely at the anode-hole transport layer interface. Very bright and efficient ( approximately 70 000 cd/m2 and approximately 2.5% forward external quantum efficiency) OLEDs have thereby been fabricated.

Location of fluorescent probes (2'-hydroxy derivatives of 2,5-diaryl-1,3-oxazole) in lipid membrane studied by fluorescence spectroscopy and molecular dynamics simulation.

PubMed

Posokhov, Yevgen; Kyrychenko, Alexander

2018-04-01

2'-Hydroxy derivatives of 2,5-diaryl-1,3-oxazole are known as environment-sensitive ratiometric excited-state intramolecular proton transfer (ESIPT) fluorescent probes, which are used to monitor physicochemical properties of lipid membranes. However, because of their heterogeneous membrane distribution, accurate experimental determination of the probe position is difficult. To estimate the location of the ESIPT probes in lipid membranes we have performed fluorescence measurements and molecular dynamics (MD) simulations. In the series composed of 2-(2'-hydroxy-phenyl)-5-phenyl-1,3-oxazole (1), 2-(2'-hydroxy-phenyl)-5-(4'-biphenyl)-1,3-oxazole (2), and 2-(2'-hydroxy-phenyl)-phenanthro[9,10-d]-1,3-oxazole (3), the structure of the ESIPT-moiety of 2-(2'-hydroxy-phenyl)-oxazole was varied by either aromatic ring substitution or annealing, leading to the systematical increase in the hydrophobic character of the probes. The comparison of the fluorescence behavior of probes 1-3 in a wide variety of solvents with those in phospholipid vesicles revealed that all three probes prefer to reside inside a membrane. Our MD results demonstrate that the probes locate from the glycerol residues and the polar carbonyl groups of phospholipids up to hydrophobic acyl chain units. It has been found that the probe location correlates well with the size of the aromatic moiety, being gradually shifted from 11.1 Å to 7.6 Å from the bilayer center for probes 1 to 3, respectively. Our results may be useful for the design of novel fluorescent probes for fluorescence sensing of specific regions within a lipid membrane. Copyright © 2018 Elsevier B.V. All rights reserved.

Foldable polymers as probes

DOEpatents

Li, Alexander D. Q. [Pullman, WA; Wang, Wei [Pullman, WA

2007-07-03

Disclosed herein are novel probes, which can be used to detect and identify target molecules of interest in a sample. The disclosed probes can be used to monitor conformational changes induced by molecular recognition events in addition to providing signaling the presence and/or identity of a target molecule. Methods, including solid phase synthesis techniques, for making probe molecules that exhibit changes in their optical properties upon target molecule binding are described in the disclosure. Also disclosed herein are novel chromophore moieties, which have tailored fluorescent emission spectra.

Foldable polymers as probes

DOEpatents

Li, Alexander D. Q. [Pullman, WA; Wang, Wei [Pullman, WA

2009-07-07

Disclosed herein are novel probes, which can be used to detect and identify target molecules of interest in a sample. The disclosed probes can be used to monitor conformational changes induced by molecular recognition events in addition to providing signaling the presence and/or identity of a target molecule. Methods, including solid phase synthesis techniques, for making probe molecules that exhibit changes in their optical properties upon target molecule binding are described in the disclosure. Also disclosed herein are novel chromophore moieties, which have tailored fluorescent emission spectra.

Super-resolved FT-IR spectroscopy: Strategies, challenges, and opportunities for membrane biophysics.

PubMed

Li, Jessica J; Yip, Christopher M

2013-10-01

Direct correlation of molecular conformation with local structure is critical to studies of protein- and peptide-membrane interactions, particularly in the context of membrane-facilitated aggregation, and disruption or disordering. Infrared spectroscopy has long been a mainstay for determining molecular conformation, following folding dynamics, and characterizing reactions. While tremendous advances have been made in improving the spectral and temporal resolution of infrared spectroscopy, it has only been with the introduction of scanned-probe techniques that exploit the raster-scanning tip as either a source, scattering tool, or measurement probe that researchers have been able to obtain sub-diffraction limit IR spectra. This review will examine the history of correlated scanned-probe IR spectroscopies, from their inception to their use in studies of molecular aggregates, membrane domains, and cellular structures. The challenges and opportunities that these platforms present for examining dynamic phenomena will be discussed. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies. Copyright © 2013 Elsevier B.V. All rights reserved.

Sounding rocket flight report, MUMP 9 and MUMP 10

NASA Technical Reports Server (NTRS)

Grassl, H. J.

1971-01-01

The results of the launching of two-Marshall-University of Michigan Probes (MUMP 9 and MUMP 10), Nike-Tomahawk sounding rocket payloads, are summarized. The MUMP is similar to the thermosphere probe, an ejectable instrument package for studying the variability of the earth's atmospheric parameters. The MUMP 9 payload included an omegatron mass analyzer, a molecular fluorescence densitometer, a mini-tilty filter, and a lunar position sensor. This complement of instruments permitted the determination of the molecular nitrogen density and temperature in the altitude range from approximately 143 to 297 km over Wallops Island, Virginia, during January 1971. The MUMP 10 payload included an omegatron mass analyzer, an electron temperature probe, a cryogenic densitometer, and a solar position sensor. These instruments permitted the determination of the molecular nitrogen density and temperature and the charged particle density and temperature in the altitude range from approximately 145 to 290 km over Wallops Island during the afternoon preceding the MUMP 9 launch.

Diffusion of uncharged probe reveals structural changes in polyacids initiated by their neutralization: poly(acrylic acids).

PubMed

Hyk, Wojciech; Masiak, Michal; Stojek, Zbigniew; Ciszkowska, Malgorzata

2005-03-17

The diffusion studies of the uncharged probe (1,1'-ferrocenedimethanol) have been successfully applied for the evaluation of the changes in the three-dimensional structure of poly(acrylic acids) of various molecular weights (ranging from 2000 to 4,000,000 g/mol) during their neutralization with a strong base. The qualitative picture of the macromolecule arrangement during the titration of the polyacids has been obtained from the conductometric measurements. The characteristic changes in the poly(acrylic acid) conductivity are practically the same for all polyacids examined and are in a very good agreement with the predictions of our theoretical model of the polyelectrolyte conductance. The transformation of the polyelectrolyte solution into the gel-like or gel phase has been investigated more quantitatively by tracing the changes in the diffusion coefficient of the uncharged probe redox system. The probe diffusivities, D, were determined using steady-state voltammetry at microelectrodes for a wide range of neutralization degree, alpha, of the polyacids tested. The dependencies of D versus alpha are of similar shape for all poly(acrylic acids). The first parts of the dependencies reflect a rapid increase in D (up to neutralization degree of either 45% for the lowest molecular-weight poly(acrylic acid) or 75-80% for other polyacids). They are followed by the parts of a slight drop in the diffusion coefficient. The changes in the probe diffusivity become stronger as the molecular weight of poly(acrylic acid) increases. The maximum probe diffusion coefficients are greater than the initial values in the pure polyacid solutions by 14, 24, 19, 30, and 28% for poly(acrylic acid) of molecular weights of 2000, 450,000, 1,250,000, 3,000,000, and 4,000,000 g/mol, respectively. The variation in the probe diffusion coefficient qualitatively follows the line of the changes in the macroscopic viscosity of the polyelectrolyte system. This is in contrast to the predictions of the Stokes-Einstein relation and, therefore, suggests that the changes in the probe diffusion rate are mainly due to the structural changes in the polyacrylate medium and the macromolecular rearrangements induced by the chemical, acid-base reaction. By adapting the obstruction model for diffusion in homogeneous gels, the transport characteristics of the probe were converted into the structural characteristics of the polyelectrolytic systems. It has been found that the most ordered structure of the polyelectrolyte, or in other words the most permeable structure, is obtained when poly(acrylic acid) is neutralized at 75-80%.

EPR spin probe and spin label studies of some low molecular and polymer micelles

NASA Astrophysics Data System (ADS)

Wasserman, A. M.; Kasaikin, V. A.; Timofeev, V. P.

1998-12-01

The rotational mobility of spin probes of different shape and size in low molecular and polymer micelles has been studied. Several probes having nitroxide fragment localized either in the vicinity of micelle interface or in the hydrocarbon core have been used. Upon increasing the number of carbon atoms in hydrocarbon chain of detergent from 7 to 13 (sodium alkyl sulfate micelles) or from 12 to 16 (alkyltrimethylammonium bromide micelles) the rotational mobility of spin probes is decreased by the factor 1.5-2.0. The spin probe rotational mobility in polymer micelles (the complexes of alkyltrimethylammonium bromides and polymethacrylic or polyacrylic acids) is less than mobility in free micelles of the same surfactants. The study of EPR-spectra of spin labeled polymethacrylic acid (PMA) indicated that formation of water soluble complexes of polymer and alkyltrimethylammonium bromides in alkaline solutions (pH 9) does not affect the polymer segmental mobility. On the other hand, the polymer complexes formation in slightly acidic water solution (pH 6) breaks down the compact PMA conformation, thus increasing the polymer segmental mobility. Possible structures of polymer micelles are discussed.

Quantum Dot-Fullerene Based Molecular Beacon Nanosensors for Rapid, Highly Sensitive Nucleic Acid Detection.

PubMed

Liu, Ye; Kannegulla, Akash; Wu, Bo; Cheng, Li-Jing

2018-05-15

Spherical fullerene (C 60 ) can quench the fluorescence of a quantum dot (QD) through energy transfer and charge transfer processes, with the quenching efficiency regulated by the number of proximate C 60 on each QD. With the quenching property and its small size compared with other nanoparticle-based quenchers, it is advantageous to group a QD reporter and multiple C 60 -labeled oligonucleotide probes to construct a molecular beacon (MB) probe for sensitive, robust nucleic acid detection. We demonstrated a rapid, high-sensitivity DNA detection method using the nanosensors composed of QD-C 60 based MBs carried by magnetic nanoparticles (MNPs). The assay was accelerated by first dispersing the nanosensors in analytes for highly efficient DNA capture resulting from short-distance 3-dimensional diffusion of targets to the sensor surface and then concentrating the nanosensors to a substrate by magnetic force to amplify the fluorescence signal for target quantification. The enhanced mass transport enabled a rapid detection (< 10 min) with a small sample volume (1-10 µl). The high signal-to-noise ratio produced by the QD-C 60 pairs and magnetic concentration yielded a detection limit of 100 fM (~106 target DNA copies for a 10 µl analyte). The rapid, sensitive, label-free detection method will benefit the applications in point-of-care molecular diagnostic technologies.

The first CO+ image: I. Probing the HI/H2 layer around the ultracompact HII region Mon R2

PubMed Central

Treviño-Morales, S. P.; Fuente, A.; Sánchez-Monge, Á.; Pilleri, P.; Goicoechea, J. R.; Ossenkopf-Okada, V.; Roueff, E.; Rizzo, J. R.; Gerin, M.; Berné, O.; Cernicharo, J.; Gónzalez-García, M.; Kramer, C.; García-Burillo, S.; Pety, J.

2016-01-01

The CO+ reactive ion is thought to be a tracer of the boundary between a HII region and the hot molecular gas. In this study, we present the spatial distribution of the CO+ rotational emission toward the Mon R2 star-forming region. The CO+ emission presents a clumpy ring-like morphology, arising from a narrow dense layer around the HII region. We compare the CO+ distribution with other species present in photon-dominated regions (PDR), such as [CII] 158 µm, H2 S(3) rotational line at 9.3 µm, polycyclic aromatic hydrocarbons (PAHs) and HCO+. We find that the CO+ emission is spatially coincident with the PAHs and [CII] emission. This confirms that the CO+ emission arises from a narrow dense layer of the HI/H2 interface. We have determined the CO+ fractional abundance, relative to C+ toward three positions. The abundances range from 0.1 to 1.9 ×10−10 and are in good agreement with previous chemical model, which predicts that the production of CO+ in PDRs only occurs in dense regions with high UV fields. The CO+ linewidth is larger than those found in molecular gas tracers, and their central velocity are blue-shifted with respect to the molecular gas velocity. We interpret this as a hint that the CO+ is probing photo-evaporating clump surfaces. PMID:27721515

Molecular orbital imaging via above-threshold ionization with circularly polarized pulses.

PubMed

Zhu, Xiaosong; Zhang, Qingbin; Hong, Weiyi; Lu, Peixiang; Xu, Zhizhan

2011-07-18

Above-threshold ionization (ATI) for aligned or orientated linear molecules by circularly polarized laser pulsed is investigated. It is found that the all-round structural information of the molecular orbital is extracted with only one shot by the circularly polarized probe pulse rather than with multi-shot detections in a linearly polarized case. The obtained photoelectron momentum spectrum directly depicts the symmetry and electron distribution of the occupied molecular orbital, which results from the strong sensitivity of the ionization probability to these structural features. Our investigation indicates that the circularly polarized probe scheme would present a simple method to study the angle-dependent ionization and image the occupied electronic orbital.

Two-dimensional fourier transform spectrometer

DOEpatents

DeFlores, Lauren; Tokmakoff, Andrei

2016-10-25

The present invention relates to a system and methods for acquiring two-dimensional Fourier transform (2D FT) spectra. Overlap of a collinear pulse pair and probe induce a molecular response which is collected by spectral dispersion of the signal modulated probe beam. Simultaneous collection of the molecular response, pulse timing and characteristics permit real time phasing and rapid acquisition of spectra. Full spectra are acquired as a function of pulse pair timings and numerically transformed to achieve the full frequency-frequency spectrum. This method demonstrates the ability to acquire information on molecular dynamics, couplings and structure in a simple apparatus. Multi-dimensional methods can be used for diagnostic and analytical measurements in the biological, biomedical, and chemical fields.

Two-dimensional fourier transform spectrometer

DOEpatents

DeFlores, Lauren; Tokmakoff, Andrei

2013-09-03

The present invention relates to a system and methods for acquiring two-dimensional Fourier transform (2D FT) spectra. Overlap of a collinear pulse pair and probe induce a molecular response which is collected by spectral dispersion of the signal modulated probe beam. Simultaneous collection of the molecular response, pulse timing and characteristics permit real time phasing and rapid acquisition of spectra. Full spectra are acquired as a function of pulse pair timings and numerically transformed to achieve the full frequency-frequency spectrum. This method demonstrates the ability to acquire information on molecular dynamics, couplings and structure in a simple apparatus. Multi-dimensional methods can be used for diagnostic and analytical measurements in the biological, biomedical, and chemical fields.

Exploring hydrophobic subdomain IIA of the protein bovine serum albumin in the native, intermediate, unfolded, and refolded states by a small fluorescence molecular reporter.

PubMed

Paul, Bijan Kumar; Samanta, Anuva; Guchhait, Nikhil

2010-05-13

A simple intramolecular charge transfer (ICT) compound, 5-(4-dimethylamino-phenyl)-penta-2,4-dienoic acid methyl ester (DPDAME), has been documented to be a potential molecular reporter for probing microheterogeneous environments of a model transport protein bovine serum albumin (BSA) using spectroscopic techniques. Meteoric modifications to the emission profile of DPDAME upon addition of BSA come out to be a result of its binding to hydrophobic subdomain IIA. The highly polarity-sensitive ICT emission of DPDAME is found to be a proficient extrinsic molecular reporter for efficient mapping of native, intermediate, unfolded, and refolded states of the protein. Experimental data coupled with a reinforcing support from theoretical simulation using CHARMM22 software confirm the binding site of the probe to be the subdomain IIA of BSA, while FRET study reveals a remarkably close approach of our extrinsic molecular reporter to Trp-212 (in domain IIA): the distance between DPDAME and Trp-212 is 1.437 nm. The caliber of DPDAME as an external fluorescence marker also extends to the depiction of protein-surfactant (BSA-SDS) interaction to commendable fruition. Additionally, the protective action of small amounts of SDS on urea-denatured protein is documented by polarity-sensitive ICT emission of the probe. The present study also reflects the enhancement of the stability of BSA with respect to chemically induced denaturation by urea as a result of binding to the probe DPDAME.

Detection of hydroxyapatite in calcified cardiovascular tissues.

PubMed

Lee, Jae Sam; Morrisett, Joel D; Tung, Ching-Hsuan

2012-10-01

The objective of this study is to develop a method for selective detection of the calcific (hydroxyapatite) component in human aortic smooth muscle cells in vitro and in calcified cardiovascular tissues ex vivo. This method uses a novel optical molecular imaging contrast dye, Cy-HABP-19, to target calcified cells and tissues. A peptide that mimics the binding affinity of osteocalcin was used to label hydroxyapatite in vitro and ex vivo. Morphological changes in vascular smooth muscle cells were evaluated at an early stage of the mineralization process induced by extrinsic stimuli, osteogenic factors and a magnetic suspension cell culture. Hydroxyapatite components were detected in monolayers of these cells in the presence of osteogenic factors and a magnetic suspension environment. Atherosclerotic plaque contains multiple components including lipidic, fibrotic, thrombotic, and calcific materials. Using optical imaging and the Cy-HABP-19 molecular imaging probe, we demonstrated that hydroxyapatite components could be selectively distinguished from various calcium salts in human aortic smooth muscle cells in vitro and in calcified cardiovascular tissues, carotid endarterectomy samples and aortic valves, ex vivo. Hydroxyapatite deposits in cardiovascular tissues were selectively detected in the early stage of the calcification process using our Cy-HABP-19 probe. This new probe makes it possible to study the earliest events associated with vascular hydroxyapatite deposition at the cellular and molecular levels. This target-selective molecular imaging probe approach holds high potential for revealing early pathophysiological changes, leading to progression, regression, or stabilization of cardiovascular diseases. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Detection of Hydroxyapatite in Calcified Cardiovascular Tissues

PubMed Central

Lee, Jae Sam; Morrisett, Joel D.; Tung, Ching-Hsuan

2012-01-01

Objective The objective of this study is to develop a method for selective detection of the calcific (hydroxyapatite) component in human aortic smooth muscle cells in vitro and in calcified cardiovascular tissues ex vivo. This method uses a novel optical molecular imaging contrast dye, Cy-HABP-19, to target calcified cells and tissues. Methods A peptide that mimics the binding affinity of osteocalcin was used to label hydroxyapatite in vitro and ex vivo. Morphological changes in vascular smooth muscle cells were evaluated at an early stage of the mineralization process induced by extrinsic stimuli, osteogenic factors and a magnetic suspension cell culture. Hydroxyapatite components were detected in monolayers of these cells in the presence of osteogenic factors and a magnetic suspension environment. Results Atherosclerotic plaque contains multiple components including lipidic, fibrotic, thrombotic, and calcific materials. Using optical imaging and the Cy-HABP-19 molecular imaging probe, we demonstrated that hydroxyapatite components could be selectively distinguished from various calcium salts in human aortic smooth muscle cells in vitro and in calcified cardiovascular tissues, carotid endarterectomy samples and aortic valves, ex vivo. Conclusion Hydroxyapatite deposits in cardiovascular tissues were selectively detected in the early stage of the calcification process using our Cy-HABP-19 probe. This new probe makes it possible to study the earliest events associated with vascular hydroxyapatite deposition at the cellular and molecular levels. This target-selective molecular imaging probe approach holds high potential for revealing early pathophysiological changes, leading to progression, regression, or stabilization of cardiovascular diseases. PMID:22877867

Deficient expression of aldehyde dehydrogenase 1A1 is consistent with increased sensitivity of Gorlin syndrome patients to radiation carcinogenesis

DOE PAGES

Wright, Aaron T.; Magnaldo, Thierry; Sontag, Ryan L.; ...

2013-11-27

Human phenotypes that are highly susceptible to radiation carcinogenesis have been identified. Sensitive phenotypes often display robust regulation of molecular features that modify biological response, which can facilitate identification of relevant pathways/networks. Here we interrogate primary dermal fibroblasts isolated from Gorlin syndrome patients (GDFs), who display a pronounced tumorigenic response to radiation, in comparison to normal human dermal fibroblasts (NHDFs). Our approach exploits newly developed thiol-reactive probes with a flexible click chemistry functional group to define changes in protein thiol profiles in live cell studies, which minimizes artifacts associated with cell lysis. We observe qualitative differences in protein thiol profilesmore » by SDS-PAGE analysis when detection by iodoacetamide vs maleimide probe chemistries are compared, and pretreatment of cells with hydrogen peroxide eliminates detection of the majority of SDS-PAGE bands. Redox probes revealed deficient expression of an apparent 55 kDa protein thiol in GDFs from independent donors, compared with NHDFs. Proteomics tentatively identified this protein as aldehyde dehydrogenase 1A1 (ALDH1A1), a key enzyme regulating retinoic acid synthesis, and this deficiency was confirmed by Western blot. Redox probes revealed additional protein thiol differences between GDFs and NHDFs, including radiation responsive annexin family members. Our results indicate a multifactorial basis for the unusual sensitivity of Gorlin syndrome to radiation carcinogenesis, and the pathways identified have plausible implications for radiation health effects.« less

Deficient expression of aldehyde dehydrogenase 1A1 is consistent with increased sensitivity of Gorlin syndrome patients to radiation carcinogenesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wright, Aaron T.; Magnaldo, Thierry; Sontag, Ryan L.

Human phenotypes that are highly susceptible to radiation carcinogenesis have been identified. Sensitive phenotypes often display robust regulation of molecular features that modify biological response, which can facilitate identification of relevant pathways/networks. Here we interrogate primary dermal fibroblasts isolated from Gorlin syndrome patients (GDFs), who display a pronounced tumorigenic response to radiation, in comparison to normal human dermal fibroblasts (NHDFs). Our approach exploits newly developed thiol-reactive probes with a flexible click chemistry functional group to define changes in protein thiol profiles in live cell studies, which minimizes artifacts associated with cell lysis. We observe qualitative differences in protein thiol profilesmore » by SDS-PAGE analysis when detection by iodoacetamide vs maleimide probe chemistries are compared, and pretreatment of cells with hydrogen peroxide eliminates detection of the majority of SDS-PAGE bands. Redox probes revealed deficient expression of an apparent 55 kDa protein thiol in GDFs from independent donors, compared with NHDFs. Proteomics tentatively identified this protein as aldehyde dehydrogenase 1A1 (ALDH1A1), a key enzyme regulating retinoic acid synthesis, and this deficiency was confirmed by Western blot. Redox probes revealed additional protein thiol differences between GDFs and NHDFs, including radiation responsive annexin family members. Our results indicate a multifactorial basis for the unusual sensitivity of Gorlin syndrome to radiation carcinogenesis, and the pathways identified have plausible implications for radiation health effects.« less

Recent Progress in Fluorescent Imaging Probes

PubMed Central

Pak, Yen Leng; Swamy, K. M. K.; Yoon, Juyoung

2015-01-01

Due to the simplicity and low detection limit, especially the bioimaging ability for cells, fluorescence probes serve as unique detection methods. With the aid of molecular recognition and specific organic reactions, research on fluorescent imaging probes has blossomed during the last decade. Especially, reaction based fluorescent probes have been proven to be highly selective for specific analytes. This review highlights our recent progress on fluorescent imaging probes for biologically important species, such as biothiols, reactive oxygen species, reactive nitrogen species, metal ions including Zn2+, Hg2+, Cu2+ and Au3+, and anions including cyanide and adenosine triphosphate (ATP). PMID:26402684

Recent Progress in Fluorescent Imaging Probes.

PubMed

Pak, Yen Leng; Swamy, K M K; Yoon, Juyoung

2015-09-22

Due to the simplicity and low detection limit, especially the bioimaging ability for cells, fluorescence probes serve as unique detection methods. With the aid of molecular recognition and specific organic reactions, research on fluorescent imaging probes has blossomed during the last decade. Especially, reaction based fluorescent probes have been proven to be highly selective for specific analytes. This review highlights our recent progress on fluorescent imaging probes for biologically important species, such as biothiols, reactive oxygen species, reactive nitrogen species, metal ions including Zn(2+), Hg(2+), Cu(2+) and Au(3+), and anions including cyanide and adenosine triphosphate (ATP).

Fluorescence Dynamics of a FRET Probe Designed for Crowding Studies.

PubMed

Currie, Megan; Leopold, Hannah; Schwarz, Jacob; Boersma, Arnold J; Sheets, Erin D; Heikal, Ahmed A

2017-06-15

Living cells are crowded with macromolecules and organelles. As a result, there is an urgent need for molecular sensors for quantitative, site-specific assessment of the macromolecular crowding effects on a myriad of biochemical processes toward quantitative cell biology and biophysics. Here we investigate the excited-state dynamics and translational diffusion of a novel FRET sensor (mCerulean-linker-mCitrine) in a buffer (PBS, pH 7.4) at room temperature. Complementary experiments were carried out on free CFP, YFP, and the cleaved FRET probe as controls. The wavelength-dependent fluorescence lifetime measurements of the donor and acceptor in the FRET probe, using the time-correlated single-photon counting technique, indicate an energy transfer efficiency of 6.8 ± 0.9% in PBS, with distinct excited-state dynamics from the recombinant CFP and YFP. The estimated mCerulean-mCitrine distance in this FRET probe is 7.7 ± 0.2 nm. The energy transfer efficiency increases (11.5 ± 0.9%) as the concentration of Ficoll-70 increases over the range of 0-300 g/L with an estimated mCerulean-mCitrine distance of 6.1 ± 0.2 nm. Complementary time-resolved anisotropy measurements suggest that the rotational diffusion of hetero-FRET in PBS is sensitive to the energy transfer from the donor to the acceptor. The results also suggest that the linker, -(GSG) 6 A(EAAAK) 6 A(GSG) 6 A(EAAAK) 6 A(GSG) 6 -, is rather flexible, and the observed rotational dynamics is likely to be due to a segmental mobility of the FRET pairs rather than an overall tumbling motion of a rigid probe. Comparative studies on a new construct of a FRET probe with a shorter, more flexible linker, mCerulean-(GSG) 18 -mCitrine, reveal enhanced energy transfer efficiency. On the millisecond time scale, fluorescence fluctuation analyses of the acceptor (excited at 488 nm) provide a means to examine the translational diffusion coefficient of the FRET probe. The results also suggest that the linker is flexible in this FRET probe, and the observed diffusion coefficient is faster than predicted as compared to the cleaved FRET probe. Our results serve as a point of reference for this FRET probe in a buffer toward its full potential as a sensor for macromolecular crowding in living cells and tissues.

Peltier cooling in molecular junctions

NASA Astrophysics Data System (ADS)

Cui, Longji; Miao, Ruijiao; Wang, Kun; Thompson, Dakotah; Zotti, Linda Angela; Cuevas, Juan Carlos; Meyhofer, Edgar; Reddy, Pramod

2018-02-01

The study of thermoelectricity in molecular junctions is of fundamental interest for the development of various technologies including cooling (refrigeration) and heat-to-electricity conversion1-4. Recent experimental progress in probing the thermopower (Seebeck effect) of molecular junctions5-9 has enabled studies of the relationship between thermoelectricity and molecular structure10,11. However, observations of Peltier cooling in molecular junctions—a critical step for establishing molecular-based refrigeration—have remained inaccessible. Here, we report direct experimental observations of Peltier cooling in molecular junctions. By integrating conducting-probe atomic force microscopy12,13 with custom-fabricated picowatt-resolution calorimetric microdevices, we created an experimental platform that enables the unified characterization of electrical, thermoelectric and energy dissipation characteristics of molecular junctions. Using this platform, we studied gold junctions with prototypical molecules (Au-biphenyl-4,4'-dithiol-Au, Au-terphenyl-4,4''-dithiol-Au and Au-4,4'-bipyridine-Au) and revealed the relationship between heating or cooling and charge transmission characteristics. Our experimental conclusions are supported by self-energy-corrected density functional theory calculations. We expect these advances to stimulate studies of both thermal and thermoelectric transport in molecular junctions where the possibility of extraordinarily efficient energy conversion has been theoretically predicted2-4,14.

In vivo near-infrared imaging of fibrin deposition in thromboembolic stroke in mice.

PubMed

Zhang, Yi; Fan, Shufeng; Yao, Yuyu; Ding, Jie; Wang, Yu; Zhao, Zhen; Liao, Lei; Li, Peicheng; Zang, Fengchao; Teng, Gao-Jun

2012-01-01

Thrombus and secondary thrombosis plays a key role in stroke. Recent molecular imaging provides in vivo imaging of activated factor XIII (FXIIIa), an important mediator of thrombosis or fibrinolytic resistance. The present study was to investigate the fibrin deposition in a thromboembolic stroke mice model by FXIIIa-targeted near-infrared fluorescence (NIRF) imaging. The experimental protocol was approved by our institutional animal use committee. Seventy-six C57B/6J mice were subjected to thromboembolic middle cerebral artery occlusion or sham operation. Mice were either intravenously injected with the FXIIIa-targeted probe or control probe. In vivo and ex vivo NIRF imaging were performed thereafter. Probe distribution was assessed with fluorescence microscopy by spectral imaging and quantification system. MR scans were performed to measure lesion volumes in vivo, which were correlated with histology after animal euthanasia. In vivo significant higher fluorescence intensity over the ischemia-affected hemisphere, compared to the contralateral side, was detected in mice that received FXIIIa-targeted probe, but not in the controlled mice. Significantly NIRF signals showed time-dependent processes from 8 to 96 hours after injection of FXIIIa-targeted probes. Ex vivo NIRF image showed an intense fluorescence within the ischemic territory only in mice injected with FXIIIa-targeted probe. The fluorescence microscopy demonstrated distribution of FXIIIa-targeted probe in the ischemic region and nearby micro-vessels, and FXIIIa-targeted probe signals showed good overlap with immune-fluorescent fibrin staining images. There was a significant correlation between total targeted signal from in vivo or ex vivo NIRF images and lesion volume. Non-invasive detection of fibrin deposition in ischemic mouse brain using NIRF imaging is feasible and this technique may provide an in vivo experimental tool in studying the role of fibrin in stroke.

In Vivo Near-Infrared Imaging of Fibrin Deposition in Thromboembolic Stroke in Mice

PubMed Central

Zhang, Yi; Fan, Shufeng; Yao, Yuyu; Ding, Jie; Wang, Yu; Zhao, Zhen; Liao, Lei; Li, Peicheng; Zang, Fengchao; Teng, Gao-Jun

2012-01-01

Objectives Thrombus and secondary thrombosis plays a key role in stroke. Recent molecular imaging provides in vivo imaging of activated factor XIII (FXIIIa), an important mediator of thrombosis or fibrinolytic resistance. The present study was to investigate the fibrin deposition in a thromboembolic stroke mice model by FXIIIa–targeted near-infrared fluorescence (NIRF) imaging. Materials and Methods The experimental protocol was approved by our institutional animal use committee. Seventy-six C57B/6J mice were subjected to thromboembolic middle cerebral artery occlusion or sham operation. Mice were either intravenously injected with the FXIIIa-targeted probe or control probe. In vivo and ex vivo NIRF imaging were performed thereafter. Probe distribution was assessed with fluorescence microscopy by spectral imaging and quantification system. MR scans were performed to measure lesion volumes in vivo, which were correlated with histology after animal euthanasia. Results In vivo significant higher fluorescence intensity over the ischemia-affected hemisphere, compared to the contralateral side, was detected in mice that received FXIIIa-targeted probe, but not in the controlled mice. Significantly NIRF signals showed time-dependent processes from 8 to 96 hours after injection of FXIIIa-targeted probes. Ex vivo NIRF image showed an intense fluorescence within the ischemic territory only in mice injected with FXIIIa-targeted probe. The fluorescence microscopy demonstrated distribution of FXIIIa-targeted probe in the ischemic region and nearby micro-vessels, and FXIIIa-targeted probe signals showed good overlap with immune-fluorescent fibrin staining images. There was a significant correlation between total targeted signal from in vivo or ex vivo NIRF images and lesion volume. Conclusion Non-invasive detection of fibrin deposition in ischemic mouse brain using NIRF imaging is feasible and this technique may provide an in vivo experimental tool in studying the role of fibrin in stroke. PMID:22272319

75 FR 51277 - Center for Scientific Review; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-19

..., Genomes, and Genetics Integrated Review Group; Molecular Genetics B Study Section. Date: October 3-4, 2010... and Urological Systems Integrated Review Group; Clinical, Integrative and Molecular Gastroenterology... Integrated Review Group; Clinical Molecular Imaging and Probe Development. Date: October 4-5, 2010. Time: 7 p...

Engineering a lifetime-based activatable probe for photoacoustic imaging

NASA Astrophysics Data System (ADS)

Morgounova, Ekaterina; Shao, Qi; Hackel, Benjamin; Ashkenazi, Shai

2013-02-01

High-resolution, high-penetration depth activatable probes are needed for in-vivo imaging of enzyme activity. In this paper, we will describe the contrast mechanism of a new photoacoustic activatable probe that changes its excitation lifetime upon activation. The excitation decay of methylene blue (MB), a chromophore commonly used in therapeutic and diagnostic applications, is probed by photoacoustic lifetime contrast imaging (PLCI). The monomer of the dye presents a high-quantum yield of intersystem-crossing and long lifetime (70 μs) whereas the dimer is statically quenched with a short lifetime (a few ns). This forms the basis of a highly sensitive contrast mechanism between monomers and dimers. Two dimerization models - one using sodium sulfate, the other using sodium dodecyl sulfate - were applied to control the monomer-to-dimer ratio in MB solutions. Preliminary results show that the photoacoustic signal of a dimer solution is efficiently suppressed (< 20 dB) due to their short lifetime compared to the monomer sample. Flash-photolysis of the same solutions reveals a 99% decrease in transient absorption confirming PLCI results. This contrast mechanism can be applied to design a MB dual-labeled activatable probe bound by an enzyme-specific cleavable peptide linker. When the probe is cleaved by its target, MB molecules will separate by molecular diffusion and recover their long excitation lifetime enabling their detection by PLCI. Our long-term goal is to investigate enzyme-specific imaging in small animals and establish pre-clinical data for translational research and implementation of the technology in clinical applications.

Single molecule localization imaging of telomeres and centromeres using fluorescence in situ hybridization and semiconductor quantum dots.

PubMed

Wang, Le; Zong, Shenfei; Wang, Zhuyuan; Lu, Ju; Chen, Chen; Zhang, Ruohu; Cui, Yiping

2018-07-13

Single molecule localization microscopy (SMLM) is a powerful tool for imaging biological targets at the nanoscale. In this report, we present SMLM imaging of telomeres and centromeres using fluorescence in situ hybridization (FISH). The FISH probes were fabricated by decorating CdSSe/ZnS quantum dots (QDs) with telomere or centromere complementary DNA strands. SMLM imaging experiments using commercially available peptide nucleic acid (PNA) probes labeled with organic fluorophores were also conducted to demonstrate the advantages of using QDs FISH probes. Compared with the PNA probes, the QDs probes have the following merits. First, the fluorescence blinking of QDs can be realized in aqueous solution or PBS buffer without thiol, which is a key buffer component for organic fluorophores' blinking. Second, fluorescence blinking of the QDs probe needs only one excitation light (i.e. 405 nm). While fluorescence blinking of the organic fluorophores usually requires two illumination lights, that is, the activation light (i.e. 405 nm) and the imaging light. Third, the high quantum yield, multiple switching times and a good optical stability make the QDs more suitable for long-term imaging. The localization precision achieved in telomeres and centromeres imaging experiments is about 30 nm, which is far beyond the diffraction limit. SMLM has enabled new insights into telomeres or centromeres on the molecular level, and it is even possible to determine the length of telomere and become a potential technique for telomere-related investigation.

Single molecule localization imaging of telomeres and centromeres using fluorescence in situ hybridization and semiconductor quantum dots

NASA Astrophysics Data System (ADS)

Wang, Le; Zong, Shenfei; Wang, Zhuyuan; Lu, Ju; Chen, Chen; Zhang, Ruohu; Cui, Yiping

2018-07-01

Single molecule localization microscopy (SMLM) is a powerful tool for imaging biological targets at the nanoscale. In this report, we present SMLM imaging of telomeres and centromeres using fluorescence in situ hybridization (FISH). The FISH probes were fabricated by decorating CdSSe/ZnS quantum dots (QDs) with telomere or centromere complementary DNA strands. SMLM imaging experiments using commercially available peptide nucleic acid (PNA) probes labeled with organic fluorophores were also conducted to demonstrate the advantages of using QDs FISH probes. Compared with the PNA probes, the QDs probes have the following merits. First, the fluorescence blinking of QDs can be realized in aqueous solution or PBS buffer without thiol, which is a key buffer component for organic fluorophores’ blinking. Second, fluorescence blinking of the QDs probe needs only one excitation light (i.e. 405 nm). While fluorescence blinking of the organic fluorophores usually requires two illumination lights, that is, the activation light (i.e. 405 nm) and the imaging light. Third, the high quantum yield, multiple switching times and a good optical stability make the QDs more suitable for long-term imaging. The localization precision achieved in telomeres and centromeres imaging experiments is about 30 nm, which is far beyond the diffraction limit. SMLM has enabled new insights into telomeres or centromeres on the molecular level, and it is even possible to determine the length of telomere and become a potential technique for telomere-related investigation.

Multicolor fluorescent intravital live microscopy (FILM) for surgical tumor resection in a mouse xenograft model.

PubMed

Thurber, Greg M; Figueiredo, Jose L; Weissleder, Ralph

2009-11-30

Complete surgical resection of neoplasia remains one of the most efficient tumor therapies. However, malignant cell clusters are often left behind during surgery due to the inability to visualize and differentiate them against host tissue. Here we establish the feasibility of multicolor fluorescent intravital live microscopy (FILM) where multiple cellular and/or unique tissue compartments are stained simultaneously and imaged in real time. Theoretical simulations of imaging probe localization were carried out for three agents with specificity for cancer cells, stromal host response, or vascular perfusion. This transport analysis gave insight into the probe pharmacokinetics and tissue distribution, facilitating the experimental design and allowing predictions to be made about the localization of the probes in other animal models and in the clinic. The imaging probes were administered systemically at optimal time points based on the simulations, and the multicolor FILM images obtained in vivo were then compared to conventional pathological sections. Our data show the feasibility of real time in vivo pathology at cellular resolution and molecular specificity with excellent agreement between intravital and traditional in vitro immunohistochemistry. Multicolor FILM is an accurate method for identifying malignant tissue and cells in vivo. The imaging probes distributed in a manner similar to predictions based on transport principles, and these models can be used to design future probes and experiments. FILM can provide critical real time feedback and should be a useful tool for more effective and complete cancer resection.

Two-probe STM experiments at the atomic level.

PubMed

Kolmer, Marek; Olszowski, Piotr; Zuzak, Rafal; Godlewski, Szymon; Joachim, Christian; Szymonski, Marek

2017-11-08

Direct characterization of planar atomic or molecular scale devices and circuits on a supporting surface by multi-probe measurements requires unprecedented stability of single atom contacts and manipulation of scanning probes over large, nanometer scale area with atomic precision. In this work, we describe the full methodology behind atomically defined two-probe scanning tunneling microscopy (STM) experiments performed on a model system: dangling bond dimer wire supported on a hydrogenated germanium (0 0 1) surface. We show that 70 nm long atomic wire can be simultaneously approached by two independent STM scanners with exact probe to probe distance reaching down to 30 nm. This allows direct wire characterization by two-probe I-V characteristics at distances below 50 nm. Our technical results presented in this work open a new area for multi-probe research, which can be now performed with precision so far accessible only by single-probe scanning probe microscopy (SPM) experiments.

Transient diffraction grating measurements of molecular diffusion in the undergraduate laboratory

NASA Astrophysics Data System (ADS)

Spiegel, Daniel R.; Tuli, Santona

2011-07-01

Diffusion is a central process in many biological, chemical, and physical systems. We describe an experiment that employs the interference of laser beams to allow the measurement of molecular diffusion on submillimeter length scales. The interference fringes of two intersecting pump beams within a dye solution create a sinusoidal distribution of long-lived molecular excited states. A third probe beam is incident at a wavelength at which the indices of refraction of the ground and excited states are different, so the probe beam diffracts from the spatially periodic excited-state pattern. After the pump beams are switched off, the excited-state periodicity washes out as the system diffuses back to equilibrium. The molecular diffusion constant is obtained from the rate constant of the exponential decay of the diffracted beam. It is also possible to measure the excited-state lifetime.

Absolute Molecular Orientation of Isopropanol at Ceria (100) Surfaces: Insight into Catalytic Selectivity from the Interfacial Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doughty, Benjamin; Goverapet Srinivasan, Sriram; Bryantsev, Vyacheslav S.

The initial mechanistic steps underlying heterogeneous chemical catalysis can be described in a framework where the composition, structure, and orientation of molecules adsorbed to reactive interfaces are known. However, extracting this vital information is the limiting step in most cases due in part to challenges in probing the interfacial monolayer with enough chemical specificity to characterize the surface molecular constituents. These challenges are exacerbated at complex or spatially heterogeneous interfaces where competing processes and a distribution of local environments can uniquely drive chemistry. To address these limitations, this work presents a distinctive combination of materials synthesis, surface specific optical experiments,more » and theory to probe and understand molecular structure at catalytic interfaces. Specifically, isopropanol was adsorbed to surfaces of the model CeO 2 catalyst that were synthesized with only the (100) facet exposed. Vibrational sum-frequency generation was used to probe the molecular monolayer, and with the guidance of density functional theory calculations, was used to extract the structure and absolute molecular orientation of isopropanol at the CeO 2 (100) surface. Our results show that isopropanol is readily deprotonated at the surface, and through the measured absolute molecular orientation of isopropanol, we obtain new insight into the selectivity of the (100) surface to form propylene. Our findings reveal key insight into the chemical and physical phenomena taking place at pristine interfaces thereby pointing to intuitive structural arguments to describe catalytic selectivity in more complex systems.« less

Absolute Molecular Orientation of Isopropanol at Ceria (100) Surfaces: Insight into Catalytic Selectivity from the Interfacial Structure

DOE PAGES

Doughty, Benjamin; Goverapet Srinivasan, Sriram; Bryantsev, Vyacheslav S.; ...

2017-06-12

The initial mechanistic steps underlying heterogeneous chemical catalysis can be described in a framework where the composition, structure, and orientation of molecules adsorbed to reactive interfaces are known. However, extracting this vital information is the limiting step in most cases due in part to challenges in probing the interfacial monolayer with enough chemical specificity to characterize the surface molecular constituents. These challenges are exacerbated at complex or spatially heterogeneous interfaces where competing processes and a distribution of local environments can uniquely drive chemistry. To address these limitations, this work presents a distinctive combination of materials synthesis, surface specific optical experiments,more » and theory to probe and understand molecular structure at catalytic interfaces. Specifically, isopropanol was adsorbed to surfaces of the model CeO 2 catalyst that were synthesized with only the (100) facet exposed. Vibrational sum-frequency generation was used to probe the molecular monolayer, and with the guidance of density functional theory calculations, was used to extract the structure and absolute molecular orientation of isopropanol at the CeO 2 (100) surface. Our results show that isopropanol is readily deprotonated at the surface, and through the measured absolute molecular orientation of isopropanol, we obtain new insight into the selectivity of the (100) surface to form propylene. Our findings reveal key insight into the chemical and physical phenomena taking place at pristine interfaces thereby pointing to intuitive structural arguments to describe catalytic selectivity in more complex systems.« less

Effect of electrostatic interaction on the location of molecular probe in polymer-surfactant supramolecular assembly: a solvent relaxation study.

PubMed

Singh, Prabhat K; Kumbhakar, Manoj; Pal, Haridas; Nath, Sukhendu

2008-07-03

Effect of electrostatic interaction on the location of a solubilized molecular probe with ionic character in a supramolecular assembly composed of a triblock copolymer, P123 ((ethylene oxide) 20-(propylene oxide) 70-(ethylene oxide) 20) and a cosurfactant cetyltrimethylammonium chloride (CTAC) in aqueous medium has been studied using steady-state and time-resolved fluorescence measurements. Coumarin-343 dye in its anionic form has been used as the molecular probe. In the absence of the surfactant, CTAC, the probe C343 prefers to reside at the surface region of the P123 micelle, showing a relatively less dynamic Stokes' shift, as a large part of the Stokes' shift is missed in the present measurements due to faster solvent relaxation at micellar surface region. As the concentration of CTAC is increased in the solution, the percentage of the total dynamic Stokes' shift observed from time-resolved measurements gradually increases until it reaches a saturation value. Observed results have been rationalized on the basis of the mixed micellar structure of the supramolecular assembly, where the hydrocarbon chain of the CTAC surfactant dissolves into the nonpolar poly(propylene oxide) (PPO) core of the P123 micelle and the positively charged headgroup of CTAC resides at the interfacial region between the central PPO core and the surrounding hydrated poly(ethylene oxide) (PEO) shell or the corona region. The electrostatic attraction between the anionic probe molecule and the positively charged surface of the PPO core developed by the presence of CTAC results in a gradual shift of the probe in the deeper region of the micellar corona region with an increase in the CTAC concentration, as clearly manifested from the solvation dynamics results.

Molecular cytogenetic mapping of 24 CEPH YACs and 24 gene-specific large insert probes to chromosome 17.

PubMed

Bärlund, M; Nupponen, N N; Karhu, R; Tanner, M M; Paavola, P; Kallioniemi, O P; Kallioniemi, A

1998-01-01

Defining boundaries of chromosomal rearrangements at the molecular level would benefit from landmarks that link the cytogenetic map to physical, genetic, and transcript maps, as well as from large-insert FISH probes for such loci to detect numerical and structural rearrangements in metaphase or interphase cells. Here, we determined the locations of 24 genetically mapped CEPH-Mega YACs along the FLpter scale (fractional length from p-telomere) by quantitative fluorescence in situ hybridization analysis. This generated a set of cytogenetically mapped probes for chromosome 17 with an average spacing of about 5 cM. We then developed large-insert YAC, BAC, PAC, or P1 clones to the following 24 known genes, and determined refined map locations along the same FLpter scale: pter-TP53-TOP3-cen-TNFAIP1-ERBB2-TOP2A- BRCA1-TCF11-NME1-HLF-ZNF147/CL N80-BCL5/MPO/SFRS1-TBX2-PECAM1-DDX5/ PRKCA-ICAM2-GH1/PRKAR1A-GRB2-CDK3 /FKHL13-qter. Taken together, these 48 cytogenetically mapped large-insert probes provide tools for the molecular analysis of chromosome 17 rearrangements, such as mapping amplification, deletion, and translocation breakpoints in this chromosome, in cancer and other diseases.

Development of PCR for screening of enteroaggregative Escherichia coli.

PubMed Central

Schmidt, H; Knop, C; Franke, S; Aleksic, S; Heesemann, J; Karch, H

1995-01-01

In this study, we determined the sequence of the EcoRI-PstI fragment of the plasmid pCVD432, also termed the enteroaggregative Escherichia coli (EAggEC) probe. A primer pair complementary to this probe was designed for PCR amplification of a 630-bp region. Comparison of the analysis of the EAggEC probe sequence with those in database libraries revealed no significant similarity to any known bacterial gene. Pure cultures of E. coli cells, as well as mixed cultures from stool specimens, were investigated with the PCR assay, the EAggEC probe test, and the adherence test. Of 50 E. coli strains which demonstrated aggregative adherence to HEp-2 cells, 43 (86%) were positive with the EAggEC PCR. All 43 of these strains reacted with the EAggEC probe. Six EAggEC strains gave negative results by both molecular techniques. In contrast, only 4 of 418 (0.96%) strains representing other categories of diarrheagenic E. coli demonstrated a positive PCR result. The PCR was also successful in screening for the presence of EAggEC in enriched cultures grown from stool specimens. Compared with cell culture assays and colony hybridization, our findings revealed that the PCR assay was more rapid, simple, and highly sensitive and can therefore be recommended as a screening method for EAggEC in the clinical laboratory. PMID:7751380

Self-Assembled Tb3+ Complex Probe for Quantitative Analysis of ATP during Its Enzymatic Hydrolysis via Time-Resolved Luminescence in Vitro and in Vivo.

PubMed

Jung, Sung Ho; Kim, Ka Young; Lee, Ji Ha; Moon, Cheol Joo; Han, Noh Soo; Park, Su-Jin; Kang, Dongmin; Song, Jae Kyu; Lee, Shim Sung; Choi, Myong Yong; Jaworski, Justyn; Jung, Jong Hwa

2017-01-11

To more accurately assess the pathways of biological systems, a probe is needed that may respond selectively to adenosine triphosphate (ATP) for both in vitro and in vivo detection modes. We have developed a luminescence probe that can provide real-time information on the extent of ATP, ADP, and AMP by virtue of the luminescence and luminescence lifetime observed from a supramolecular polymer based on a C 3 symmetrical terpyridine complex with Tb 3+ (S1-Tb). The probe shows remarkable selective luminescence enhancement in the presence of ATP compared to other phosphate-displaying nucleotides including adenosine diphosphate (ADP), adenosine monophosphate (AMP), guanosine triphosphate (GTP), thymidine triphosphate (TTP), H 2 PO 4 - (Pi), and pyrophosphate (PPi). In addition, the time-resolved luminescence lifetime and luminescence spectrum of S1-Tb could facilitate the quantitative measurement of the exact amount of ATP and similarly ADP and AMP within living cells. The time-resolved luminescence lifetime of S1-Tb could also be used to quantitatively monitor the amount of ATP, ADP, and AMP in vitro following the enzymatic hydrolysis of ATP. The long luminescence lifetime, which was observed into the millisecond range, makes this S1-Tb-based probe particularly attractive for monitoring biological ATP levels in vivo, because any short lifetime background fluorescence arising from the complex molecular environment may be easily eliminated.

Studies on the formation and stability of triplex DNA using fluorescence correlation spectroscopy.

PubMed

Hu, Hongyan; Huang, Xiangyi; Ren, Jicun

2016-05-01

Triplex DNA has become one of the most useful recognition motifs in the design of new molecular biology tools, therapeutic agents and sophisticated DNA-based nanomaterials because of its direct recognition of natural double-stranded DNA. In this paper, we developed a sensitive and microscale method to study the formation and stability characterization of triplex DNA using fluorescence correlation spectroscopy (FCS). The principle of this method is mainly based on the excellent capacity of FCS for sensitively distinguishing between free single-strand DNA (ssDNA) fluorescent probes and fluorescent probe-double-strand DNA (dsDNA) hybridized complexes. First, we systematically investigated the experimental conditions of triplex DNA formation. Then, we evaluated the equilibrium association constants (K(a)) under different ssDNA probe lengths, composition and pH. Finally, we used FCS to measure the hybridization fraction of a 20-mer perfectly matched ssDNA probe and three single-base mismatched ssDNA probes with 146-mer dsDNA. Our data illustrated that FCS is a useful tool for the direct determination of the thermodynamic parameters of triplex DNA formation and discrimination of a single-base mismatch of triplex DNA without denaturation. Compared with current methods, our method is characterized by high sensitivity, good universality and small sample and reagent requirements. More importantly, our method has the potential to become a platform for triplex DNA research in vitro. Copyright © 2015 John Wiley & Sons, Ltd.

Intravascular Raman spectroscopic catheter for molecular diagnosis of atherosclerotic coronary disease

NASA Astrophysics Data System (ADS)

Komachi, Yuichi; Sato, Hidetoshi; Tashiro, Hideo

2006-10-01

An intravascular catheter for Raman spectroscopic detection and analysis of coronary atherosclerotic disease has been developed. The catheter, having an outer diameter of 2 mm, consisted of a side-view-type micro-Raman probe, an imaging fiber bundle, a working channel (injection drain), and a balloon. By inflating the balloon, the probe was brought close to the inner wall of a modeled blood flow system and detected a phantom target buried in the wall. Results obtained demonstrate the possibility of using the spectroscopic catheter for molecular diagnosis of coronary lesions.

Piezoelectric tuning fork biosensors for the quantitative measurement of biomolecular interactions

NASA Astrophysics Data System (ADS)

Gonzalez, Laura; Rodrigues, Mafalda; Benito, Angel Maria; Pérez-García, Lluïsa; Puig-Vidal, Manel; Otero, Jorge

2015-12-01

The quantitative measurement of biomolecular interactions is of great interest in molecular biology. Atomic force microscopy (AFM) has proved its capacity to act as a biosensor and determine the affinity between biomolecules of interest. Nevertheless, the detection scheme presents certain limitations when it comes to developing a compact biosensor. Recently, piezoelectric quartz tuning forks (QTFs) have been used as laser-free detection sensors for AFM. However, only a few studies along these lines have considered soft biological samples, and even fewer constitute quantified molecular recognition experiments. Here, we demonstrate the capacity of QTF probes to perform specific interaction measurements between biotin-streptavidin complexes in buffer solution. We propose in this paper a variant of dynamic force spectroscopy based on representing adhesion energies E (aJ) against pulling rates v (nm s-1). Our results are compared with conventional AFM measurements and show the great potential of these sensors in molecular interaction studies.

Ion-Pair States in Triplet Molecular Hydrogen

NASA Astrophysics Data System (ADS)

Setzer, W.; Baker, B. C.; Ashman, S.; Morgan, T. J.

2016-05-01

An experimental search is underway to observe the long range triplet ionic states H+ H- of molecular hydrogen. Resonantly enhanced multi-photon ionization of the metastable c 3∏u- 2 pπ state is used access to the R(1)nd1 n = 21 Rydberg state that serves as an intermediate stepping stone state to probe the energy region above the ionization limit with a second tunable laser photon. The metastable state is prepared by electron capture of 6 keV H2+ions in potassium in a molecular beam. Formation of the H+ H- triplet configuration involves triplet excited states of the H- ion, especially the 2p23Pe state, the second bound state of H- predicted to exist with a lifetime long compared to typical auto ionization lifetimes but not yet observed experimentally. Details of the experiment and preliminary results to date will be presented at the conference.

Bacterial Phytochromes, Cyanobacteriochromes and Allophycocyanins as a Source of Near-Infrared Fluorescent Probes

PubMed Central

Oliinyk, Olena S.; Chernov, Konstantin G.

2017-01-01

Bacterial photoreceptors absorb light energy and transform it into intracellular signals that regulate metabolism. Bacterial phytochrome photoreceptors (BphPs), some cyanobacteriochromes (CBCRs) and allophycocyanins (APCs) possess the near-infrared (NIR) absorbance spectra that make them promising molecular templates to design NIR fluorescent proteins (FPs) and biosensors for studies in mammalian cells and whole animals. Here, we review structures, photochemical properties and molecular functions of several families of bacterial photoreceptors. We next analyze molecular evolution approaches to develop NIR FPs and biosensors. We then discuss phenotypes of current BphP-based NIR FPs and compare them with FPs derived from CBCRs and APCs. Lastly, we overview imaging applications of NIR FPs in live cells and in vivo. Our review provides guidelines for selection of existing NIR FPs, as well as engineering approaches to develop NIR FPs from the novel natural templates such as CBCRs. PMID:28771184

Holographic grating relaxation technique for soft matter science

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lesnichii, Vasilii, E-mail: vasilii.lesnichii@physchem.uni-freiburg.de; ITMO University, Kronverksky prospekt 49, Saint-Petersburg 197101; Kiessling, Andy

2016-06-17

The holographic grating relaxation technique also known as forced Rayleigh scattering consists basically in writing a holographic grating in the specimen of interest and monitoring its diffraction efficiency as a function of time, from which valuable information on mass or heat transfer and photoinduced transformations can be extracted. In a more detailed view, the shape of the relaxation curve and the relaxation rate as a function of the grating period were found to be affected by the architecture of diffusing species (molecular probes) that constitute the grating, as well as that of the environment they diffuse in, thus making itmore » possible to access and study spatial heterogeneity of materials and different modes of e.g., polymer motion. Minimum displacements and spatial domains approachable by the technique are in nanometer range, well below spatial periods of holographic gratings. In the present paper, several cases of holographic relaxation in heterogeneous media and complex motions are exemplified. Nano- to micro-structures or inhomogeneities comparable in spatial scale with holographic gratings manifest themselves in relaxation experiments via non-exponential decay (stepwise or stretched), spatial-period-dependent apparent diffusion coefficient, or unusual dependence of diffusion coefficient on molecular volume of diffusing probes.« less

Adsorption and Exchange Dynamics in Aging Hydroxyethylcellulose Layers on Silica.

PubMed

Mubarekyan; Santore

2000-07-15

The adsorption kinetics of hydroxyethylcellulose (HEC) on silica and relaxations in adsorbed HEC layers were probed using total internal reflectance fluorescence and near-Brewster reflectivity. Like many random-coil polymers, HEC was found to adsorb at the transport-limited rate. Relaxations occurred at nearly constant interfacial mass when HEC layers were exposed to aqueous solvent, causing the subsequent exchange of chains between the layer and the free solution to become increasingly hindered. Eventually, on the time scale of a day, layers became immobilized and unable to accommodate chains from free solution. A continued fluorescence decay, beyond time scales that could be probed with self exchange, suggested further relaxations of the adsorbed HEC. The polydisperse HEC system (with an average molecular weight near 450,000) behaved qualitatively similar to molecular weight standard polyethylene oxide (PEO) layers on silica. For instance, relaxations in PEO layers occurred on a time scale of 10-20 h, like the HEC layers. Young layers of the latter, however, exhibited self-exchange kinetics that were an order of magnitude slower than PEO layers of similar age. This difference in adsorbed layer dynamics was attributed to HEC's stiffer backbone, compared with flexible PEO. Copyright 2000 Academic Press.

Control of femtosecond laser driven retro-Diels-Alder-like reaction of dicyclopentadiene

PubMed Central

Das, Dipak Kumar; Goswami, Tapas; Goswami, Debabrata

2013-01-01

Using femtosecond time resolved degenerate pump-probe mass spectrometry coupled with simple linearly chirped frequency modulated pulse, we elucidate that the dynamics of retro-Diels-Alder-like reaction of diclopentadiene (DCPD) to cyclopentadiene (CPD) in supersonic molecular beam occurs in ultrafast time scale. Negatively chirped pulse enhances the ion yield of CPD, as compared to positively chirped pulse. This indicates that by changing the frequency (chirp) of the laser pulse we can control the ion yield of a chemical reaction. PMID:23814449

Coexpression of CdSe and CdSe/CdS quantum dots in live cells using molecular hyperspectral imaging technology

NASA Astrophysics Data System (ADS)

Li, Qingli; Peng, Hui; Wang, Jing; Wang, Yiting; Guo, Fangmin

2015-11-01

A direct spatial and spectral observation of CdSe and CdSe/CdS quantum dots (QDs) as probes in live cells is performed by using a custom molecular hyperspectral imaging (MHI) system. Water-soluble CdSe and CdSe/CdS QDs are synthesized in aqueous solution under the assistance of high-intensity ultrasonic irradiation and incubated with colon cancer cells for bioimaging. Unlike the traditional fluorescence microscopy methods, MHI technology can identify QD probes according to their spectral signatures and generate coexpression and stain titer maps by a clustering method. The experimental results show that the MHI method has potential to unmix biomarkers by their spectral information, which opens up a pathway of optical multiplexing with many different QD probes.

Transport mirages in single-molecule devices

NASA Astrophysics Data System (ADS)

Gaudenzi, R.; Misiorny, M.; Burzurí, E.; Wegewijs, M. R.; van der Zant, H. S. J.

2017-03-01

Molecular systems can exhibit a complex, chemically tailorable inner structure which allows for targeting of specific mechanical, electronic, and optical properties. At the single-molecule level, two major complementary ways to explore these properties are molecular quantum-dot structures and scanning probes. This article outlines comprehensive principles of electron-transport spectroscopy relevant to both these approaches and presents a new, high-resolution experiment on a high-spin single-molecule junction exemplifying these principles. Such spectroscopy plays a key role in further advancing our understanding of molecular and atomic systems, in particular, the relaxation of their spin. In this joint experimental and theoretical analysis, particular focus is put on the crossover between the resonant regime [single-electron tunneling] and the off-resonant regime [inelastic electron (co)tunneling spectroscopy (IETS)]. We show that the interplay of these two processes leads to unexpected mirages of resonances not captured by either of the two pictures alone. Although this turns out to be important in a large fraction of the possible regimes of level positions and bias voltages, it has been given little attention in molecular transport studies. Combined with nonequilibrium IETS—four-electron pump-probe excitations—these mirages provide crucial information on the relaxation of spin excitations. Our encompassing physical picture is supported by a master-equation approach that goes beyond weak coupling. The present work encourages the development of a broader connection between the fields of molecular quantum-dot and scanning probe spectroscopy.

Miniature and Molecularly Specific Optical Screening Technologies for Breast Cancer

DTIC Science & Technology

2008-10-01

commercially available dual-channel transimpedance amplifier circuit boards (Boston Electronics, TWAMP). Preliminary results with the imaging probe...connected to a current amplifier via a coaxial cable for diffuse reflectance measurements. This new probe is named P4-3 and schematics of the system and...probe. With the single pixel device a single-channel current amplifier (Terahertz Technologies, PDA-750) could easily read and collect the photocurrent

Experimental study of the evanescent-wave photonic sensors response in presence of molecular beacon conformational changes.

PubMed

Ruiz-Tórtola, Ángela; Prats-Quílez, Francisco; Gónzalez-Lucas, Daniel; Bañuls, María-José; Maquieira, Ángel; Wheeler, Guy; Dalmay, Tamas; Griol, Amadeu; Hurtado, Juan; Bohlmann, Helge; Götzen, Reiner; García-Rupérez, Jaime

2018-04-17

An experimental study of the influence of the conformational change suffered by molecular beacon (MB) probes -upon the biorecognition of nucleic acid target oligonucleotides over evanescent wave photonic sensors- is reported. To this end, high sensitivity photonic sensors based on silicon photonic bandgap (PBG) structures were used, where the MB probes were immobilized via their 5' termination. Those MBs incorporate a biotin moiety close to their 3' termination in order to selectively bind a streptavidin molecule to them. The different photonic sensing responses obtained towards the target oligonucleotide detection, when the streptavidin molecule was bound to the MB probes or not, demonstrate the conformational change suffered by the MB upon hybridization, which promotes the displacement of the streptavidin molecule away from the surface of the photonic sensing structure. Schematic diagram of the PBG sensing structure on which the streptavidin-labeled MB probes were immobilized. This article is protected by copyright. All rights reserved.

Modelling heat conduction in polycrystalline hexagonal boron-nitride films

PubMed Central

Mortazavi, Bohayra; Pereira, Luiz Felipe C.; Jiang, Jin-Wu; Rabczuk, Timon

2015-01-01

We conducted extensive molecular dynamics simulations to investigate the thermal conductivity of polycrystalline hexagonal boron-nitride (h-BN) films. To this aim, we constructed large atomistic models of polycrystalline h-BN sheets with random and uniform grain configuration. By performing equilibrium molecular dynamics (EMD) simulations, we investigated the influence of the average grain size on the thermal conductivity of polycrystalline h-BN films at various temperatures. Using the EMD results, we constructed finite element models of polycrystalline h-BN sheets to probe the thermal conductivity of samples with larger grain sizes. Our multiscale investigations not only provide a general viewpoint regarding the heat conduction in h-BN films but also propose that polycrystalline h-BN sheets present high thermal conductivity comparable to monocrystalline sheets. PMID:26286820

Comparative evaluation of probing depth and clinical attachment level using a manual probe and Florida probe.

PubMed

Kour, Amandeep; Kumar, Ashish; Puri, Komal; Khatri, Manish; Bansal, Mansi; Gupta, Geeti

2016-01-01

To compare and evaluate the intra- and inter-examiner efficacy and reproducibility of the first-generation manual (Williams) probe and the third-generation Florida probe in terms of measuring pocket probing depth (PD) and clinical attachment level (CAL). Forty subjects/4000 sites were included in this comparative, cross-sectional study. Group- and site-wise categorizations were done. Based on gingival index, PD, and CAL, patients were divided into four groups, i.e., periodontally healthy, gingivitis, mild to moderate periodontitis, and severe periodontitis. Further, based on these parameters, a total of 4000 sites, with 1000 sites in each category randomly selected from these 40 patients, were taken. Full mouth PD and CAL measurements were recorded with two probes, by Examiner 1 and on Ramfjord teeth by Examiner 2. Full mouth and Ramfjord teeth group- and site-wise PD obtained with the manual probe by both the examiners were statistically significantly deeper than that obtained with the Florida probe. The full mouth and Ramfjord teeth mean CAL measurement by Florida probe was higher as compared to manual probe in mild to moderate periodontitis group and sites, whereas in severe periodontitis group and sites, manual probe recorded higher CAL as compared to Florida probe. Mean PD and CAL measurements were deeper with the manual probe as compared to the Florida probe in all the groups and sites, except for the mild-moderate periodontitis group and sites where the CAL measurements with the manual probe were less than the Florida probe. Manual probe was more reproducible and showed less interexaminer variability as compared to the Florida probe.

Carbon Nanotubules: Building Blocks for Nanometer-Scale Engineering

NASA Technical Reports Server (NTRS)

Sinnott, Susan B.

1997-01-01

Proximal probe technology has provided researchers with new ways to investigate and manipulate matter on the nanometer scale. We have studied, through molecular dynamics simulations, using a many-body empirical potential, the indentation of a hydrogen-terminated, diamond (111 ) surface, with a proximal probe tip that consists of an open, hydrogen-terminated, (10,10) carbon nanotubule. The simulations showed that upon indenting 1.8 A, the tubule deforms but returns to its original shape upon retraction. The Young's modulus of the tubule was determined using the predicted Euler buckling force and was found to be comparable to measured and calculated values. In a second series of simulations, an open (10, 10) nanotubule was heated to 4500 K and allowed to close. We find that at this temperature the resulting cap contains numerous imperfections, including some not mentioned previously in the literature.

Interpreting atom probe data from chromium oxide scales.

PubMed

La Fontaine, Alexandre; Gault, Baptiste; Breen, Andrew; Stephenson, Leigh; Ceguerra, Anna V; Yang, Limei; Nguyen, Thuan Dinh; Zhang, Jianqiang; Young, David J; Cairney, Julie M

2015-12-01

Picosecond-pulsed ultraviolet-laser (UV-355 nm) assisted atom probe tomography (APT) was used to analyze protective, thermally grown chromium oxides formed on stainless steel. The influence of analysis parameters on the thermal tail observed in the mass spectra and the chemical composition is investigated. A new parameter termed "laser sensitivity factor" is introduced in order to quantify the effect of laser energy on the extent of the thermal tail. This parameter is used to compare the effect of increasing laser energy on thermal tails in chromia and chromite samples. Also explored is the effect of increasing laser energy on the measured oxygen content and the effect of specimen base temperature and laser pulse frequency on the mass spectrum. Finally, we report a preliminary analysis of molecular ion dissociations in chromia. Copyright © 2015 Elsevier B.V. All rights reserved.

Optical setup for two-colour experiments at the low density matter beamline of FERMI

NASA Astrophysics Data System (ADS)

Finetti, Paola; Demidovich, Alexander; Plekan, Oksana; Di Fraia, Michele; Cucini, Riccardo; Callegari, Carlo; Cinquegrana, Paolo; Sigalotti, Paolo; Ivanov, Rosen; Danailov, Miltcho B.; Fava, Claudio; De Ninno, Giovanni; Coreno, Marcello; Grazioli, Cesare; Feifel, Raimund; Squibb, Richard J.; Mazza, Tommaso; Meyer, Michael; Prince, Kevin C.

2017-11-01

The low density matter beamline of the free electron laser facility FERMI is dedicated to the study of atomic, molecular and cluster systems, and here we describe the optical setup available for two-colour experiments. Samples can be exposed to ultrashort pulses from a Ti:Sapphire source (fundamental, or second or third harmonic), and ultrashort light pulses of FERMI in the EUV/soft x-ray region with a well-defined temporal delay, and negligible jitter (<10 fs) compared to the pulse durations (40-100 fs). Detection schemes available include electron, ion and optical spectroscopy. The majority of experiments using this apparatus are pump-and-probe, where either wavelength can be pump or probe, but the system is also useful for other techniques, such as multi-photon spectroscopy, cross-correlation measurements and alignment of molecules in space.

Low-intensity focused ultrasound (LIFU)-induced acoustic droplet vaporization in phase-transition perfluoropentane nanodroplets modified by folate for ultrasound molecular imaging.

PubMed

Liu, Jianxin; Shang, Tingting; Wang, Fengjuan; Cao, Yang; Hao, Lan; Ren, JianLi; Ran, Haitao; Wang, Zhigang; Li, Pan; Du, Zhiyu

2017-01-01

The commonly used ultrasound (US) molecular probes, such as targeted microbubbles and perfluorocarbon emulsions, present a number of inherent problems including the conflict between US visualization and particle penetration. This study describes the successful fabrication of phase changeable folate-targeted perfluoropentane nanodroplets (termed FA-NDs), a novel US molecular probe for tumor molecular imaging with US. Notably, these FA-NDs can be triggered by low-intensity focused US (LIFU) sonication, providing excellent US enhancement in B-mode and contrast-enhanced US mode in vitro. After intravenous administration into nude mice bearing SKOV3 ovarian carcinomas, 1,1'-dioctadecyl-3,3,3',3' -tetramethylindotricarbocya-nine iodide-labeled FA-NDs were found to accumulate in the tumor region. FA-NDs injection followed by LIFU sonication exhibited remarkable US contrast enhancement in the tumor region. In conclusion, combining our elaborately developed FA-NDs with LIFU sonication provides a potential protocol for US molecular imaging in folate receptor-overexpressing tumors.

Low-intensity focused ultrasound (LIFU)-induced acoustic droplet vaporization in phase-transition perfluoropentane nanodroplets modified by folate for ultrasound molecular imaging

PubMed Central

Liu, Jianxin; Shang, Tingting; Wang, Fengjuan; Cao, Yang; Hao, Lan; Ren, JianLi; Ran, Haitao; Wang, Zhigang; Li, Pan; Du, Zhiyu

2017-01-01

The commonly used ultrasound (US) molecular probes, such as targeted microbubbles and perfluorocarbon emulsions, present a number of inherent problems including the conflict between US visualization and particle penetration. This study describes the successful fabrication of phase changeable folate-targeted perfluoropentane nanodroplets (termed FA-NDs), a novel US molecular probe for tumor molecular imaging with US. Notably, these FA-NDs can be triggered by low-intensity focused US (LIFU) sonication, providing excellent US enhancement in B-mode and contrast-enhanced US mode in vitro. After intravenous administration into nude mice bearing SKOV3 ovarian carcinomas, 1,1′-dioctadecyl-3,3,3′,3′ -tetramethylindotricarbocya-nine iodide-labeled FA-NDs were found to accumulate in the tumor region. FA-NDs injection followed by LIFU sonication exhibited remarkable US contrast enhancement in the tumor region. In conclusion, combining our elaborately developed FA-NDs with LIFU sonication provides a potential protocol for US molecular imaging in folate receptor-overexpressing tumors. PMID:28184161

Single molecule spectroscopy reveals heterogeneous transport mechanisms for molecular ions in a polyelectrolyte polymer brush.

PubMed

Reznik, Carmen; Estillore, Nicel; Advincula, Rigoberto C; Landes, Christy F

2009-11-05

Single molecule polarization and fluorescence correlation spectroscopy were used to evaluate heterogeneous transport mechanisms of molecular ions within supported polyelectrolyte brushes. Modes of diffusive transport include periods of significantly restricted rotational motion, often maintained over tens of milliseconds; periods of fast molecular rotation; and occasional adsorption of fluorescent probe molecules in the brush. The studies reveal rapid switching between orientational states during each observed mode of motion. Through quantitative analysis of state occupation times, the rate constants for transitions from weakly associated to strongly associated states were extracted. Additionally, the pH dependence of the ion transport rates in the brush exhibits an abrupt, rather than continuous, trend. These single molecule studies demonstrate the presence of dynamic anisotropic interactions between the charged molecular probe and the polymer brush and provide experimental evidence of stimuli responsive switchable transport functionality in the polyelectrolyte brush.

Analyte-Triggered DNA-Probe Release from a Triplex Molecular Beacon for Nanopore Sensing.

PubMed

Guo, Bingyuan; Sheng, Yingying; Zhou, Ke; Liu, Quansheng; Liu, Lei; Wu, Hai-Chen

2018-03-26

A new nanopore sensing strategy based on triplex molecular beacon was developed for the detection of specific DNA or multivalent proteins. The sensor is composed of a triplex-forming molecular beacon and a stem-forming DNA component that is modified with a host-guest complex. Upon target DNA hybridizing with the molecular beacon loop or multivalent proteins binding to the recognition elements on the stem, the DNA probe is released and produces highly characteristic current signals when translocated through α-hemolysin. The frequency of current signatures can be used to quantify the concentrations of the target molecules. This sensing approach provides a simple, quick, and modular tool for the detection of specific macromolecules with high sensitivity and excellent selectivity. It may find useful applications in point-of-care diagnostics with a portable nanopore kit in the future. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular organization and dynamics of micellar phase of polyelectrolyte-surfactant complexes: ESR spin probe study

NASA Astrophysics Data System (ADS)

Wasserman, A. M.; Kasaikin, V. A.; Zakharova, Yu. A.; Aliev, I. I.; Baranovsky, V. Yu.; Doseva, V.; Yasina, L. L.

2002-04-01

Molecular dynamics and organization of the micellar phase of complexes of linear polyelectrolytes with ionogenic and non-ionogenic surfactants was studied by the ESR spin probe method. Complexes of polyacrylic acid (PAA) and sodium polystyrenesulfonate (PSS) with alkyltrimethylammonium bromides (ATAB), as well as complexes of poly- N, N'-dimethyldiallylammonium chloride (PDACL) with sodium dodecylsulfate (SDS) were studied. The micellar phase of such complexes is highly organized molecular system, molecular ordering of which near the polymeric chain is much higher than in the 'center' of the micelle, it depends on the polymer-detergent interaction, flexibility of polymeric chain and length of carbonic part of the detergent molecule. Complexes of polymethacrylic acid (PMAA) with non-ionic detergent (dodecyl-substituted polyethyleneglycol), show that the local mobility of surfactant in such complexes is significantly lower than in 'free' micelles and depends on the number of micellar particles participating in formation of complexes.

The Evolutionary Connection Bewtween z~2-3 Submillimeter Galaxies and AGN as Probed by Molecular Gas Excitation

NASA Astrophysics Data System (ADS)

Sharon, Chelsea E.; Riechers, Dominik A.; Carilli, Chris Luke; Hodge, Jacqueline; Walter, Fabian

2016-01-01

Theoretical work has suggested that active galactic nuclei (AGN) play an important role in quenching star formation in massive galaxies. Direct evidence for AGN affecting the molecular ISM has so far been limited to detections of molecular outflows in low-redshift systems and extreme excitation regions which represent a tiny fraction of the total gas. Indirect evidence for AGN's impact on their host galaxies' cold gas phase may be provided by measurements of the gas excitation and dynamics. At z~2-3, the peak epoch of star formation and AGN activity, previous observations of the CO(1-0) line revealed that submillimeter galaxies (SMGs) have multi-phase molecular gas, including substantial reservoirs of cold-phase gas. However, the entirety of the molecular gas in AGN-host galaxies appears highly excited, potentially supporting an evolutionary connection between these two populations. I will present a new VLA sample that nearly doubles the number of CO(1-0) detections in z~2-3 SMGs and AGN-host galaxies that allows us to better compare the cold gas properties of these systems and further investigate evidence for the effects of AGN on the star-forming molecular gas.

Practical implementation, characterization and applications of a multi-colour time-gated luminescence microscope.

PubMed

Zhang, Lixin; Zheng, Xianlin; Deng, Wei; Lu, Yiqing; Lechevallier, Severine; Ye, Zhiqiang; Goldys, Ewa M; Dawes, Judith M; Piper, James A; Yuan, Jingli; Verelst, Marc; Jin, Dayong

2014-10-13

Time-gated luminescence microscopy using long-lifetime molecular probes can effectively eliminate autofluorescence to enable high contrast imaging. Here we investigate a new strategy of time-gated imaging for simultaneous visualisation of multiple species of microorganisms stained with long-lived complexes under low-background conditions. This is realized by imaging two pathogenic organisms (Giardia lamblia stained with a red europium probe and Cryptosporidium parvum with a green terbium probe) at UV wavelengths (320-400 nm) through synchronization of a flash lamp with high repetition rate (1 kHz) to a robust time-gating detection unit. This approach provides four times enhancement in signal-to-background ratio over non-time-gated imaging, while the average signal intensity also increases six-fold compared with that under UV LED excitation. The high sensitivity is further confirmed by imaging the single europium-doped Y₂O₂S nanocrystals (150 nm). We report technical details regarding the time-gating detection unit and demonstrate its compatibility with commercial epi-fluorescence microscopes, providing a valuable and convenient addition to standard laboratory equipment.

Practical Implementation, Characterization and Applications of a Multi-Colour Time-Gated Luminescence Microscope

NASA Astrophysics Data System (ADS)

Zhang, Lixin; Zheng, Xianlin; Deng, Wei; Lu, Yiqing; Lechevallier, Severine; Ye, Zhiqiang; Goldys, Ewa M.; Dawes, Judith M.; Piper, James A.; Yuan, Jingli; Verelst, Marc; Jin, Dayong

2014-10-01

Time-gated luminescence microscopy using long-lifetime molecular probes can effectively eliminate autofluorescence to enable high contrast imaging. Here we investigate a new strategy of time-gated imaging for simultaneous visualisation of multiple species of microorganisms stained with long-lived complexes under low-background conditions. This is realized by imaging two pathogenic organisms (Giardia lamblia stained with a red europium probe and Cryptosporidium parvum with a green terbium probe) at UV wavelengths (320-400 nm) through synchronization of a flash lamp with high repetition rate (1 kHz) to a robust time-gating detection unit. This approach provides four times enhancement in signal-to-background ratio over non-time-gated imaging, while the average signal intensity also increases six-fold compared with that under UV LED excitation. The high sensitivity is further confirmed by imaging the single europium-doped Y2O2S nanocrystals (150 nm). We report technical details regarding the time-gating detection unit and demonstrate its compatibility with commercial epi-fluorescence microscopes, providing a valuable and convenient addition to standard laboratory equipment.

Structural design of intrinsically fluorescent oxysterols.

PubMed

Nåbo, Lina J; Modzel, Maciej; Krishnan, Kathiresan; Covey, Douglas F; Fujiwara, Hideji; Ory, Daniel S; Szomek, Maria; Khandelia, Himanshu; Wüstner, Daniel; Kongsted, Jacob

2018-05-01

Oxysterols are oxidized derivatives of cholesterol with many important biological functions. Trafficking of oxysterols in and between cells is not well studied, largely due to the lack of appropriate oxysterol analogs. Intrinsically fluorescent oxysterols present a new route towards direct observation of intracellular oxysterol trafficking by fluorescence microscopy. We characterize the fluorescence properties of the existing fluorescent 25-hydroxycholesterol analog 25-hydroxycholestatrienol, and propose a new probe with an extended conjugated system. The location of both probes inside a membrane is analyzed and compared with that of 25-hydroxycholesterol using molecular dynamics simulations. The analogs' one- and two-photon absorption properties inside the membrane are evaluated using electronic structure calculations with polarizable embedding. Due to predicted keto-enol tautomerisation of the new oxysterol analog, we also evaluate the keto form. Both analogs are found to be good probe candidates for 25-hydroxycholesterol, provided that the new analog remains in the enol-form. Only the new analog with extended conjugated system shows significant two-photon absorption, which is strongly enhanced by the presence of the membrane. Copyright © 2018 Elsevier B.V. All rights reserved.

Electron Paramagnetic Resonance of a Single NV Nanodiamond Attached to an Individual Biomolecule

NASA Astrophysics Data System (ADS)

Teeling-Smith, Richelle M.; Jung, Young Woo; Scozzaro, Nicolas; Cardellino, Jeremy; Rampersaud, Isaac; North, Justin A.; Šimon, Marek; Bhallamudi, Vidya P.; Rampersaud, Arfaan; Johnston-Halperin, Ezekiel; Poirier, Michael G.; Hammel, P. Chris

2016-05-01

A key limitation of electron paramagnetic resonance (EPR), an established and powerful tool for studying atomic-scale biomolecular structure and dynamics is its poor sensitivity, samples containing in excess of 10^12 labeled biomolecules are required in typical experiments. In contrast, single molecule measurements provide improved insights into heterogeneous behaviors that can be masked by ensemble measurements and are often essential for illuminating the molecular mechanisms behind the function of a biomolecule. We report EPR measurements of a single labeled biomolecule that merge these two powerful techniques. We selectively label an individual double-stranded DNA molecule with a single nanodiamond containing nitrogen-vacancy (NV) centers, and optically detect the paramagnetic resonance of NV spins in the nanodiamond probe. Analysis of the spectrum reveals that the nanodiamond probe has complete rotational freedom and that the characteristic time scale for reorientation of the nanodiamond probe is slow compared to the transverse spin relaxation time. This demonstration of EPR spectroscopy of a single nanodiamond labeled DNA provides the foundation for the development of single molecule magnetic resonance studies of complex biomolecular systems.

Study of Molecular-Shape Selectivity of Zeolites by Gas Chromatography

ERIC Educational Resources Information Center

Chao, Pei-Yu; Chuang, Yao-Yuan; Ho, Grace Hsiuying; Chuang, Shiow-Huey; Tsai, Tseng-Chang; Lee, Chi-Young; Tsai, Shang-Tien; Huang, Jun-Fu

2008-01-01

A sorption experiment using a gas chromatograph is described that can help students understand the "molecular-shape selectivity" behavior of zeolites in the subnano regime. Hexane isomers are used as probe molecules to demonstrate the sorption phenomena. In the experiment, a zeolite adsorbs certain hexane isomers with molecular sizes smaller than…

Development and Comparison of a Rapid Isothermal Nucleic Acid Amplification Test for Typing of Herpes Simplex Virus Types 1 and 2 on a Portable Fluorescence Detector

PubMed Central

Tong, Yanhong; McCarthy, Kaitlin; Kong, Huimin; Lemieux, Bertrand

2013-01-01

We have developed a rapid and simple molecular test, the IsoGlow HSV Typing assay, for the detection and typing of herpes simplex virus (type 1 and 2) from genital or oral lesions. Clinical samples suspended in viral transport mediums are simply diluted and then added to a helicase-dependent amplification master mix. The amplification and detection were performed on a portable fluorescence detector called the FireFly instrument. Detection of amplification products is based on end-point analysis using cycling probe technology. An internal control nucleic acid was included in the amplification master mix to monitor the presence of amplification inhibitors in the samples. Because the device has only two fluorescence detection channels, two strategies were developed and compared to detect the internal control template: internal control detected by melting curve analysis using a dual-labeled probe, versus internal control detection using end-point fluorescence release by a CPT probe at a lower temperature. Both have a total turnaround time of about 1 hour. Clinical performance relative to herpes viral culture was evaluated using 176 clinical specimens. Both formats of the IsoGlow HSV typing assay had sensitivities comparable to that of the Food and Drug Administration–cleared IsoAmp HSV (BioHelix Corp., Beverly MA) test and specificity for the two types of HSV comparable to that of ELVIS HSV (Diagnostic Hybrids, Athens, OH). PMID:22951487

SERS Detection of Dopamine Using Label-Free Acridine Red as Molecular Probe in Reduced Graphene Oxide/Silver Nanotriangle Sol Substrate

NASA Astrophysics Data System (ADS)

Luo, Yanghe; Ma, Lu; Zhang, Xinghui; Liang, Aihui; Jiang, Zhiliang

2015-05-01

The reduced graphene oxide/silver nanotriangle (rGO/AgNT) composite sol was prepared by the reduction of silver ions with sodium borohydride in the presence of H2O2 and sodium citrate. In the nanosol substrate, the molecular probe of acridine red (AR) exhibited a weak surface-enhanced Raman scattering (SERS) peak at 1506 cm-1 due to its interaction with the rGO of rGO/AgNT. Upon addition of dopamine (DA), the competitive adsorption between DA and AR with the rGO took place, and the AR molecules were adsorbed on the AgNT aggregates with a strong SERS peak at 1506 cm-1 that caused the SERS peak increase. The increased SERS intensity is linear to the DA concentration in the range of 2.5-500 μmol/L. This new analytical system was investigated by SERS, fluorescence, absorption, transmission electron microscope (TEM), and scanning electron microscope (SEM) techniques, and a SERS quantitative analysis method for DA was established, using AR as a label-free molecular probe.

Molecular Modeling of a Probe in 2D IR Spectroscopy

NASA Astrophysics Data System (ADS)

Cooper, Anthony; Larini, Luca

Proteins must adopt a precise three dimensional structure in the folding process in order to perform its designated function. Although much has been learned about folding, there are still many details in structural dynamics that are difficult to characterize by existing experimental techniques. In order to overcome these challenges, novel infrared and fluorescent spectroscopic techniques have recently been employed to probe the molecular structure at the atomistic scale. These techniques rely on the spectroscopic properties of the nitrile group attached to a phenylalanine. In this study, we model this probe and we compute its properties in different solvents. This is done by performing Molecular Dynamics simulations with a PheCN solvated in water, urea and TMAO. We measure the decay rate of the vibrational stretching of the CN group in order to characterize the effects of different solvents on the local structure of the molecule. This data can be used to identify non-trivial conformational changes of the protein in the folding process. Preliminary results show agreement with current experimental data on 2D IR spectroscopy.

DNA detection and single nucleotide mutation identification using SERS for molecular diagnostics and global health

NASA Astrophysics Data System (ADS)

Ngo, Hoan T.; Gandra, Naveen; Fales, Andrew M.; Taylor, Steve M.; Vo-Dinh, Tuan

2017-02-01

Nucleic acid-based molecular diagnostics at the point-of-care (POC) and in resource-limited settings is still a challenge. We present a sensitive yet simple DNA detection method with single nucleotide polymorphism (SNP) identification capability. The detection scheme involves sandwich hybridization of magnetic beads conjugated with capture probes, target sequences, and ultrabright surface-enhanced Raman Scattering (SERS) nanorattles conjugated with reporter probes. Upon hybridization, the sandwich probes are concentrated at the detection focus controlled by a magnetic system for SERS measurements. The ultrabright SERS nanorattles, consisting of a core and a shell with resonance Raman reporters loaded in the gap space between the core and the shell, serve as SERS tags for ultrasensitive signal detection. Specific DNA sequences of the malaria parasite Plasmodium falciparum and dengue virus 1 (DENV1) were used as the model marker system. Detection limit of approximately 100 attomoles was achieved. Single nucleotide polymorphism (SNP) discrimination of wild type malaria DNA and mutant malaria DNA, which confers resistance to artemisinin drugs, was also demonstrated. The results demonstrate the molecular diagnostic potential of the nanorattle-based method to both detect and genotype infectious pathogens. The method's simplicity makes it a suitable candidate for molecular diagnosis at the POC and in resource-limited settings.

Far-red fluorescent probes for canonical and non-canonical nucleic acid structures: current progress and future implications.

PubMed

Suseela, Y V; Narayanaswamy, Nagarjun; Pratihar, Sumon; Govindaraju, Thimmaiah

2018-02-05

The structural diversity and functional relevance of nucleic acids (NAs), mainly deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are indispensable for almost all living organisms, with minute aberrations in their structure and function becoming causative factors in numerous human diseases. The standard structures of NAs, termed canonical structures, are supported by Watson-Crick hydrogen bonding. Under special physiological conditions, NAs adopt distinct spatial organisations, giving rise to non-canonical conformations supported by hydrogen bonding other than the Watson-Crick type; such non-canonical structures have a definite function in controlling gene expression and are considered as novel diagnostic and therapeutic targets. Development of molecular probes for these canonical and non-canonical DNA/RNA structures has been an active field of research. Among the numerous probes studied, probes with turn-on fluorescence in the far-red (600-750 nm) region are highly sought-after due to minimal autofluorescence and cellular damage. Far-red fluorescent probes are vital for real-time imaging of NAs in live cells as they provide good resolution and minimal perturbation of the cell under investigation. In this review, we present recent advances in the area of far-red fluorescent probes of DNA/RNA and non-canonical G-quadruplex structures. For the sake of continuity and completeness, we provide a brief overview of visible fluorescent probes. Utmost importance is given to design criteria, characteristic properties and biological applications, including in cellulo imaging, apart from critical discussion on limitations of the far-red fluorescent probes. Finally, we offer current and future prospects in targeting canonical and non-canonical NAs specific to cellular organelles, through sequence- and conformation-specific far-red fluorescent probes. We also cover their implications in chemical and molecular biology, with particular focus on decoding various disease mechanisms involving NAs.

Activateable Imaging Probes Light Up Inside Cancer Cells | Center for Cancer Research

Cancer.gov

Imaging can be used to help diagnose cancer as well as monitor tumor progression and response to treatment. The field of molecular imaging focuses on techniques capable of detecting specific molecular targets associated with cancer; the agents used for molecular imaging—often called probes—are multifunctional, with components that allow them to both interact with their molecular target and emit a detectable signal.

The Transferrin Receptor: A Potential Molecular Imaging Marker for Human Cancer1

PubMed Central

Högemann-Savellano, Dagmar; Bos, Erik; Blondet, Cyrille; Sato, Fuminori; Abe, Tatsuya; Josephson, Lee; Weissleder, Ralph; Gaudet, Justin; Sgroi, Dennis; Peters, Peter J.; Basilion, James P.

2003-01-01

Abstract Noninvasive imaging of differences between the molecular properties of cancer and normal tissue has the potential to enhance the detection of tumors. Because overexpression of endogenous transferrin receptor (TfR) has been qualitatively described for various cancers and is presumably due to malignant transformation of cells, TfR may represent a suitable target for application of molecular imaging technologies to increase detection of smaller tumors. In the work reported here, investigation into the biology of this receptor using electron microscopy has demonstrated that iron oxide particles targeted to TfR are internalized and accumulate in lysosomal vesicles within cells. Biochemical analysis of the interaction of imaging probes with cells overexpressing the TfR demonstrated that the extent of accumulation, and therefore probe efficacy, is dependent on the nature of the chemical cross-link between transferrin and the iron oxide particle. These data were utilized to design and synthesize an improved imaging probe. Experiments demonstrate that the novel magnetic resonance imaging (MRI) probe is sensitive enough to detect small differences in endogenous TfR expression in human cancer cell lines. Quantitative measurement of TfR overexpression in a panel of 27 human breast cancer patients demonstrated that 74% of patient cancer tissues overexpressed the TfR and that the sensitivity of the new imaging agent was suitable to detect TfR overexpression in greater than 40% of these cases. Based on a biochemical and cell biological approach, these studies have resulted in the synthesis and development of an improved MRI probe with the best in vitro and in vivo imaging properties reported to date. PMID:14965443

Polarization-controlled optimal scatter suppression in transient absorption spectroscopy

PubMed Central

Malý, Pavel; Ravensbergen, Janneke; Kennis, John T. M.; van Grondelle, Rienk; Croce, Roberta; Mančal, Tomáš; van Oort, Bart

2017-01-01

Ultrafast transient absorption spectroscopy is a powerful technique to study fast photo-induced processes, such as electron, proton and energy transfer, isomerization and molecular dynamics, in a diverse range of samples, including solid state materials and proteins. Many such experiments suffer from signal distortion by scattered excitation light, in particular close to the excitation (pump) frequency. Scattered light can be effectively suppressed by a polarizer oriented perpendicular to the excitation polarization and positioned behind the sample in the optical path of the probe beam. However, this introduces anisotropic polarization contributions into the recorded signal. We present an approach based on setting specific polarizations of the pump and probe pulses, combined with a polarizer behind the sample. Together, this controls the signal-to-scatter ratio (SSR), while maintaining isotropic signal. We present SSR for the full range of polarizations and analytically derive the optimal configuration at angles of 40.5° between probe and pump and of 66.9° between polarizer and pump polarizations. This improves SSR by (or compared to polarizer parallel to probe). The calculations are validated by transient absorption experiments on the common fluorescent dye Rhodamine B. This approach provides a simple method to considerably improve the SSR in transient absorption spectroscopy. PMID:28262765

Investigation of the Binding Profiles of AZD2184 and Thioflavin T with Amyloid-β(1-42) Fibril by Molecular Docking and Molecular Dynamics Methods.

PubMed

Kuang, Guanglin; Murugan, N Arul; Tu, Yaoquan; Nordberg, Agneta; Ågren, Hans

2015-09-03

Detecting deposits of amyloid β fibrils in the brain is of paramount importance for an early diagnosis of Alzheimer's disease. A number of PET tracers have been developed for amyloid imaging, but many suffer from poor specificity and large signal to background ratio. Design of tracers with specificity and improved binding affinity requires knowledge about various potential binding sites in the amyloid β fibril available for the tracers and the nature of the local microenvironment of these sites. In this study we investigate the local structure of fibrils using two important probes, namely, thioflavin T (a fluorescent probe) and AZD2184 (a PET tracer). The target structures for amyloid-β(1-42) fibril are based on reported NMR solution models. By explicitly considering the effect of fibril flexibility on the available binding sites for all these models, the binding affinity of these probes has been investigated. The binding profiles of AZD2184 and thioflavin T were studied by molecular docking and molecular dynamics simulation methods. The two compounds were found to bind at the same sites of the fibril: three of which are within the fibril, and one is on the two sides of the Met35 residue on the surface. The binding affinity of AZD2184 and thioflavin T is found to be higher at the core sites than on the surface due to more contact residues. The binding affinity of AZD2184 is much higher than that of thioflavin T at every site due to electrostatic interaction and spatial restriction, which is in good agreement with experimental observation. However, the structural change of thioflavin T is much more significant than that of AZD2184, which is the chemical basis for its usage as a fluorescent probe. The ramifications of these results for the design and optimization of PET radioligands and fluorescent probes are briefly discussed.

Exploratory Project: Rigid nanostructured organic polymer monolith for in situ collection and analysis of plant metabolites from soil matrices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tharayil, Nishanth

Plant metabolites released from litter leachates and root exudates enable plants to adapt and survive in a wide range of habitats by facilitating resource foraging and plant-organismal interactions, and could influence soil carbon storage. The biological functions of these plant inputs and the organismal interactions they facilitate in soil are strictly governed by their composition and molecular identity. Our current understanding about the molecular identity of exudates is based on physiological studies that are done in soil-less axenic cultures. On the other hand, ecological studies that rely on isotope labeling to track the fluxes of carbon from plants to soilmore » have found the complexities of soil-microbe matrices as an insurmountable barrier to undertake any meaningful molecular level characterization of plant inputs. Although it is constantly advocated to undertake a molecular level identification of the dynamicity of plant metabolites in soils, the complexity of soil system has thus far prevented any such endeavors. We developed polymeric probes through in-situ polymerization of poly(styrene-co-vinylbenzyl chloride-co-divinylbenzene) to elucidate the chemical environment of the soil to which the plant roots are exposed. Hypercrosslinking of the polymeric probes through an in-situ Friedel-Crafts alkylation significantly increased the surface area and the sorption capacity of the probes. Surface functionalization of the probes using a hybrid approach was also attempted. The efficacy of these probes was tested using batch equilibration. Scanning electron microscopy revealed extensive modification of the surface of the probes through hypercrosslinking. The probes exhibited a lower site specific sorption (slope of Freundlich adsorption isotherm close to unity) and percent recovery of the sorbed compounds from the probes were >70, indicating a predominance of reversible sorption. Further we imparted specificity to this copolymer matrix by using molecular-template imprinting approach for the selective capture of less abundant plant metabolites from a crowded soil/litter leachate. Our results suggests that i) the root exudate pattern of plants is highly dependent on the nutrient status of the plant, with greater specificity of root exudation occurring in growing medium with low available form of nutrients, ii) the chemical composition of root exudation is a function of the distance of sampling from the source-roots, with the composition of root exudation being more enriched in polar metabolites farther from the source-roots, iii) Further we demonstrated that the compounds present in real root exudates diffuse farther from the source roots than those in artificial root exudates that are traditionally used. Thus, our project highlights how the soil matrix is instrumental in modifying the chemical composition of root exudates, and highlights that, apart from the plant physiology, the specificity and function of root exudates is also modified by environmental factors.« less

Shock compression and flash-heating of molecular adsorbates on the picosecond time scale

NASA Astrophysics Data System (ADS)

Berg, Christopher Michael

An ultrafast nonlinear coherent laser spectroscopy termed broadband multiplex vibrational sum-frequency generation (SFG) with nonresonant suppression was employed to monitor vibrational transitions of molecular adsorbates on metallic substrates during laser-driven shock compression and flash-heating. Adsorbates were in the form of well-ordered self-assembled monolayers (SAMs) and included molecular explosive simulants, such as nitroaromatics, and long chain-length alkanethiols. Based on reflectance measurements of the metallic substrates, femtosecond flash-heating pulses were capable of producing large-amplitude temperature jumps with DeltaT = 500 K. Laser-driven shock compression of SAMs produced pressures up to 2 GPa, where 1 GPa ≈ 1 x 104 atm. Shock pressures were estimated via comparison with frequency shifts observed in the monolayer vibrational transitions during hydrostatic pressure measurements in a SiC anvil cell. Molecular dynamics during flash-heating and shock loading were probed with vibrational SFG spectroscopy with picosecond temporal resolution and sub-nanometer spatial resolution. Flash-heating studies of 4-nitrobenzenethiolate (NBT) on Au provided insight into effects from hot-electron excitation of the molecular adsorbates at early pump-probe delay times. At longer delay times, effects from the excitation of SAM lattice modes and lower-energy NBT vibrations were shown. In addition, flash-heating studies of alkanethiolates demonstrated chain disordering behaviors as well as interface thermal conductances across the Au-SAM junction, which was of specific interest within the context of molecular electronics. Shock compression studies of molecular explosive simulants, such as 4-nitrobenzoate (NBA), demonstrated the proficiency of this technique to observe shock-induced molecular dynamics, in this case orientational dynamics, on the picosecond time scale. Results validated the utilization of these refined shock loading techniques to probe the shock initiation or first bond-breaking reactions in molecular explosives such as delta-HMX: a necessary study for the development of safer and more effective energetic materials.

A Streamlined Protocol for Molecular Testing of the DMD Gene within a Diagnostic Laboratory: A Combination of Array Comparative Genomic Hybridization and Bidirectional Sequence Analysis

PubMed Central

Marquis-Nicholson, Renate; Lai, Daniel; Love, Jennifer M.; Love, Donald R.

2013-01-01

Purpose. The aim of this study was to develop a streamlined mutation screening protocol for the DMD gene in order to confirm a clinical diagnosis of Duchenne or Becker muscular dystrophy in affected males and to clarify the carrier status of female family members. Methods. Sequence analysis and array comparative genomic hybridization (aCGH) were used to identify mutations in the dystrophin DMD gene. We analysed genomic DNA from six individuals with a range of previously characterised mutations and from eight individuals who had not previously undergone any form of molecular analysis. Results. We successfully identified the known mutations in all six patients. A molecular diagnosis was also made in three of the four patients with a clinical diagnosis who had not undergone prior genetic screening, and testing for familial mutations was successfully completed for the remaining four patients. Conclusion. The mutation screening protocol described here meets best practice guidelines for molecular testing of the DMD gene in a diagnostic laboratory. The aCGH method is a superior alternative to more conventional assays such as multiplex ligation-dependent probe amplification (MLPA). The combination of aCGH and sequence analysis will detect mutations in 98% of patients with the Duchenne or Becker muscular dystrophy. PMID:23476807

A Pan-GTPase Inhibitor as a Molecular Probe

PubMed Central

Hong, Lin; Guo, Yuna; BasuRay, Soumik; Agola, Jacob O.; Romero, Elsa; Simpson, Denise S.; Schroeder, Chad E.; Simons, Peter; Waller, Anna; Garcia, Matthew; Carter, Mark; Ursu, Oleg; Gouveia, Kristine; Golden, Jennifer E.; Aubé, Jeffrey; Wandinger-Ness, Angela; Sklar, Larry A.

2015-01-01

Overactive GTPases have often been linked to human diseases. The available inhibitors are limited and have not progressed far in clinical trials. We report here a first-in-class small molecule pan-GTPase inhibitor discovered from a high throughput screening campaign. The compound CID1067700 inhibits multiple GTPases in biochemical, cellular protein and protein interaction, as well as cellular functional assays. In the biochemical and protein interaction assays, representative GTPases from Rho, Ras, and Rab, the three most generic subfamilies of the GTPases, were probed, while in the functional assays, physiological processes regulated by each of the three subfamilies of the GTPases were examined. The chemical functionalities essential for the activity of the compound were identified through structural derivatization. The compound is validated as a useful molecular probe upon which GTPase-targeting inhibitors with drug potentials might be developed. PMID:26247207

FRET-based small-molecule fluorescent probes: rational design and bioimaging applications.

PubMed

Yuan, Lin; Lin, Weiying; Zheng, Kaibo; Zhu, Sasa

2013-07-16

Fluorescence imaging has emerged as a powerful tool for monitoring biomolecules within the context of living systems with high spatial and temporal resolution. Researchers have constructed a large number of synthetic intensity-based fluorescent probes for bio-imaging. However, intensity-based fluorescent probes have some limitations: variations in probe concentration, probe environment, and excitation intensity may influence the fluorescence intensity measurements. In principle, the use of ratiometric fluorescent probes can alleviate this shortcoming. Förster resonance energy transfer (FRET) is one of the most widely used sensing mechanisms for ratiometric fluorescent probes. However, the development of synthetic FRET probes with favorable photophysical properties that are also suitable for biological imaging applications remains challenging. In this Account, we review the rational design and biological applications of synthetic FRET probes, focusing primarily on studies from our laboratory. To construct useful FRET probes, it is a pre-requisite to develop a FRET platform with favorable photophysical properties. The design criteria of a FRET platform include (1) well-resolved absorption spectra of the donor and acceptor, (2) well-separated emission spectra of the donor and acceptor, (3) donors and acceptors with comparable brightness, (4) rigid linkers, and (5) near-perfect efficiency in energy transfer. With an efficient FRET platform in hand, it is then necessary to modulate the donor-acceptor distance or spectral overlap integral in an analyte-dependent fashion for development of FRET probes. Herein, we emphasize our most recent progress on the development of FRET probes by spectral overlap integral, in particular by changing the molar absorption coefficient of the donor dyes such as rhodamine dyes, which undergo unique changes in the absorption profiles during the ring-opening and -closing processes. Although partial success has been obtained in design of first-generation rhodamine-based FRET probes via modulation of acceptor molar absorption coefficient, further improvements in terms of versatility, sensitivity, and synthetic accessibility are required. To address these issues with the first-generation rhodamine-based FRET probes, we have proposed a strategy for the design of second-generation probes. As a demonstration, we have developed FRET imaging probes for diverse targets including Cu²⁺, NO, HOCl, cysteine, and H₂O₂. This discussion of the methods for successfully designing synthetic FRET probes underscores the rational basis for further development of new FRET probes as a molecular toolbox for probing and manipulating a wide variety of biomolecules in living systems.

Unveiling molecular events in the brain by noninvasive imaging.

PubMed

Klohs, Jan; Rudin, Markus

2011-10-01

Neuroimaging allows researchers and clinicians to noninvasively assess structure and function of the brain. With the advances of imaging modalities such as magnetic resonance, nuclear, and optical imaging; the design of target-specific probes; and/or the introduction of reporter gene assays, these technologies are now capable of visualizing cellular and molecular processes in vivo. Undoubtedly, the system biological character of molecular neuroimaging, which allows for the study of molecular events in the intact organism, will enhance our understanding of physiology and pathophysiology of the brain and improve our ability to diagnose and treat diseases more specifically. Technical/scientific challenges to be faced are the development of highly sensitive imaging modalities, the design of specific imaging probe molecules capable of penetrating the CNS and reporting on endogenous cellular and molecular processes, and the development of tools for extracting quantitative, biologically relevant information from imaging data. Today, molecular neuroimaging is still an experimental approach with limited clinical impact; this is expected to change within the next decade. This article provides an overview of molecular neuroimaging approaches with a focus on rodent studies documenting the exploratory state of the field. Concepts are illustrated by discussing applications related to the pathophysiology of Alzheimer's disease.

Recent patents on self-quenching DNA probes.

PubMed

Knemeyer, Jens-Peter; Marmé, Nicole

2007-01-01

In this review, we report on patents concerning self-quenching DNA probes for assaying DNA during or after amplification as well as for direct assaying DNA or RNA, for example in living cells. Usually the probes consist of fluorescently labeled oligonucleotides whose fluorescence is quenched in the absence of the matching target DNA. Thereby the fluorescence quenching is based on fluorescence resonance energy transfer (FRET), photoinduced electron transfer (PET), or electronically interactions between dye and quencher. However, upon hybridization to the target or after the degradation during a PCR, the fluorescence of the dye is restored. Although the presented probes were originally developed for use in homogeneous assay formats, most of them are also appropriate to improve surface-based assay methods. In particular we describe patents for self-quenching primers, self-quenching probes for TaqMan assays, probes based on G-quartets, Molecular Beacons, Smart Probes, and Pleiades Probes.

Integrated signal probe based aptasensor for dual-analyte detection.

PubMed

Xiang, Juan; Pi, Xiaomei; Chen, Xiaoqing; Xiang, Lei; Yang, Minghui; Ren, Hao; Shen, Xiaojuan; Qi, Ning; Deng, Chunyan

2017-10-15

For the multi-analyte detection, although the sensitivity has commonly met the practical requirements, the reliability, reproducibility and stability need to be further improved. In this work, two different aptamer probes labeled with redox tags were used as signal probe1 (sP1) and signal probe2 (sP2), which were integrated into one unity DNA architecture to develop the integrated signal probe (ISP). Comparing with the conventional independent signal probes for the simultaneous multi-analyte detection, the proposed ISP was more reproducible and accurate. This can be due to that ISP in one DNA structure can ensure the completely same modification condition and an equal stoichiometric ratio between sP1 and sP2, and furthermore the cross interference between sP1 and sP2 can be successfully prevented by regulating the complementary position of sP1 and sP2. The ISP-based assay system would be a great progress for the dual-analyte detection. Combining with gold nanoparticles (AuNPs) signal amplification, the ISP/AuNPs-based aptasensor for the sensitive dual-analyte detection was explored. Based on DNA structural switching induced by targets binding to aptamer, the simultaneous dual-analyte detection was simply achieved by monitoring the electrochemical responses of methylene blue (MB) and ferrocene (Fc) This proposed detection system possesses such advantages as simplicity in design, easy operation, good reproducibility and accuracy, high sensitivity and selectivity, which indicates the excellent application of this aptasensor in the field of clinical diagnosis or other molecular sensors. Copyright © 2017 Elsevier B.V. All rights reserved.

The association of low-molecular-weight hydrophobic compounds with native casein micelles in bovine milk

PubMed Central

Cheema, M.; Mohan, M. S.; Campagna, S. R.; Jurat-Fuentes, J. L.; Harte, F. M.

2015-01-01

The agreed biological function of the casein micelles in milk is to carry minerals (calcium, magnesium, and phosphorus) from mother to young along with amino acids for growth and development. Recently, native and modified casein micelles were used as encapsulating and delivery agents for various hydrophobic low-molecular-weight probes. The ability of modified casein micelles to bind certain probes may derive from the binding affinity of native casein micelles. Hence, a study with milk from single cows was conducted to further elucidate the association of hydrophobic molecules into native casein micelles and further understand their biological function. Hydrophobic and hydrophilic extraction followed by ultraperformance liquid chromatography-high resolution mass spectrometry analysis were performed over protein fractions obtained from size exclusion fractionation of raw skim milk. Hydrophobic compounds, including phosphatidylcholine, lyso-phosphatidylcholine, phosphatidylethanolamine, and sphingomyelin, showed strong association exclusively to casein micelles as compared with whey proteins, whereas hydrophilic compounds did not display any preference for their association among milk proteins. Further analysis using liquid chromatography-tandem mass spectrometry detected 42 compounds associated solely with the casein-micelles fraction. Mass fragments in tandem mass spectrometry identified 4 of these compounds as phosphatidylcholine with fatty acid composition of 16:0/18:1, 14:0/16:0, 16:0/16:0, and 18:1/18:0. These results support that transporting low-molecular-weight hydrophobic molecules is also a biological function of the casein micelles in milk. PMID:26074238

Brain transcriptome atlases: a computational perspective.

PubMed

Mahfouz, Ahmed; Huisman, Sjoerd M H; Lelieveldt, Boudewijn P F; Reinders, Marcel J T

2017-05-01

The immense complexity of the mammalian brain is largely reflected in the underlying molecular signatures of its billions of cells. Brain transcriptome atlases provide valuable insights into gene expression patterns across different brain areas throughout the course of development. Such atlases allow researchers to probe the molecular mechanisms which define neuronal identities, neuroanatomy, and patterns of connectivity. Despite the immense effort put into generating such atlases, to answer fundamental questions in neuroscience, an even greater effort is needed to develop methods to probe the resulting high-dimensional multivariate data. We provide a comprehensive overview of the various computational methods used to analyze brain transcriptome atlases.

Targeted Capture and High-Throughput Sequencing Using Molecular Inversion Probes (MIPs).

PubMed

Cantsilieris, Stuart; Stessman, Holly A; Shendure, Jay; Eichler, Evan E

2017-01-01

Molecular inversion probes (MIPs) in combination with massively parallel DNA sequencing represent a versatile, yet economical tool for targeted sequencing of genomic DNA. Several thousand genomic targets can be selectively captured using long oligonucleotides containing unique targeting arms and universal linkers. The ability to append sequencing adaptors and sample-specific barcodes allows large-scale pooling and subsequent high-throughput sequencing at relatively low cost per sample. Here, we describe a "wet bench" protocol detailing the capture and subsequent sequencing of >2000 genomic targets from 192 samples, representative of a single lane on the Illumina HiSeq 2000 platform.

Selenium- and tellurium-containing fluorescent molecular probes for the detection of biologically important analytes.

PubMed

Manjare, Sudesh T; Kim, Youngsam; Churchill, David G

2014-10-21

As scientists in recent decades have discovered, selenium is an important trace element in life. The element is now known to play an important role in biology as an enzymatic antioxidant. In this case, it sits at the active site and converts biological hydrogen peroxides to water. Mimicking this reaction, chemists have synthesized several organoselenium compounds that undergo redox transformations. As such, these types of compounds are important in the future of both medicinal and materials chemistry. One main challenge for organochalcogen chemists has been to synthesize molecular probes that are soluble in water where a selenium or tellurium center can best modify electronics of the molecule based on a chemical oxidation or reduction event. In this Account, we discuss chemists' recent efforts to create chalcogen-based chemosensors through synthetic means and current photophysical understanding. Our work has focused on small chromophoric or fluorophoric molecules, in which we incorporate discrete organochalcogen atoms (e.g., R-Se-R, R-Te-R) in predesigned sites. These synthetic molecules, involving rational synthetic pathways, allow us to chemoselectively oxidize compounds and to study the level of analyte selectivity by way of their optical responses. All the reports we discussed here deal with well-defined and small synthetic molecular systems. With a large number of reports published over the last few years, many have notably originated from the laboratory of K. Han (P. R. China). This growing body of research has given chemists new ideas for the previously untenable reversible reactive oxygen species detection. While reversibility of the probe is technically important from the stand-point of the chalcogen center, facile regenerability of the probe using a secondary analyte to recover the initial probe is a very promising avenue. This is because (bio)chalcogen chemistry is extremely rich and bioinspired and continues to yield important developments across many scientific fields. Organochalcogen (R-E-R) chemistry in such chemical recognition and supramolecular pursuits is a fundamental tool to allow chemists to explore stable organic-based probe modalities of interest to develop better spectroscopic tools for (neuro)biological applications. Chalcogen donor sites also provide sites where metals can coordinate, and facile oxidation may extend to the sulfone analogues (R-EO2-R) or beyond. Consequently, chemists can then make use of reliable reversible chemical probing platforms based on the chemical redox properties valence state switching principally from 2 to 4 (and back to 2) of selenium and tellurium atoms. The main organic molecular skeletons have involved chemical frames including boron-dipyrromethene (BODIPY) systems, extended cyanine groups, naphthalimide, rhodamine, and fluorescein cores, and isoselenazolone, pyrene, coumarin, benzoselenadiazole, and selenoguanine systems. Our group has tested many such molecular probe systems in cellular milieu and under a series of conditions and competitive environments. We have found that the most important analytes have been reactive oxygen species (ROS) such as superoxide and hypochlorite. Reactive nitrogen species (RNS) such as peroxynitrite are also potential targets. In addition, we have also considered Fenton chemistry systems. Our research and that of others shows that the action of ROS is often reversible with H2S or biothiols such as glutathione (GSH). We have also found that a second class of analytes are the thiols (RSH), in particular, biothiols. Here, the target group might involve an R-Se-Se-R group. The study of analytes also extends to metal ions, for example, Hg(2+), and anions such as fluoride (F(-)), and we have developed NIR-based systems as well. These work through various photomechanisms, including photoinduced electron transfer (PET), twisted internal charge transfer (TICT), and internal charge transfer (ICT). The growing understanding of this class of probe suggests that there is much room for creative thinking regarding modular designs or unexpected organic chemical synthesis designs, interplay between analytes, new analyte selectivity, biological targeting, and chemical switching, which can also serve to further the neurological probing and molecular logic gating frontiers.

Long-stem shaped multifunctional molecular beacon for highly sensitive nucleic acids determination via intramolecular and intermolecular interactions based strand displacement amplification.

PubMed

Xu, Jianguo; Zheng, Tingting; Le, Jingqing; Jia, Lee

2017-11-20

Occurrence and application of oligonucleotide probes have promoted great progress in the biochemical analysis field due to their unique biological and chemical properties. In this work, a long-stem shaped multifunctional molecular beacon (LS-MMB) that is responsive to a cancer-related gene, p53, is well-prepared. By designing the probe with long-paired bases at its two ends and short-paired bases between the middle region and the 3' end, the LS-MMB is intelligently endowed with the ability to recognize the target analyte, serve as the polymerization primer/template, and signal the hybridization event synchronously, which is distinctly advantageous over the traditional molecular beacons (MBs). Moreover, it is excitingly found that the LS-MMB can be employed to exert intramolecular and intermolecular interactions for strand displacement amplification (SDA) without the involvement of any assistant probes; this therapy results in a really easy and rapid sensing system that provides an extremely low background noise and high target output signal. In this case, an excellent sensitivity and specificity to detect target gene down to picomolar level and resolution to even one nucleotide variation are achieved, respectively. In addition, the application potential for real genomic DNA analysis is realized. We envision that the probe of LS-MMB can act as a universal platform for biosensing and biomedical research.

Development of new PTK7-targeting aptamer-fluorescent and -radiolabelled probes for evaluation as molecular imaging agents: Lymphoma and melanoma in vivo proof of concept.

PubMed

Calzada, Victoria; Moreno, María; Newton, Jessica; González, Joel; Fernández, Marcelo; Gambini, Juan Pablo; Ibarra, Manuel; Chabalgoity, Alejandro; Deutscher, Susan; Quinn, Thomas; Cabral, Pablo; Cerecetto, Hugo

2017-02-01

Aptamers are single-stranded oligonucleotides that recognize molecular targets with high affinity and specificity. Aptamer that selectively bind to the protein tyrosine kinase-7 (PTK7) receptor, overexpressed on many cancers, has been labelled as probes for molecular imaging of cancer. Two new PTK7-targeting aptamer probes were developed by coupling frameworks from the fluorescent dye AlexaFluor647 or the 6-hydrazinonicotinamide (HYNIC) chelator-labelled to 99m Tc. The derivatizations via a 5'-aminohexyl terminal linker were done at room temperature and under mild buffer conditions. Physicochemical and biological controls for both imaging agents were performed verifying the integrity of the aptamer-conjugates by HPLC. Recognition of melanoma (B16F1) and lymphoma (A20) mouse cell lines by the aptamer was studied using cell binding, flow cytometry and confocal microscopy. Finally, in vivo imaging studies in tumour-bearing mice were performed. The new probes were able to bind to melanoma and lymphoma cell lines in vitro, the in vivo imaging in tumour-bearing mice showed different uptake behaviours showing for the fluorescent conjugate good uptake by B cell lymphoma while the radiolabelled conjugate did not display tumour uptake due to its high extravascular distribution, and both showed rapid clearance properties in tumour-bearing mice. Copyright © 2016 Elsevier Ltd. All rights reserved.

Improved molecular fingerprint analysis employing multi-branched gold nanoparticles in conjunction with surface-enhanced Raman scattering.

PubMed

Johnston, Jencilin; Taylor, Erik N; Gilbert, Richard J; Webster, Thomas J

2016-01-01

Vibrational spectroscopy is a powerful analytical tool that assesses molecular properties based on spectroscopic signatures. In this study, the effect of gold nanoparticle morphology (spherical vs multi-branched) was assessed for the characterization of a Raman signal (ie, molecular fingerprint) that may be helpful for numerous medical applications. Multi-branched gold nanoparticles (MBAuNPs) were fabricated using a green chemistry method which employed the reduction of gold ion solute by 2-[4-(2-hydroxyethyl)-1-piperazyl] ethane sulfonic acid. Two types of reporter dyes, indocyanine (IR820 and IR792) and carbocyanine (DTTC [3,3'-diethylthiatricarbocyanine iodide] and DTDC [3,3'-diethylthiadicarbocyanine iodide]), were functionalized to the surface of the MBAuNPs and stabilized with denatured bovine serum albumin, thus forming the surface-enhanced Raman spectroscopy tag. Fluorescein isothiocyanate-conjugated anti-epidermal growth factor receptor to the surface-enhanced Raman spectroscopy tags and the properties of the resulting conjugates were assessed through determination of the Raman signal. Using the MBAuNP Raman probes synthesized in this manner, we demonstrated that MBAuNP provided significantly more surface-enhanced Raman scattering signal when compared with the associated spherical gold nanoparticle of similar size and concentration. MBAuNP enhancements were retained in the surface-enhanced Raman spectroscopy tags complexed to anti-epidermal growth factor receptor, providing evidence that this could be a useful biological probe for enhanced Raman molecular fingerprinting. Furthermore, while utilizing IR820 as a novel reporter dye linked with MBAuNP, superior Raman signal fingerprint results were obtained. Such results provide significant promise for the use of MBAuNP in the detection of numerous diseases for which biologically specific surface markers exist.

Improved molecular fingerprint analysis employing multi-branched gold nanoparticles in conjunction with surface-enhanced Raman scattering

PubMed Central

Johnston, Jencilin; Taylor, Erik N; Gilbert, Richard J; Webster, Thomas J

2016-01-01

Vibrational spectroscopy is a powerful analytical tool that assesses molecular properties based on spectroscopic signatures. In this study, the effect of gold nanoparticle morphology (spherical vs multi-branched) was assessed for the characterization of a Raman signal (ie, molecular fingerprint) that may be helpful for numerous medical applications. Multi-branched gold nanoparticles (MBAuNPs) were fabricated using a green chemistry method which employed the reduction of gold ion solute by 2-[4-(2-hydroxyethyl)-1-piperazyl] ethane sulfonic acid. Two types of reporter dyes, indocyanine (IR820 and IR792) and carbocyanine (DTTC [3,3′-diethylthiatricarbocyanine iodide] and DTDC [3,3′-diethylthiadicarbocyanine iodide]), were functionalized to the surface of the MBAuNPs and stabilized with denatured bovine serum albumin, thus forming the surface-enhanced Raman spectroscopy tag. Fluorescein isothiocyanate-conjugated anti-epidermal growth factor receptor to the surface-enhanced Raman spectroscopy tags and the properties of the resulting conjugates were assessed through determination of the Raman signal. Using the MBAuNP Raman probes synthesized in this manner, we demonstrated that MBAuNP provided significantly more surface-enhanced Raman scattering signal when compared with the associated spherical gold nanoparticle of similar size and concentration. MBAuNP enhancements were retained in the surface-enhanced Raman spectroscopy tags complexed to anti-epidermal growth factor receptor, providing evidence that this could be a useful biological probe for enhanced Raman molecular fingerprinting. Furthermore, while utilizing IR820 as a novel reporter dye linked with MBAuNP, superior Raman signal fingerprint results were obtained. Such results provide significant promise for the use of MBAuNP in the detection of numerous diseases for which biologically specific surface markers exist. PMID:26730189

Molecular Tracking, through Processing, of Campylobacter Strains Colonizing Broiler Flocks▿

PubMed Central

Elvers, Karen T.; Morris, Victoria K.; Newell, Diane G.; Allen, Vivien M.

2011-01-01

Many of the poultry flocks produced in the United Kingdom are colonized with Campylobacter, and the intensive nature of poultry processing usually results in contaminated carcasses. In this study, a previously reported molecular oligonucleotide probe method was used to track a specific flock-colonizing strain(s) on broiler carcasses during processing in two United Kingdom commercial poultry processing plants. Five Campylobacter-positive flocks were sampled at four points along the processing line, postbleed, postpluck, prechill, and postchill, and two Campylobacter-negative flocks processed immediately after positive flocks were sampled prechill. flaA was sequenced from Campylobacter strains isolated from these flocks, and strain-specific probes were synthesized. Skin and cecal samples were plated onto selective agar to give individual colonies, which were transferred onto membranes. These were then hybridized with the strain- and genus-specific probes. For all the 5 positive flocks, there was a significant reduction in campylobacters postbleed compared to postpluck but no subsequent fall on sampling pre- and postchill, and the strain(s) predominating on the carcasses throughout processing came from the flock being processed. This indicates that strains from the abattoir environment were not a significant cause of carcass contamination in flocks with well-established campylobacter colonization. However, negative flocks that were preceded by positive flocks were contaminated by strains that did not generally originate from the predominating strains recovered from the ceca of the previous positive flocks. This suggests that the abattoir environment has a significant role in the contamination of carcasses from negative but not fully colonized flocks. PMID:21705532

Recent Development of Inorganic Nanoparticles for Biomedical Imaging

PubMed Central

2018-01-01

Inorganic nanoparticle-based biomedical imaging probes have been studied extensively as a potential alternative to conventional molecular imaging probes. Not only can they provide better imaging performance but they can also offer greater versatility of multimodal, stimuli-responsive, and targeted imaging. However, inorganic nanoparticle-based probes are still far from practical use in clinics due to safety concerns and less-optimized efficiency. In this context, it would be valuable to look over the underlying issues. This outlook highlights the recent advances in the development of inorganic nanoparticle-based probes for MRI, CT, and anti-Stokes shift-based optical imaging. Various issues and possibilities regarding the construction of imaging probes are discussed, and future research directions are suggested. PMID:29632878

Spectroscopic and molecular docking studies on N,N-di-tert-butoxycarbonyl (Boc)-2-amino pyridine: A potential bioactive agent for lung cancer treatment

NASA Astrophysics Data System (ADS)

Mohamed Asath, R.; Premkumar, R.; Mathavan, T.; Milton Franklin Benial, A.

2017-09-01

Potential energy surface scan was performed and the most stable molecular structure of the N,N-di-tert-butoxycarbonyl (Boc)-2-amino pyridine (DBAP) molecule was predicted. The most stable molecular structure of the molecule was optimized using B3LYP method with cc-pVTZ basis set. Anticancer activity of the DBAP molecule was evaluated by molecular docking analysis. The structural parameters and vibrational wavenumbers were calculated for the optimized molecular structure. The experimental and theoretical wavenumbers were assigned and compared. Ultraviolet-Visible spectrum was simulated and validated experimentally. The molecular electrostatic potential surface was simulated and Fukui function calculations were also carried out to investigate the reactive nature of the DBAP molecule. The natural bond orbital analysis was also performed to probe the intramolecular interactions and confirm the bioactivity of the DBAP molecule. The molecular docking analysis reveals the better inhibitory nature of the DBAP molecule against the epidermal growth factor receptor (EGFR) protein which causes lung cancer. Hence, the present study unveils the structural and bioactive nature of the title molecule. The DBAP molecule was identified as a potential inhibitor against the lung cancer which may be useful in further development of drug designing in the treatment of lung cancer.

Pump-Probe Noise Spectroscopy of Molecular Junctions.

PubMed

Ochoa, Maicol A; Selzer, Yoram; Peskin, Uri; Galperin, Michael

2015-02-05

The slow response of electronic components in junctions limits the direct applicability of pump-probe type spectroscopy in assessing the intramolecular dynamics. Recently the possibility of getting information on a sub-picosecond time scale from dc current measurements was proposed. We revisit the idea of picosecond resolution by pump-probe spectroscopy from dc measurements and show that any intramolecular dynamics not directly related to charge transfer in the current direction is missed by current measurements. We propose a pump-probe dc shot noise spectroscopy as a suitable alternative. Numerical examples of time-dependent and average responses of junctions are presented for generic models.

Molecular imaging reveals elevated VEGFR-2 expression in retinal capillaries in diabetes: a novel biomarker for early diagnosis.

PubMed

Sun, Dawei; Nakao, Shintaro; Xie, Fang; Zandi, Souska; Bagheri, Abouzar; Kanavi, Mozhgan Rezaei; Samiei, Shahram; Soheili, Zahra-Soheila; Frimmel, Sonja; Zhang, Zhongyu; Ablonczy, Zsolt; Ahmadieh, Hamid; Hafezi-Moghadam, Ali

2014-09-01

Diabetic retinopathy (DR) is a microvascular complication of diabetes and a leading cause of vision loss. Biomarkers and methods for early diagnosis of DR are urgently needed. Using a new molecular imaging approach, we show up to 94% higher accumulation of custom designed imaging probes against vascular endothelial growth factor receptor 2 (VEGFR-2) in retinal and choroidal vessels of diabetic animals (P<0.01), compared to normal controls. More than 80% of the VEGFR-2 in the diabetic retina was in the capillaries, compared to 47% in normal controls (P<0.01). Angiography in rabbit retinas revealed microvascular capillaries to be the location for VEGF-A-induced leakage, as expressed by significantly higher rate of fluorophore spreading with VEGF-A injection when compared to vehicle control (26±2 vs. 3±1 μm/s, P<0.05). Immunohistochemistry showed VEGFR-2 expression in capillaries of diabetic animals but not in normal controls. Macular vessels from diabetic patients (n=7) showed significantly more VEGFR-2 compared to nondiabetic controls (n=5) or peripheral retinal regions of the same retinas (P<0.01 in both cases). Here we introduce a new approach for early diagnosis of DR and VEGFR-2 as a molecular marker. VEGFR-2 could become a key diagnostic target, one that might help to prevent retinal vascular leakage and proliferation in diabetic patients. © FASEB.

Novel nano-OLED based probes for very high resolution optical microscopy

NASA Astrophysics Data System (ADS)

Zhao, Yiying

Near-field scanning optical microscopy (NSOM) has been applied in the study of nanomaterials, microelectronics, photonics, plasmonics, cells, and molecules. However, conventional NSOM relies on optically pumped probes, suffering low optical transmission, heating of the tip, and poor reproducibility of probe fabrication, increasing the cost, impeding usability, reducing practical imaging resolution, and limiting NSOM's utility. In this thesis, I demonstrate a novel probe based on a nanoscale, electrically pumped organic light-emitting device (OLED) formed on the tip of a low-cost, commercially available atomic force microscopy (AFM) probe. I describe the structure, fabrication, and principles of this novel probe's operation, and discuss its potential to overcome the limitations of conventional NSOM probes. The broader significance of this work in the field of organic optoelectronics is also discussed. Briefly, OLEDs consist of organic thin films sandwiched between two electrodes. Under bias, electrons and holes are injected into the organic layers, leading to radiative recombination. Depositing a small molecular OLED in vacuum onto a pyramid-tipped AFM probe results in a laminar structure that is highly curved at the tip. Simple electrical modeling predicts concentration of electric field and localized electron injection into the organic layers at the tip, improving the local charge balance in an otherwise electron-starved OLED. Utilizing an "inverted" OLED structure (i.e. cathode on the "bottom"), light emission is localized to sub-200 nm sized, green light emitting regions on probe vertices; light output power in the range of 0.1-0.5 nanowatts was observed, comparable to that of typical fiber based NSOM probes but with greater power efficiency. Massive arrays of similar sub-micron OLEDs were also fabricated by depositing onto textured silicon substrates, demonstrating the superior scalability of the probe fabrication process (e.g. relative to pulled glass fibers). The investigation of the effect of non-planar substrate geometry on charge injection, transport and recombination provides broader insights into OLEDs made on rough substrates, general understanding of OLED operation (e.g. filamentary charge conduction) and degradation, and potentially helps to improve technologically important "inverted" OLED structures.

Molecular cytogenetic definition of the chicken genome: the first complete avian karyotype.

PubMed Central

Masabanda, Julio S; Burt, Dave W; O'Brien, Patricia C M; Vignal, Alain; Fillon, Valerie; Walsh, Philippa S; Cox, Helen; Tempest, Helen G; Smith, Jacqueline; Habermann, Felix; Schmid, Michael; Matsuda, Yoichi; Ferguson-Smith, Malcolm A; Crooijmans, Richard P M A; Groenen, Martien A M; Griffin, Darren K

2004-01-01

Chicken genome mapping is important for a range of scientific disciplines. The ability to distinguish chromosomes of the chicken and other birds is thus a priority. Here we describe the molecular cytogenetic characterization of each chicken chromosome using chromosome painting and mapping of individual clones by FISH. Where possible, we have assigned the chromosomes to known linkage groups. We propose, on the basis of size, that the NOR chromosome is approximately the size of chromosome 22; however, we suggest that its original assignment of 16 should be retained. We also suggest a definitive chromosome classification system and propose that the probes developed here will find wide utility in the fields of developmental biology, DT40 studies, agriculture, vertebrate genome organization, and comparative mapping of avian species. PMID:15082555

Optical imaging of reporter gene expression using a positron-emission-tomography probe

NASA Astrophysics Data System (ADS)

Liu, Hongguang; Ren, Gang; Liu, Shuanglong; Zhang, Xiaofen; Chen, Luxi; Han, Peizhen; Cheng, Zhen

2010-11-01

Reporter gene/reporter probe technology is one of the most important techniques in molecular imaging. Lately, many reporter gene/reporter probe systems have been coupled to different imaging modalities such as positron emission tomography (PET) and optical imaging (OI). It has been recently found that OI techniques could be used to monitor radioactive tracers in vitro and in living subjects. In this study, we further demonstrate that a reporter gene/nuclear reporter probe system [herpes simplex virus type-1 thymidine kinase (HSV1-tk) and 9-(4-18F-fluoro-3-[hydroxymethyl] butyl) guanine ([18F]FHBG)] could be successfully imaged by OI in vitro and in vivo. OI with radioactive reporter probes will facilitate and broaden the applications of reporter gene/reporter probe techniques in medical research.

A Simple Refraction Experiment for Probing Diffusion in Ternary Mixtures

ERIC Educational Resources Information Center

Coutinho, Cecil A.; Mankidy, Bijith D.; Gupta, Vinay K.

2010-01-01

Diffusion is a fundamental phenomenon that is vital in many chemical processes such as mass transport in living cells, corrosion, and separations. We describe a simple undergraduate-level experiment based on Weiner's Method to probe diffusion in a ternary aqueous mixture of small molecular-weight molecules. As an illustration, the experiment…

Use of molecular probes to detect parasites and retrotransposons in gypsy moths

Treesearch

John H. Werren; Thomas O' Dell

1991-01-01

Retrotransposon screen: Gypsy moth families containing straggling and nonstraggling individuals were divided into categories of straggling, medium, and nonstraggling individuals, from which DNA was extracted. Four families were tested by southern hybridization and probing with ribosomal sequences designed to detect R1 and R2 retrotransposon insertions. Results showed...

Time-resolved ion imaging at free-electron lasers using TimepixCam.

PubMed

Fisher-Levine, Merlin; Boll, Rebecca; Ziaee, Farzaneh; Bomme, Cédric; Erk, Benjamin; Rompotis, Dimitrios; Marchenko, Tatiana; Nomerotski, Andrei; Rolles, Daniel

2018-03-01

The application of a novel fast optical-imaging camera, TimepixCam, to molecular photoionization experiments using the velocity-map imaging technique at a free-electron laser is described. TimepixCam is a 256 × 256 pixel CMOS camera that is able to detect and time-stamp ion hits with 20 ns timing resolution, thus making it possible to record ion momentum images for all fragment ions simultaneously and avoiding the need to gate the detector on a single fragment. This allows the recording of significantly more data within a given amount of beam time and is particularly useful for pump-probe experiments, where drifts, for example, in the timing and pulse energy of the free-electron laser, severely limit the comparability of pump-probe scans for different fragments taken consecutively. In principle, this also allows ion-ion covariance or coincidence techniques to be applied to determine angular correlations between fragments.

Upconversion particles coated with molecularly imprinted polymers as fluorescence probe for detection of clenbuterol.

PubMed

Tang, Yiwei; Gao, Ziyuan; Wang, Shuo; Gao, Xue; Gao, Jingwen; Ma, Yong; Liu, Xiuying; Li, Jianrong

2015-09-15

A novel fluorescence probe based on upconversion particles, YF3:Yb(3+), Er(3+), coating with molecularly imprinted polymers (MIPs@UCPs) has been synthesized for selective recognition of the analyte clenbuterol (CLB), which was characterized by scan electron microscope and X-ray powder diffraction. The fluorescence of the MIPs@UCPs probe is quenched specifically by CLB, and the effect is much stronger than the NIPs@UCPs (non-imprinting polymers, NIPs). Good linear correlation was obtained for CLB over the concentration range of 5.0-100.0 μg L(-1) with a detection limit of 0.12 μg L(-1) (S/N=3). The developed method was also used in the determination of CLB in water and pork samples, and the recoveries ranged from 81.66% to 102.46% were obtained with relative standard deviation of 2.96-4.98% (n=3). The present study provides a new and general tactics to synthesize MIPs@UCPs fluorescence probe with highly selective recognition ability to the CLB and is desirable for application widely in the near future. Copyright © 2015 Elsevier B.V. All rights reserved.

Design Mechanism and Property of the Novel Fluorescent Probes for the Identification of Microthrix parvicella In Situ

PubMed Central

Jiao, Xiumei; Fei, Xuening; Li, Songya; Lin, Dayong; Ma, Huaji; Zhang, Baolian

2017-01-01

In this study, two novel fluorescent probes, probe A and probe B were designed, synthesized and characterized, based on Microthrix parvicella (M. parvicella) preferring to utilize long-chain fatty acid (LCFA), for the labeling of M. parvicella in activated sludge. The molecular structure of probe A and probe B include long-chain alkane and LCFA, respectively. The results indicated that probe A and probe B had a large stokes shift of 118 nm and 120 nm and high quantum yield of 0.1043 and 0.1058, respectively, which were significantly helpful for the fluorescent labeling. As probe A was more stable than probe B in activated sludge, and the fluorescence intensity keep stable during 24 h, probe A was more suitable for labeling M. parvicella in situ. In addition, through the Image Pro Plus 6 (IPP 6) analysis, a quantitative relationship was established between sludge volume index (SVI) and integral optical density (IOD) of the labeled M. parvicella in activated sludge samples. The relationship between IOD and SVI conforms to Logistic curve (R2 = 0.94). PMID:28773166

A peptide-based positron emission tomography probe for in vivo detection of caspase activity in apoptotic cells.

PubMed

Hight, Matthew R; Cheung, Yiu-Yin; Nickels, Michael L; Dawson, Eric S; Zhao, Ping; Saleh, Samir; Buck, Jason R; Tang, Dewei; Washington, M Kay; Coffey, Robert J; Manning, H Charles

2014-04-15

Apoptosis, or programmed cell death, can be leveraged as a surrogate measure of response to therapeutic interventions in medicine. Cysteine aspartic acid-specific proteases, or caspases, are essential determinants of apoptosis signaling cascades and represent promising targets for molecular imaging. Here, we report development and in vivo validation of [(18)F]4-fluorobenzylcarbonyl-Val-Ala-Asp(OMe)-fluoromethylketone ([(18)F]FB-VAD-FMK), a novel peptide-based molecular probe suitable for quantification of caspase activity in vivo using positron emission tomography (PET). Supported by molecular modeling studies and subsequent in vitro assays suggesting probe feasibility, the labeled pan-caspase inhibitory peptide, [(18)F]FB-VAD-FMK, was produced in high radiochemical yield and purity using a simple two-step, radiofluorination. The biodistribution of [(18)F]FB-VAD-FMK in normal tissue and its efficacy to predict response to molecularly targeted therapy in tumors was evaluated using microPET imaging of mouse models of human colorectal cancer. Accumulation of [(18)F]FB-VAD-FMK was found to agree with elevated caspase-3 activity in response to Aurora B kinase inhibition as well as a multidrug regimen that combined an inhibitor of mutant BRAF and a dual PI3K/mTOR inhibitor in (V600E)BRAF colon cancer. In the latter setting, [(18)F]FB-VAD-FMK PET was also elevated in the tumors of cohorts that exhibited reduction in size. These studies illuminate [(18)F]FB-VAD-FMK as a promising PET imaging probe to detect apoptosis in tumors and as a novel, potentially translatable biomarker for predicting response to personalized medicine. ©2014 AACR.

Multimodal Molecular Imaging Reveals High Target Uptake and Specificity of 111In- and 68Ga-Labeled Fibrin-Binding Probes for Thrombus Detection in Rats.

PubMed

Oliveira, Bruno L; Blasi, Francesco; Rietz, Tyson A; Rotile, Nicholas J; Day, Helen; Caravan, Peter

2015-10-01

We recently showed the high target specificity and favorable imaging properties of 64Cu and Al18F PET probes for noninvasive imaging of thrombosis. Here, our aim was to evaluate new derivatives labeled with either with 68Ga, 111In, or 99mTc as thrombus imaging agents for PET and SPECT. In this study, the feasibility and potential of these probes for thrombus imaging was assessed in detail in 2 animal models of arterial thrombosis. The specificity of the probes was further evaluated using a triple-isotope approach with multimodal SPECT/PET/CT imaging. Radiotracers were synthesized using a known fibrin-binding peptide conjugated to 1,4,7-triazacyclononane,1-glutaric acid-4,7-acetic acid (NODAGA), 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid monoamide (DOTA-MA), or a diethylenetriamine ligand (DETA-propanoic acid [PA]), followed by labeling with 68Ga (FBP14, 68Ga-NODAGA), 111In (FBP15, 111In-DOTA-MA), or 99mTc (FBP16, 99mTc(CO)3-DETA-PA), respectively. PET or SPECT imaging, biodistribution, pharmacokinetics, and metabolic stability were evaluated in rat models of mural and occlusive carotid artery thrombosis. In vivo target specificity was evaluated by comparing the distribution of the SPECT and PET probes with preformed 125I-labeled thrombi and with a nonbinding control probe using SPECT/PET/CT imaging. All 3 radiotracers showed affinity similar to soluble fibrin fragment DD(E) (inhibition constant=0.53-0.83 μM). After the kidneys, the highest uptake of 68Ga-FBP14 and 111In-FBP15 was in the thrombus (1.0±0.2 percentage injected dose per gram), with low off-target accumulation. Both radiotracers underwent fast systemic elimination (half-life, 8-15 min) through the kidneys, which led to highly conspicuous thrombi on PET and SPECT images. 99mTc-FBP16 displayed low target uptake and distribution consistent with aggregation or degradation. Triple-isotope imaging experiments showed that both 68Ga-FBP14 and 111In-FBP15, but not the nonbinding derivative 64Cu-D-Cys-FBP8, detected the location of the 125I-labeled thrombus, confirming high target specificity. 68Ga-FBP14 and 111In-FBP15 have high fibrin affinity and thrombus specificity and represent useful PET and SPECT probes for thrombus detection. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Molecular Probes: An Innovative Technology for Monitoring Membrane Processes

NASA Astrophysics Data System (ADS)

Santoro, Sergio

The ultimate objective of this study is to use molecular probes as an innovative and alternative technology contributing to the advance of membrane science by monitoring membrane processes in-situ, on-line and at sub-micron scale. An optical sensor for oxygen sensing was developed by the immobilization of tris (1,10-phenanthroline) ruthenium (II) (Ru(phen)3) in a dense polymeric membrane made of polystyrene (PS) or Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). The emission of the probe was quenched by both the temperature and by the oxygen. Moreover, the oxygen sensitivity was affected by the oxygen permeability of the membrane. The evaluation of the oxygen concentration is prone to errors since the emission of a single probe depends on several parameters (i.e. optical path, source intensity). The correction of these artefacts was obtained by the immobilization of a second luminescent molecule non-sensitive to the oxygen, Coumarin. The potential of the luminescent ratiometric sensor for the non-invasive monitoring of oxygen in food packaging using polymeric films with different oxygen permeability was evaluated. Emphasis was given to the efficiency of the optical sensor for the on-line, in-situ and non invasive monitoring of the oxygen by comparing the experimental data with a model which takes into account the oxygen permeability of the packaging materials evaluated independently. A nano-thermometer based on silica nano-particles doped with Ru(phen)3 was developed. A systematic study shows how it is possible to control the properties of the nano-particles as well as their temperature sensitivity. The nano-thermometer was immobilized on a membrane surface by dip-coating providing information about the temperature on the membrane surface. Hydrophobic porous membrane made of Poly(vinylidene fluoride) was prepared via electrospinning and employed in a direct contact membrane distillation process. Using a designed membrane module and a membrane doped with Ru(phen)3 the on-line mapping of the temperature on the membrane's surface was evaluated. None None None None

Method of identifying hairpin DNA probes by partial fold analysis

DOEpatents

Miller, Benjamin L [Penfield, NY; Strohsahl, Christopher M [Saugerties, NY

2009-10-06

Method of identifying molecular beacons in which a secondary structure prediction algorithm is employed to identify oligonucleotide sequences within a target gene having the requisite hairpin structure. Isolated oligonucleotides, molecular beacons prepared from those oligonucleotides, and their use are also disclosed.

Method of identifying hairpin DNA probes by partial fold analysis

DOEpatents

Miller, Benjamin L.; Strohsahl, Christopher M.

2008-10-28

Methods of identifying molecular beacons in which a secondary structure prediction algorithm is employed to identify oligonucleotide sequences within a target gene having the requisite hairpin structure. Isolated oligonucleotides, molecular beacons prepared from those oligonucleotides, and their use are also disclosed.

Coupling Molecular Beacons to Barcoded Metal Nanowires for Multiplexed, Sealed Chamber DNA Bioassays

PubMed Central

Stoermer, Rebecca L.; Cederquist, Kristin B.; McFarland, Sean K.; Sha, Michael Y.; Penn, Sharron G.

2010-01-01

We have combined molecular beacon (MB) probes with barcoded metal nanowires to enable no-wash, sealed chamber, multiplexed detection of nucleic acids. Probe design and experimental parameters important in nanowire-based MB assays are discussed. Loop regions of 24 bases and 5 base pair stem regions in the beacon probes gave optimal performance. Our results suggest that thermodynamic predictions for secondary structure stability of solution-phase MB can guide probe design for nanowire-based assays. Dengue virus-specific probes with predicted solution-phase ΔG of folding in 500 mM buffered NaCl of approximately −4 kcal/mol performed better than those with ΔG > −2 or < −6 kcal/mol. Buffered 300–500 mM NaCl was selected after comparison of several buffers previously reported for similar types of assays, and 200–500 mM NaCl was found to be the optimal ionic strength for the hybridization temperatures (25 and 50 °C) and probe designs used here. Target binding to the surface as a function of solution concentration fit a Sips isotherm with Kd = 1.7 ± 0.3 nM. The detection limit was ∼100 pM, limited by incomplete quenching. Single base mismatches could be discriminated from fully complementary targets. Oligonucleotide target sequences specific for human immunodeficiency, hepatitis C, and severe acute respiratory viruses were assayed simultaneously in a no-wash, sealed chamber, multiplexed experiment in which each of three probe sequences was attached to a different pattern of encoded nanowires. Finally, we demonstrated that probe-coated nanowires retain their selectivity and sensitivity in a triplexed assay after storage for over 3 months. PMID:17177440

Development and cytotoxicity of Schiff base derivative as a fluorescence probe for the detection of L-Arginine

NASA Astrophysics Data System (ADS)

Shang, Xuefang; Li, Jie; Guo, Kerong; Ti, Tongyu; Wang, Tianyun; Zhang, Jinlian

2017-04-01

Inspired from biological counter parts, chemical modification of Schiff base derivatives with function groups may provide a highly efficient method to detect amino acids. Therefore, a fluorescent probe involving Schiff base and hydroxyl group has been designed and prepared, which showed high response and specificity for Arginine (Arg) among normal eighteen standard kinds of amino acids (Alanine, Valine, Leucine, Isoleucine, Methionine, Asparticacid, Glutamicacid, Arginine, Glycine, Serine, Threonine, Asparagine, Phenylalanine, Histidine, Tryptophan, Proline, Lysine, Glutamine, Tyrosine and Cysteine). Furthermore, theoretical investigation further illustrated the possible binding mode in the host-guest interaction and the roles of molecular frontier orbitals in molecular interplay. In addition, the synthesized fluorescent probe exhibited high binding ability for Arg and low cytotoxicity to MCF-7 cells over a concentration range of 0-200 μg mL-1 which can be also used as a biosensor for the Arg detection in vivo.

Molecular Imaging of Apoptosis: From Micro to Macro

PubMed Central

Zeng, Wenbin; Wang, Xiaobo; Xu, Pengfei; Liu, Gang; Eden, Henry S.; Chen, Xiaoyuan

2015-01-01

Apoptosis, or programmed cell death, is involved in numerous human conditions including neurodegenerative diseases, ischemic damage, autoimmune disorders and many types of cancer, and is often confused with other types of cell death. Therefore strategies that enable visualized detection of apoptosis would be of enormous benefit in the clinic for diagnosis, patient management, and development of new therapies. In recent years, improved understanding of the apoptotic machinery and progress in imaging modalities have provided opportunities for researchers to formulate microscopic and macroscopic imaging strategies based on well-defined molecular markers and/or physiological features. Correspondingly, a large collection of apoptosis imaging probes and approaches have been documented in preclinical and clinical studies. In this review, we mainly discuss microscopic imaging assays and macroscopic imaging probes, ranging in complexity from simple attachments of reporter moieties to proteins that interact with apoptotic biomarkers, to rationally designed probes that target biochemical changes. Their clinical translation will also be our focus. PMID:25825597

Probing of some compounds as anti-aggregatory additives in the protein refolding process from Escherichia coli inclusion bodies.

PubMed

Zilinskas, Albinas; Sereikaite, Jolanta

2011-01-01

Five compounds of different chemical structure were tested for aggregation suppression during the refolding of porcine and mink growth hormones as model proteins from Escherichia coli inclusion bodies by the dilution method. Of all compounds tested in this work, 3-guanidinopropionic acid (GPA) containing a guanidinium group was the most effective additive for aggregation suppression. Anti-aggregatory properties of GPA were compared with the ones of l-arginine. Copyright © 2011 International Union of Biochemistry and Molecular Biology, Inc.

Selective fluorescence quenching of 2,3-diazabicyclo[2.2.2]oct-2-ene by nucleotides.

PubMed

Marquez, Cesar; Pischel, Uwe; Nau, Werner M

2003-10-16

[reaction: see text] The fluorescence quenching of 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) by nucleotides has been studied. The quenching mechanism was analyzed on the basis of deuterium isotope effects, tendencies for exciplex formation, and the quenching efficiency in the presence of a molecular container (cucurbit[7]uril). Exciplex-induced quenching appears to prevail for adenosine, cytidine, and uridine, while hydrogen abstraction becomes competitive for thymidine and guanosine. Compared to other fluorescent probes, DBO responds very selectively to the type of nucleotide.

Chain exchange in triblock copolymer micelles

NASA Astrophysics Data System (ADS)

Lu, Jie; Lodge, Timothy; Bates, Frank

2015-03-01

Block polymer micelles offer a host of technological applications including drug delivery, viscosity modification, toughening of plastics, and colloidal stabilization. Molecular exchange between micelles directly influences the stability, structure and access to an equilibrium state in such systems and this property recently has been shown to be extraordinarily sensitive to the core block molecular weight in diblock copolymers. The dependence of micelle chain exchange dynamics on molecular architecture has not been reported. The present work conclusively addresses this issue using time-resolved small-angle neutron scattering (TR-SANS) applied to complimentary S-EP-S and EP-S-EP triblock copolymers dissolved in squalane, a selective solvent for the EP blocks, where S and EP refer to poly(styrene) and poly(ethylenepropylene), respectively. Following the overall SANS intensity as a function of time from judiciously deuterium labelled polymer and solvent mixtures directly probes the rate of molecular exchange. Remarkably, the two triblocks display exchange rates that differ by approximately ten orders of magnitude, even though the solvophobic S blocks are of comparable size. This discovery is considered in the context of a model that successfully explains S-EP diblock exchange dynamics.

Molecular approaches to Taenia asiatica.

PubMed

Jeon, Hyeong-Kyu; Eom, Keeseon S

2013-02-01

Taenia solium, T. saginata, and T. asiatica are taeniid tapeworms that cause taeniasis in humans and cysticercosis in intermediate host animals. Taeniases remain an important public health concerns in the world. Molecular diagnostic methods using PCR assays have been developed for rapid and accurate detection of human infecting taeniid tapeworms, including the use of sequence-specific DNA probes, PCR-RFLP, and multiplex PCR. More recently, DNA diagnosis using PCR based on histopathological specimens such as 10% formalin-fixed paraffin-embedded and stained sections mounted on slides has been applied to cestode infections. The mitochondrial gene sequence is believed to be a very useful molecular marker for not only studying evolutionary relationships among distantly related taxa, but also for investigating the phylo-biogeography of closely related species. The complete sequence of the human Taenia tapeworms mitochondrial genomes were determined, and its organization and structure were compared to other human-tropic Taenia tapeworms for which complete mitochondrial sequence data were available. The multiplex PCR assay with the Ta4978F, Ts5058F, Tso7421F, and Rev7915 primers will be useful for differential diagnosis, molecular characterization, and epidemiological surveys of human Taenia tapeworms.

Probing the effects of surface hydrophobicity and tether orientation on antibody-antigen binding

NASA Astrophysics Data System (ADS)

Bush, Derek B.; Knotts, Thomas A.

2017-04-01

Antibody microarrays have the potential to revolutionize molecular detection for many applications, but their current use is limited by poor reliability, and efforts to change this have not yielded fruitful results. One difficulty which limits the rational engineering of next-generation devices is that little is known, at the molecular level, about the antibody-antigen binding process near solid surfaces. Atomic-level structural information is scant because typical experimental techniques (X-ray crystallography and NMR) cannot be used to image proteins bound to surfaces. To overcome this limitation, this study uses molecular simulation and an advanced, experimentally validated, coarse-grain, protein-surface model to compare fab-lysozyme binding in bulk solution and when the fab is tethered to hydrophobic and hydrophilic surfaces. The results show that the tether site in the fab, as well as the surface hydrophobicity, significantly impacts the binding process and suggests that the optimal design involves tethering fabs upright on a hydrophilic surface. The results offer an unprecedented, molecular-level picture of the binding process and give hope that the rational design of protein-microarrays is possible.

AIE active multianalyte fluorescent probe for the detection of Cu2+, Ni2+ and Hg2+ ions.

PubMed

Pannipara, Mehboobali; Al-Sehemi, Abdullah G; Irfan, Ahmad; Assiri, Mohammed; Kalam, Abul; Al-Ammari, Yahya S

2018-08-05

A novel pyrazolyl chromene derivative (Probe 1) displaying aggregation induced emission (AIE) properties that capable of sensing of multiple metal ions has been designed and synthesized. The multi analyte probe exhibits selective sensing for Cu 2+ and Ni 2+ ions via fluorescence turn-off mechanism and ratiometric selectivity for Hg 2+ ions in aqueous media. The extent of binding of the probe with sensitive metal ions has been demonstrated. The experimental results were further investigated by computational means by optimizing the ground state geometries of Probe 1 and its various metal complexes for Probe 1-Ni, Probe 1-Hg and Probe 1-Cu using density functional theory (DFT) at B3LYP/6-31+g(d,p) (LANL2DZ) level. On the basis of binding energies, the stability of metal complexes has been studied. In Probe 1-Ni and Probe 1-Cu complexes, charge transfer has been observed from Probe 1 to metal ions revealing ligand to metal charge transfer (LMCT) while in Probe1-Hg complex LMCT as well as intra-molecular charge tranfer (ICT) within Probe 1. Copyright © 2018 Elsevier B.V. All rights reserved.

Designing topological defects in 2D materials using scanning probe microscopy and a self-healing mechanism: a density functional-based molecular dynamics study

NASA Astrophysics Data System (ADS)

Popov, Igor; Đurišić, Ivana; Belić, Milivoj R.

2017-12-01

Engineering of materials at the atomic level is one of the most important aims of nanotechnology. The unprecedented ability of scanning probe microscopy to address individual atoms opened up the possibilities for nanomanipulation and nanolitography of surfaces and later on of two-dimensional materials. While the state-of-the-art scanning probe lithographic methods include, primarily, adsorption, desorption and repositioning of adatoms and molecules on substrates or tailoring nanoribbons by etching of trenches, the precise modification of the intrinsic atomic structure of materials is yet to be advanced. Here we introduce a new concept, scanning probe microscopy with a rotating tip, for engineering of the atomic structure of membranes based on two-dimensional materials. In order to indicate the viability of the concept, we present our theoretical research, which includes atomistic modeling, molecular dynamics simulations, Fourier analysis and electronic transport calculations. While stretching can be employed for fabrication of atomic chains only, our comprehensive molecular dynamics simulations indicate that nanomanipulation by scanning probe microscopy with a rotating tip is capable of assembling a wide range of topological defects in two-dimensional materials in a rather controllable and reproducible manner. We analyze two possibilities. In the first case the probe tip is retracted from the membrane while in the second case the tip is released beneath the membrane allowing graphene to freely relax and self-heal the pore made by the tip. The former approach with the tip rotation can be achieved experimentally by rotation of the sample, which is equivalent to rotation of the tip, whereas irradiation of the membrane by nanoclusters can be utilized for the latter approach. The latter one has the potential to yield a yet richer diversity of topological defects on account of a lesser determinacy. If successfully realized experimentally the concept proposed here could be an important step toward controllable nanostructuring of two-dimensional materials.

Designing topological defects in 2D materials using scanning probe microscopy and a self-healing mechanism: a density functional-based molecular dynamics study.

PubMed

Popov, Igor; Đurišić, Ivana; Belić, Milivoj R

2017-12-08

Engineering of materials at the atomic level is one of the most important aims of nanotechnology. The unprecedented ability of scanning probe microscopy to address individual atoms opened up the possibilities for nanomanipulation and nanolitography of surfaces and later on of two-dimensional materials. While the state-of-the-art scanning probe lithographic methods include, primarily, adsorption, desorption and repositioning of adatoms and molecules on substrates or tailoring nanoribbons by etching of trenches, the precise modification of the intrinsic atomic structure of materials is yet to be advanced. Here we introduce a new concept, scanning probe microscopy with a rotating tip, for engineering of the atomic structure of membranes based on two-dimensional materials. In order to indicate the viability of the concept, we present our theoretical research, which includes atomistic modeling, molecular dynamics simulations, Fourier analysis and electronic transport calculations. While stretching can be employed for fabrication of atomic chains only, our comprehensive molecular dynamics simulations indicate that nanomanipulation by scanning probe microscopy with a rotating tip is capable of assembling a wide range of topological defects in two-dimensional materials in a rather controllable and reproducible manner. We analyze two possibilities. In the first case the probe tip is retracted from the membrane while in the second case the tip is released beneath the membrane allowing graphene to freely relax and self-heal the pore made by the tip. The former approach with the tip rotation can be achieved experimentally by rotation of the sample, which is equivalent to rotation of the tip, whereas irradiation of the membrane by nanoclusters can be utilized for the latter approach. The latter one has the potential to yield a yet richer diversity of topological defects on account of a lesser determinacy. If successfully realized experimentally the concept proposed here could be an important step toward controllable nanostructuring of two-dimensional materials.

Partitioning of 2,6-Bis(1H-Benzimidazol-2-yl)pyridine Fluorophore into a Phospholipid Bilayer: Complementary Use of Fluorescence Quenching Studies and Molecular Dynamics Simulations

PubMed Central

Kyrychenko, Alexander; Sevriukov, Igor Yu.; Syzova, Zoya A.; Ladokhin, Alexey S.; Doroshenko, Andrey O.

2014-01-01

Successful use of fluorescence sensing in elucidating the biophysical properties of lipid membranes requires knowledge of the distribution and location of an emitting molecule in the bilayer. We report here that 2,6-bis(1H-benzimidazol-2-yl)pyridine (BBP), which is almost non-fluorescent in aqueous solutions, reveals a strong emission enhancement in a hydrophobic environment of a phospholipid bilayer, making it interesting for fluorescence probing of water content in a lipid membrane. Comparing the fluorescence behavior of BBP in a wide variety of solvents with those in phospholipid vesicles, we suggest that the hydrogen bonding interactions between a BBP fluorophore and water molecules play a crucial role in the observed “light switch effect”. Therefore, the loss of water-induced fluorescence quenching inside a membrane are thought to be due to deep penetration of BBP into the hydrophobic, water-free region of a bilayer. Characterized by strong quenching by transition metal ions in solution, BBP also demonstrated significant shielding from the action of the quencher in the presence of phospholipid vesicles. We used the increase in fluorescence intensity, measured upon titration of probe molecules with lipid vesicles, to estimate the partition constant and the Gibbs free energy (ΔG) of transfer of BBP from aqueous buffer into a membrane. Partitioning BBP revealed strongly favorable ΔG, which depends only slightly on the lipid composition of a bilayer, varying in a range from -6.5 to -7.0 kcal/mol. To elucidate the binding interactions of the probe with a membrane on the molecular level, a distribution and favorable location of BBP in a POPC bilayer were modeled via atomistic molecular dynamics (MD) simulations using two different approaches: (i) free, diffusion-driven partitioning of the probe molecules into a bilayer and (ii) constrained umbrella sampling of a penetration profile of the dye molecule across a bilayer. Both of these MD approaches agreed with regard to the preferred location of a BBP fluorophore within the interfacial region of a bilayer, located between the hydrocarbon acyl tails and the initial portion of the lipid headgroups. MD simulations also revealed restricted permeability of water molecules into this region of a POPC bilayer, determining the strong fluorescence enhancement observed experimentally for the membrane-partitioned form of BBP. PMID:21211898

Ligation-rolling circle amplification combined with γ-cyclodextrin mediated stemless molecular beacon for sensitive and specific genotyping of single-nucleotide polymorphism.

PubMed

Zou, Zhen; Qing, Zhihe; He, Xiaoxiao; Wang, Kemin; He, Dinggeng; Shi, Hui; Yang, Xue; Qing, Taiping; Yang, Xiaoxiao

2014-07-01

A novel approach for highly sensitive and selective genotyping of single-nucleotide polymorphism (SNP) has been developed based on ligation-rolling circle amplification (L-RCA) and stemless molecular beacon. In this approach, two tailored DNA probes were involved. The stemless molecular beacon, formed through the inclusion interactions of γ-cyclodextrin (γ-CD) and bis-pyrene labeled DNA fragment, was served as signal probe. In the absence of mutant target, the two pyrene molecules were bound in the γ-CD cavity to form an excimer and showed a strong fluorescence at 475 nm. It was here named γ-CD-P-MB. The padlock DNA probe was designed as recognition probe. Upon the recognition of a point mutation DNA targets, the padlock probe was ligated to generate a circular template. An RCA amplification was then initiated using the circular template in the presence of Phi29 polymerase and dNTPs. The L-RCA products, containing repetitive sequence units, subsequently hybridized with the γ-CD-P-MB. This made pyrene molecules away from γ-CD cavity and caused a decrease of excimer fluorescence. As a proof-of-concept, SNP typing of β-thalassemia gene at position -28 was investigated using this approach. The detection limit of mutated target was determined to be 40 fM. In addition, DNA ligase offered high fidelity in distinguishing the mismatched bases at the ligation site, resulting in positive detection of mutant target even when the ratio of the wildtype to the mutant is 999:1. Given these attractive characteristics, the developed approach might provide a great genotyping platform for pathogenic diagnosis and genetic analysis. Copyright © 2014 Elsevier B.V. All rights reserved.

Planck intermediate results: XXXV. Probing the role of the magnetic field in the formation of structure in molecular clouds

DOE PAGES

Ade, P. A. R.; Aghanim, N.; Alves, M. I. R.; ...

2016-02-09

Within ten nearby (d < 450 pc) Gould belt molecular clouds we evaluate in this paper statistically the relative orientation between the magnetic field projected on the plane of sky, inferred from the polarized thermal emission of Galactic dust observed by Planck at 353 GHz, and the gas column density structures, quantified by the gradient of the column density, N H. The selected regions, covering several degrees in size, are analysed at an effective angular resolution of 10' FWHM, thus sampling physical scales from 0.4 to 40 pc in the nearest cloud. The column densities in the selected regions rangemore » from N H≈ 10 21 to10 23 cm -2, and hence they correspond to the bulk of the molecular clouds. The relative orientation is evaluated pixel by pixel and analysed in bins of column density using the novel statistical tool called “histogram of relative orientations”. Throughout this study, we assume that the polarized emission observed by Planck at 353 GHz is representative of the projected morphology of the magnetic field in each region, i.e., we assume a constant dust grain alignment efficiency, independent of the local environment. Within most clouds we find that the relative orientation changes progressively with increasing N H, from mostly parallel or having no preferred orientation to mostly perpendicular. In simulations of magnetohydrodynamic turbulence in molecular clouds this trend in relative orientation is a signature of Alfvénic or sub-Alfvénic turbulence, implying that the magnetic field is significant for the gas dynamics at the scales probed by Planck. Finally, we compare the deduced magnetic field strength with estimates we obtain from other methods and discuss the implications of the Planck observations for the general picture of molecular cloud formation and evolution.« less

Challenges for Super-Resolution Localization Microscopy and Biomolecular Fluorescent Nano-Probing in Cancer Research

PubMed Central

Ilić, Nataša; Pilarczyk, Götz; Lee, Jin-Ho; Logeswaran, Abiramy; Borroni, Aurora Paola; Krufczik, Matthias; Theda, Franziska; Waltrich, Nadine; Bestvater, Felix; Hildenbrand, Georg; Cremer, Christoph; Blank, Michael

2017-01-01

Understanding molecular interactions and regulatory mechanisms in tumor initiation, progression, and treatment response are key requirements towards advanced cancer diagnosis and novel treatment procedures in personalized medicine. Beyond decoding the gene expression, malfunctioning and cancer-related epigenetic pathways, investigations of the spatial receptor arrangements in membranes and genome organization in cell nuclei, on the nano-scale, contribute to elucidating complex molecular mechanisms in cells and tissues. By these means, the correlation between cell function and spatial organization of molecules or molecular complexes can be studied, with respect to carcinogenesis, tumor sensitivity or tumor resistance to anticancer therapies, like radiation or antibody treatment. Here, we present several new applications for bio-molecular nano-probes and super-resolution, laser fluorescence localization microscopy and their potential in life sciences, especially in biomedical and cancer research. By means of a tool-box of fluorescent antibodies, green fluorescent protein (GFP) tagging, or specific oligonucleotides, we present tumor relevant re-arrangements of Erb-receptors in membranes, spatial organization of Smad specific ubiquitin protein ligase 2 (Smurf2) in the cytosol, tumor cell characteristic heterochromatin organization, and molecular re-arrangements induced by radiation or antibody treatment. The main purpose of this article is to demonstrate how nano-scaled distance measurements between bio-molecules, tagged by appropriate nano-probes, can be applied to elucidate structures and conformations of molecular complexes which are characteristic of tumorigenesis and treatment responses. These applications open new avenues towards a better interpretation of the spatial organization and treatment responses of functionally relevant molecules, at the single cell level, in normal and cancer cells, offering new potentials for individualized medicine. PMID:28956810

Challenges for Super-Resolution Localization Microscopy and Biomolecular Fluorescent Nano-Probing in Cancer Research.

PubMed

Hausmann, Michael; Ilić, Nataša; Pilarczyk, Götz; Lee, Jin-Ho; Logeswaran, Abiramy; Borroni, Aurora Paola; Krufczik, Matthias; Theda, Franziska; Waltrich, Nadine; Bestvater, Felix; Hildenbrand, Georg; Cremer, Christoph; Blank, Michael

2017-09-28

Understanding molecular interactions and regulatory mechanisms in tumor initiation, progression, and treatment response are key requirements towards advanced cancer diagnosis and novel treatment procedures in personalized medicine. Beyond decoding the gene expression, malfunctioning and cancer-related epigenetic pathways, investigations of the spatial receptor arrangements in membranes and genome organization in cell nuclei, on the nano-scale, contribute to elucidating complex molecular mechanisms in cells and tissues. By these means, the correlation between cell function and spatial organization of molecules or molecular complexes can be studied, with respect to carcinogenesis, tumor sensitivity or tumor resistance to anticancer therapies, like radiation or antibody treatment. Here, we present several new applications for bio-molecular nano-probes and super-resolution, laser fluorescence localization microscopy and their potential in life sciences, especially in biomedical and cancer research. By means of a tool-box of fluorescent antibodies, green fluorescent protein (GFP) tagging, or specific oligonucleotides, we present tumor relevant re-arrangements of Erb-receptors in membranes, spatial organization of Smad specific ubiquitin protein ligase 2 (Smurf2) in the cytosol, tumor cell characteristic heterochromatin organization, and molecular re-arrangements induced by radiation or antibody treatment. The main purpose of this article is to demonstrate how nano-scaled distance measurements between bio-molecules, tagged by appropriate nano-probes, can be applied to elucidate structures and conformations of molecular complexes which are characteristic of tumorigenesis and treatment responses. These applications open new avenues towards a better interpretation of the spatial organization and treatment responses of functionally relevant molecules, at the single cell level, in normal and cancer cells, offering new potentials for individualized medicine.

Molecular dynamics approach to probe PKCβII-ligand interactions and influence of crystal water molecules on these interactions.

PubMed

Grewal, Baljinder K; Bhat, Jyotsna; Sobhia, Masilamani Elizabeth

2015-01-01

PKCβII is a potential target for therapeutic intervention against pandemic diabetic complications. Present study probes the molecular interactions of PKCβII with its clinically important ligands, viz. ruboxistaurin, enzastaurin and co-crystallized ligand, 2-methyl-1H-indol-3-yl-BIM-1. The essentials of PKCβII-ligand interaction, crystal water-induced alterations in these interactions and key interacting flexible residues are analyzed. Computational methodologies, viz. molecular docking and molecular simulation coupled with molecular mechanics-Poisson-Boltzmann surface area and generalized born surface area (MM-PB[GB]SA) are employed. The structural changes in the presence and absence of crystal water molecules in PKCβII ATP binding site residues, and its interaction with bound ligand, are identified. Difference in interaction of selective and nonselective ligand with ATP binding site residues of PKCβII is reported. The study showed that the nonbonding interactions contribute significantly in PKCβII-ligand binding and presence of crystal water molecules affects the interactions. The findings of present work may integrate the new aspects in the drug design process of PKCβII inhibitors.

Clinically compatible flexible wide-field multi-color fluorescence endoscopy with a porcine colon model

PubMed Central

Oh, Gyugnseok; Park, Youngrong; Yoo, Su Woong; Hwang, Soonjoo; Chin-Yu, Alexey V. Dan; Ryu, Yeon-Mi; Kim, Sang-Yeob; Do, Eun-Ju; Kim, Ki Hean; Kim, Sungjee; Myung, Seung-Jae; Chung, Euiheon

2017-01-01

Early detection of structural or molecular changes in dysplastic epithelial tissues is crucial for cancer screening and surveillance. Multi-targeting molecular endoscopic fluorescence imaging may improve noninvasive detection of precancerous lesions in the colon. Here, we report the first clinically compatible, wide-field-of-view, multi-color fluorescence endoscopy with a leached fiber bundle scope using a porcine model. A porcine colon model that resembles the human colon is used for the detection of surrogate tumors composed of multiple biocompatible fluorophores (FITC, ICG, and heavy metal-free quantum dots (hfQDs)). With an ex vivo porcine colon tumor model, molecular imaging with hfQDs conjugated with MMP14 antibody was achieved by spraying molecular probes on a mucosa layer that contains xenograft tumors. With an in vivo porcine colon embedded with surrogate tumors, target-to-background ratios of 3.36 ± 0.43, 2.70 ± 0.72, and 2.10 ± 0.13 were achieved for FITC, ICG, and hfQD probes, respectively. This promising endoscopic technology with molecular contrast shows the capacity to reveal hidden tumors and guide treatment strategy decisions. PMID:28270983

Cytogenetic and molecular analysis in Angelman syndrome.

PubMed

Zackowski, J L; Nicholls, R D; Gray, B A; Bent-Williams, A; Gottlieb, W; Harris, P J; Waters, M F; Driscoll, D J; Zori, R T; Williams, C A

1993-04-01

We report on cytogenetic and molecular analyses of 29 Angelman syndrome (AS) individuals ascertained in 1990 through the first National Angelman Syndrome Conference. High resolution GTG- and GBG-banded chromosomes were studied. Standard molecular analysis with six 15q11q13 DNA sequences was used to analyze copy number and parental origin of 15q11q13. Concordance between molecular and cytogenetic data was excellent. The combined data showed that 23 of the 27 probands (85%) on whom we had definitive results have deletions of the chromosome 15q11q13 region. Two classes of deletion were detected molecularly: most patients were deleted for the 5 more proximal probes, but in 2 cases the deletion extended distally to include in sixth probe. In the 13 cases where the parental origin of the deleted chromosome 15 could be established, it was maternal. There were no cases of uniparental disomy. Cytological observations of the relative sizes of the heterochromatic regions of the short arm of chromosome 15 suggested that chromosomes with large heterochromatic blocks may be more prone to de novo deletion.

An in silico pan-genomic probe for the molecular traits behind Lactobacillus ruminis gut autochthony.

PubMed

Kant, Ravi; Palva, Airi; von Ossowski, Ingemar

2017-01-01

As an ecological niche, the mammalian intestine provides the ideal habitat for a variety of bacterial microorganisms. Purportedly, some commensal genera and species offer a beneficial mix of metabolic, protective, and structural processes that help sustain the natural digestive health of the host. Among these sort of gut inhabitants is the Gram-positive lactic acid bacterium Lactobacillus ruminis, a strict anaerobe with both pili and flagella on its cell surface, but also known for being autochthonous (indigenous) to the intestinal environment. Given that the molecular basis of gut autochthony for this species is largely unexplored and unknown, we undertook a study at the genome level to pinpoint some of the adaptive traits behind its colonization behavior. In our pan-genomic probe of L. ruminis, the genomes of nine different strains isolated from human, bovine, porcine, and equine host guts were compiled and compared for in silico analysis. For this, we conducted a geno-phenotypic assessment of protein-coding genes, with an emphasis on those products involved with cell-surface morphology and anaerobic fermentation and respiration. We also categorized and examined the core and accessory genes that define the L. ruminis species and its strains. Here, we made an attempt to identify those genes having ecologically relevant phenotypes that might support or bring about intestinal indigenousness.

Integrin-Targeted Hybrid Fluorescence Molecular Tomography/X-ray Computed Tomography for Imaging Tumor Progression and Early Response in Non-Small Cell Lung Cancer.

PubMed

Ma, Xiaopeng; Phi Van, Valerie; Kimm, Melanie A; Prakash, Jaya; Kessler, Horst; Kosanke, Katja; Feuchtinger, Annette; Aichler, Michaela; Gupta, Aayush; Rummeny, Ernst J; Eisenblätter, Michel; Siveke, Jens; Walch, Axel K; Braren, Rickmer; Ntziachristos, Vasilis; Wildgruber, Moritz

2017-01-01

Integrins play an important role in tumor progression, invasion and metastasis. Therefore we aimed to evaluate a preclinical imaging approach applying ανβ3 integrin targeted hybrid Fluorescence Molecular Tomography/X-ray Computed Tomography (FMT-XCT) for monitoring tumor progression as well as early therapy response in a syngeneic murine Non-Small Cell Lung Cancer (NSCLC) model. Lewis Lung Carcinomas were grown orthotopically in C57BL/6 J mice and imaged in-vivo using a ανβ3 targeted near-infrared fluorescence (NIRF) probe. ανβ3-targeted FMT-XCT was able to track tumor progression. Cilengitide was able to substantially block the binding of the NIRF probe and suppress the imaging signal. Additionally mice were treated with an established chemotherapy regimen of Cisplatin and Bevacizumab or with a novel MEK inhibitor (Refametinib) for 2 weeks. While μCT revealed only a moderate slowdown of tumor growth, ανβ3 dependent signal decreased significantly compared to non-treated mice already at one week post treatment. ανβ3 targeted imaging might therefore become a promising tool for assessment of early therapy response in the future. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Evaluation of glycophenotype in breast cancer by quantum dot-lectin histochemistry

PubMed Central

Andrade, Camila G; Cabral Filho, Paulo E; Tenório, Denise PL; Santos, Beate S; Beltrão, Eduardo IC; Fontes, Adriana; Carvalho, Luiz B

2013-01-01

Cell surface glycoconjugates play an important role in differentiation/dedifferentiation processes and lectins are employed to evaluate them by several methodologies. Fluorescent probes are considered a valuable tool because of their ability to provide a particular view, and are more detailed and sensitive in terms of cell structure and molecular content. The aim of this study was to evaluate and compare the expression and distribution of glycoconjugates in normal human breast tissue, and benign (fibroadenoma), and malignantly transformed (invasive ductal carcinoma) breast tissues. For this, we used mercaptosuccinic acid-coated Cadmium Telluride (CdTe) quantum dots (QDs) conjugated with concanavalin A (Con A) or Ulex europaeus agglutinin I (UEA I) lectins to detect α-D-glucose/mannose and L-fucose residues, respectively. The QD-lectin conjugates were evaluated by hemagglutination activity tests and carbohydrate inhibition assays, and were found to remain functional, keeping their fluorescent properties and carbohydrate recognition ability. Fluorescence images showed that different regions of breast tissue expressed particular types of carbohydrates. While the stroma was preferentially and intensely stained by QD-Con A, ductal cells were preferentially labeled by QD-UEA I. These results indicate that QD-lectin conjugates can be used as molecular probes and can help to elucidate the glycoconjugate profile in biological processes. PMID:24324334

Activateable Imaging Probes Light Up Inside Cancer Cells | Center for Cancer Research

Cancer.gov

Imaging can be used to help diagnose cancer as well as monitor tumor progression and response to treatment. The field of molecular imaging focuses on techniques capable of detecting specific molecular targets associated with cancer; the agents used for molecular imaging—often called probes—are multifunctional, with components that allow them to both interact with their

Humidity-controlled rectification switching in ruthenium-complex molecular junctions

NASA Astrophysics Data System (ADS)

Atesci, Huseyin; Kaliginedi, Veerabhadrarao; Celis Gil, Jose A.; Ozawa, Hiroaki; Thijssen, Joseph M.; Broekmann, Peter; Haga, Masa-aki; van der Molen, Sense Jan

2018-02-01

Although molecular rectifiers were proposed over four decades ago1,2, until recently reported rectification ratios (RR) were rather moderate2-11 (RR 101). This ceiling was convincingly broken using a eutectic GaIn top contact12 to probe molecular monolayers of coupled ferrocene groups (RR 105), as well as using scanning tunnelling microscopy-break junctions13-16 and mechanically controlled break junctions17 to probe single molecules (RR 102-103). Here, we demonstrate a device based on a molecular monolayer in which the RR can be switched by more than three orders of magnitude (between RR 100 and RR ≥ 103) in response to humidity. As the relative humidity is toggled between 5% and 60%, the current-voltage (I-V) characteristics of a monolayer of di-nuclear Ru-complex molecules reversibly change from symmetric to strongly asymmetric (diode-like). Key to this behaviour is the presence of two localized molecular orbitals in series, which are nearly degenerate in dry circumstances but become misaligned under high humidity conditions, due to the displacement of counter ions (PF6-). This asymmetric gating of the two relevant localized molecular orbital levels results in humidity-controlled diode-like behaviour.

Two-dimensional ice mapping of molecular cores

NASA Astrophysics Data System (ADS)

Noble, J. A.; Fraser, H. J.; Pontoppidan, K. M.; Craigon, A. M.

2017-06-01

We present maps of the column densities of H2O, CO2 and CO ices towards the molecular cores B 35A, DC 274.2-00.4, BHR 59 and DC 300.7-01.0. These ice maps, probing spatial distances in molecular cores as low as 2200 au, challenge the traditional hypothesis that the denser the region observed, the more ice is present, providing evidence that the relationships between solid molecular species are more varied than the generic picture we often adopt to model gas-grain chemical processes and explain feedback between solid phase processes and gas phase abundances. We present the first combined solid-gas maps of a single molecular species, based upon observations of both CO ice and gas phase C18O towards B 35A, a star-forming dense core in Orion. We conclude that molecular species in the solid phase are powerful tracers of 'small-scale' chemical diversity, prior to the onset of star formation. With a component analysis approach, we can probe the solid phase chemistry of a region at a level of detail greater than that provided by statistical analyses or generic conclusions drawn from single pointing line-of-sight observations alone.

Molecularly Imprinted Core-Shell CdSe@SiO2/CDs as a Ratiometric Fluorescent Probe for 4-Nitrophenol Sensing

NASA Astrophysics Data System (ADS)

Liu, Mingyue; Gao, Zhao; Yu, Yanjun; Su, Rongxin; Huang, Renliang; Qi, Wei; He, Zhimin

2018-01-01

4-Nitrophenol (4-NP) is a priority pollutant in water and is both carcinogenic and genotoxic to humans and wildlife even at very low concentrations. Thus, we herein fabricated a novel molecularly imprinted core-shell nanohybrid as a ratiometric fluorescent sensor for the highly sensitive and selective detection of 4-NP. This sensor was functioned by the transfer of fluorescence resonance energy between photoluminescent carbon dots (CDs) and 4-NP. This sensor was synthesized by linking organosilane-functionalized CDs to silica-coated CdSe quantum dots (CdSe@SiO2) via Si-O bonds. The nanohybrids were further modified by anchoring a molecularly imprinted polymer (MIP) layer on the ratiometric fluorescent sensor through a facile sol-gel polymerization method. The morphology, chemical structure, and optical properties of the resulting molecularly imprinted dual-emission fluorescent probe were characterized by transmission electron microscopy and spectroscopic analysis. The probe was then applied in the detection of 4-NP and exhibited good linearity between 0.051 and 13.7 μg/mL, in addition to a low detection limit of 0.026 μg/mL. Furthermore, the simplicity, reliability, high selectivity, and high sensitivity of the developed sensor demonstrate that the combination of MIPs and ratiometric fluorescence allows the preparation of excellent fluorescent sensors for the detection of trace or ultra-trace analytes.

MMP-13 In-Vivo Molecular Imaging Reveals Early Expression in Lung Adenocarcinoma

PubMed Central

Salaün, Mathieu; Peng, Jing; Hensley, Harvey H.; Roder, Navid; Flieder, Douglas B.; Houlle-Crépin, Solène; Abramovici-Roels, Olivia; Sabourin, Jean-Christophe; Thiberville, Luc; Clapper, Margie L.

2015-01-01

Introduction Several matrix metalloproteinases (MMPs) are overexpressed in lung cancer and may serve as potential targets for the development of bioactivable probes for molecular imaging. Objective To characterize and monitor the activity of MMPs during the progression of lung adenocarcinoma. Methods K-rasLSL-G12D mice were imaged serially during the development of adenocarcinomas using fluorescence molecular tomography (FMT) and a probe specific for MMP-2, -3, -9 and -13. Lung tumors were identified using FMT and MRI co-registration, and the probe concentration in each tumor was assessed at each time-point. The expression of Mmp2, -3, -9, -13 was quantified by qRT-PCR using RNA isolated from microdissected tumor cells. Immunohistochemical staining of overexpressed MMPs in animals was assessed on human lung tumors. Results In mice, 7 adenomas and 5 adenocarcinomas showed an increase in fluorescent signal on successive FMT scans, starting between weeks 4 and 8. qRT-PCR assays revealed significant overexpression of only Mmp-13 in mice lung tumors. In human tumors, a high MMP-13 immunostaining index was found in tumor cells from invasive lesions (24/27), but in none of the non-invasive (0/4) (p=0.001). Conclusion MMP-13 is detected in early pulmonary invasive adenocarcinomas and may be a potential target for molecular imaging of lung cancer. PMID:26193700

Probing the emitter site of Renilla luciferase using small organic molecules; an attempt to understand the molecular architecture of the emitter site.

PubMed

Salehi, Farajollah; Emamzadeh, Rahman; Nazari, Mahboobeh; Rasa, Seyed Mohammad Mahdi

2016-12-01

Renilla luciferase is a sensitive enzyme and has wide applications in biotechnology such as drug screening. Previous studies have tried to show the catalytic residues, nevertheless, the accurate architecture and molecular behavior of its emitter site remains uncharacterized. In this study, the activity of Renilla luciferase, in the presence of two small organic molecules including dimethyl sulfoxide (DMSO) and isopropanol was considered and the structure was studied by circular dichroism (CD) and fluorescence spectroscopy. Moreover, the interaction of small organic molecules with the Renilla luciferase was studied using molecular dynamics simulations. Kinetics studies showed that at low concentration of DMSO (16.6-66mM) and isopropanol (19.3-76mM) the K m changed and a competitive inhibition pattern was observed. Moreover, spectroscopy studies reveled that the changes of activity of Renilla luciferase in the presence of low concentrations of small organic molecules was not associated with structural collapse or severe changes in the enzyme conformation. Molecular dynamics simulations indicated that DMSO and isopropanol, as probing molecules, were both able to bind to the emitter site and remained with the residues of the emitter site. Based on the probing data, the architecture of the emitter site in the "non-binding" model was proposed. Copyright © 2016 Elsevier B.V. All rights reserved.

Implantation of Neural Probes in the Brain Elicits Oxidative Stress

PubMed Central

Ereifej, Evon S.; Rial, Griffin M.; Hermann, John K.; Smith, Cara S.; Meade, Seth M.; Rayyan, Jacob M.; Chen, Keying; Feng, He; Capadona, Jeffrey R.

2018-01-01

Clinical implantation of intracortical microelectrodes has been hindered, at least in part, by the perpetual inflammatory response occurring after device implantation. The neuroinflammatory response observed after device implantation has been correlated to oxidative stress that occurs due to neurological injury and disease. However, there has yet to be a definitive link of oxidative stress to intracortical microelectrode implantation. Thus, the objective of this study is to give direct evidence of oxidative stress following intracortical microelectrode implantation. This study also aims to identify potential molecular targets to attenuate oxidative stress observed postimplantation. Here, we implanted adult rats with silicon non-functional microelectrode probes for 4 weeks and compared the oxidative stress response to no surgery controls through postmortem gene expression analysis and qualitative histological observation of oxidative stress markers. Gene expression analysis results at 4 weeks postimplantation indicated that EH domain-containing 2, prion protein gene (Prnp), and Stearoyl-Coenzyme A desaturase 1 (Scd1) were all significantly higher for animals implanted with intracortical microelectrode probes compared to no surgery control animals. To the contrary, NADPH oxidase activator 1 (Noxa1) relative gene expression was significantly lower for implanted animals compared to no surgery control animals. Histological observation of oxidative stress showed an increased expression of oxidized proteins, lipids, and nucleic acids concentrated around the implant site. Collectively, our results reveal there is a presence of oxidative stress following intracortical microelectrode implantation compared to no surgery controls. Further investigation targeting these specific oxidative stress linked genes could be beneficial to understanding potential mechanisms and downstream therapeutics that can be utilized to reduce oxidative stress-mediated damage following microelectrode implantation. PMID:29487848

Seven novel probe systems for real-time PCR provide absolute single-base discrimination, higher signaling, and generic components.

PubMed

Murray, James L; Hu, Peixu; Shafer, David A

2014-11-01

We have developed novel probe systems for real-time PCR that provide higher specificity, greater sensitivity, and lower cost relative to dual-labeled probes. The seven DNA Detection Switch (DDS)-probe systems reported here employ two interacting polynucleotide components: a fluorescently labeled probe and a quencher antiprobe. High-fidelity detection is achieved with three DDS designs: two internal probes (internal DDS and Flip probes) and a primer probe (ZIPR probe), wherein each probe is combined with a carefully engineered, slightly mismatched, error-checking antiprobe. The antiprobe blocks off-target detection over a wide range of temperatures and facilitates multiplexing. Other designs (Universal probe, Half-Universal probe, and MacMan probe) use generic components that enable low-cost detection. Finally, single-molecule G-Force probes employ guanine-mediated fluorescent quenching by forming a hairpin between adjacent C-rich and G-rich sequences. Examples provided show how these probe technologies discriminate drug-resistant Mycobacterium tuberculosis mutants, Escherichia coli O157:H7, oncogenic EGFR deletion mutations, hepatitis B virus, influenza A/B strains, and single-nucleotide polymorphisms in the human VKORC1 gene. Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Overtone spectroscopy of N2H+ molecular ions—application of cavity ring-down spectroscopy

NASA Astrophysics Data System (ADS)

Kálosi, Á.; Dohnal, P.; Shapko, D.; Roučka, Š.; Plašil, R.; Johnsen, R.; Glosík, J.

2017-10-01

A stationary afterglow apparatus in conjunction with a laser absorption cavity ring-down spectrometer has been employed to observe absorption lines in the P- and R-branches of the (200) <-- (000) and (2110) <-- (0110) vibrational bands of the N2H+ molecular ion as a part of an ongoing study of the electron-ion recombination of N2H+ in afterglow plasmas. The probed absorption lines lie in the near-infrared spectral region around 1580 nm. The observed transition wavenumbers were fitted to experimental accuracy and improved molecular constants for the (200) vibrational state were obtained. The employed experimental technique enables probing of the translational, rotational and vibrational temperature of the studied ions as well as the determination of the number densities of different quantum states of the ion in discharge and afterglow plasma.

Temporal mapping of photochemical reactions and molecular excited states with carbon specificity

NASA Astrophysics Data System (ADS)

Wang, K.; Murahari, P.; Yokoyama, K.; Lord, J. S.; Pratt, F. L.; He, J.; Schulz, L.; Willis, M.; Anthony, J. E.; Morley, N. A.; Nuccio, L.; Misquitta, A.; Dunstan, D. J.; Shimomura, K.; Watanabe, I.; Zhang, S.; Heathcote, P.; Drew, A. J.

2017-04-01

Photochemical reactions are essential to a large number of important industrial and biological processes. A method for monitoring photochemical reaction kinetics and the dynamics of molecular excitations with spatial resolution within the active molecule would allow a rigorous exploration of the pathway and mechanism of photophysical and photochemical processes. Here we demonstrate that laser-excited muon pump-probe spin spectroscopy (photo-μSR) can temporally and spatially map these processes with a spatial resolution at the single-carbon level in a molecule with a pentacene backbone. The observed time-dependent light-induced changes of an avoided level crossing resonance demonstrate that the photochemical reactivity of a specific carbon atom is modified as a result of the presence of the excited state wavefunction. This demonstrates the sensitivity and potential of this technique in probing molecular excitations and photochemistry.

Light propagation analysis for fluorescence measurements of a molecular probe in the brain

NASA Astrophysics Data System (ADS)

Asai, Kota; Togashi, Takuya; Okada, Eiji

2017-04-01

Light propagation in the slab head model that consists of five types of tissues was calculated to estimate the fluorescent intensity emerged from a molecular probe in the brain by a Monte Carlo simulation. The thickness of the scalp, skull and cerebrospinal fluid layer was varied to analyze the influence of the thickness of the superficial tissues on the fluorescent intensity detected on the scalp surface. The fluorescent intensity is exponentially reduced with increasing the depth of the brain surface. The thickness of the cerebrospinal fluid layer more significantly affects the fluorescent intensity than that of the scalp and skull.

Probing the Inelastic Interactions in Molecular Junctions by Scanning Tunneling Microscope

NASA Astrophysics Data System (ADS)

Xu, Chen

With a sub-Kelvin scanning tunneling microscope, the energy resolution of spectroscopy is improved dramatically. Detailed studies of finer features of spectrum become possible. The asymmetry in the line shape of carbon monoxide vibrational spectra is observed to correlate with the couplings of the molecule to the tip and substrates. The spin-vibronic coupling in the molecular junctions is revisited with two metal phthalocyanine molecules, unveiling sharp spin-vibronic peaks. Finally, thanks to the improved spectrum resolution, the bonding structure of the acyclic compounds molecules is surveyed with STM inelastic tunneling probe, expanding the capability of the innovative high resolution imaging technique.

Gold nanoparticles: enhanced optical trapping and sensitivity coupled with significant heating.

PubMed

Seol, Yeonee; Carpenter, Amanda E; Perkins, Thomas T

2006-08-15

Gold nanoparticles appear to be superior handles in optical trapping assays. We demonstrate that relatively large gold particles (R(b)=50 nm) indeed yield a sixfold enhancement in trapping efficiency and detection sensitivity as compared to similar-sized polystyrene particles. However, optical absorption by gold at the most common trapping wavelength (1064 nm) induces dramatic heating (266 degrees C/W). We determined this heating by comparing trap stiffness from three different methods in conjunction with detailed modeling. Due to this heating, gold nanoparticles are not useful for temperature-sensitive optical-trapping experiments, but may serve as local molecular heaters. Also, such particles, with their increased detection sensitivity, make excellent probes for certain zero-force biophysical assays.

Vibronic dephasing model for coherent-to-incoherent crossover in DNA

NASA Astrophysics Data System (ADS)

Karasch, Patrick; Ryndyk, Dmitry A.; Frauenheim, Thomas

2018-05-01

In this paper, we investigate the interplay between coherent and incoherent charge transport in cytosine-guanine (GC-) rich DNA molecules. Our objective is to introduce a physically grounded approach to dephasing in large molecules and to understand the length-dependent charge transport characteristics, and especially the crossover from the coherent tunneling to incoherent hopping regime at different temperatures. Therefore, we apply the vibronic dephasing model and compare the results to the Büttiker probe model which is commonly used to describe decoherence effects in charge transport. Using the full ladder model and simplified one-dimensional model of DNA, we consider molecular junctions with alternating and stacked GC sequences and compare our results to recent experimental measurements.

Nanoparticle assembled microcapsules for application as pH and ammonia sensor.

PubMed

Amali, Arlin Jose; Awwad, Nour H; Rana, Rohit Kumar; Patra, Digambara

2011-12-05

The encapsulation of molecular probes in a suitable nanostructured matrix can be exploited to alter their optical properties and robustness for fabricating efficient chemical sensors. Despite high sensitivity, simplicity, selectivity and cost effectiveness, the photo-destruction and photo-bleaching are the serious concerns while utilizing molecular probes. Herein we demonstrate that hydroxy pyrene trisulfonate (HPTS), a pH sensitive molecular probe, when encapsulated in a microcapsule structure prepared via the assembly of silica nanoparticles mediated by poly-L-lysine and trisodium citrate, provides a robust sensing material for pH sensing under the physiological conditions. The temporal evolution under continuous irradiation indicates that the fluorophore inside the silica microcapsule is extraordinarily photostable. The fluorescence intensity alternation at dual excitation facilitates for a ratiometic sensing of the pH, however, the fluorescence lifetime is insensitive to hydrogen ion concentration. The sensing scheme is found to be robust, fast and simple for the measurement of pH in the range 5.8-8.0, and can be successfully applied for the determination of ammonia in the concentration range 0-1.2 mM, which is important for aquatic life and the environment. Copyright © 2011 Elsevier B.V. All rights reserved.

Firefly Luciferin-Inspired Biocompatible Chemistry for Protein Labeling and In Vivo Imaging.

PubMed

Wang, Yuqi; An, Ruibing; Luo, Zhiliang; Ye, Deju

2018-04-17

Biocompatible reactions have emerged as versatile tools to build various molecular imaging probes that hold great promise for the detection of biological processes in vitro and/or in vivo. In this Minireview, we describe the recent advances in the development of a firefly luciferin-inspired biocompatible reaction between cyanobenzothiazole (CBT) and cysteine (Cys), and highlight its versatility to label proteins and build multimodality molecular imaging probes. The review starts from the general introduction of biocompatible reactions, which is followed by briefly describing the development of the firefly luciferin-inspired biocompatible chemistry. We then discuss its applications for the specific protein labeling and for the development of multimodality imaging probes (fluorescence, bioluminescence, MRI, PET, photoacoustic, etc.) that enable high sensitivity and spatial resolution imaging of redox environment, furin and caspase-3/7 activity in living cells and mice. Finally, we offer the conclusions and our perspective on the various and potential applications of this reaction. We hope that this review will contribute to the research of biocompatible reactions for their versatile applications in protein labeling and molecular imaging. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular Level Structure and Dynamics of Electrolytes Using 17O Nuclear Magnetic Resonance Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murugesan, Vijayakumar; Han, Kee Sung; Hu, Jianzhi

2017-03-19

Electrolytes help harness the energy from electrochemical processes by serving as solvents and transport media for redox-active ions. Molecular-level interactions between ionic solutes and solvent molecules – commonly referred to as solvation phenomena – give rise to many functional properties of electrolytes such as ionic conductivity, viscosity, and stability. It is critical to understand the evolution of solvation phenomena as a function of competing counterions and solvent mixtures to predict and design the optimal electrolyte for a target application. Probing oxygen environments is of great interest as oxygens are located at strategic molecular sites in battery solvents and are directlymore » involved in inter- and intramolecular solvation interactions. NMR signals from 17O nuclei in battery electrolytes offer nondestructive bulk measurements of isotropic shielding, electric field gradient tensors, and transverse and longitudinal relaxation rates, which are excellent means for probing structure, bonding, and dynamics of both solute and solvent molecules. This article describes the use of 17O NMR spectroscopy in probing the solvation structures of various electrolyte systems ranging from transition metal ions in aqueous solution to lithium cations in organic solvent mixtures.« less

Understanding API-polymer proximities in amorphous stabilized composite drug products using fluorine-carbon 2D HETCOR solid-state NMR.

PubMed

Abraham, Anuji; Crull, George

2014-10-06

A simple and robust method for obtaining fluorine-carbon proximities was established using a (19)F-(13)C heteronuclear correlation (HETCOR) two-dimensional (2D) solid-state nuclear magnetic resonance (ssNMR) experiment under magic-angle spinning (MAS). The method was applied to study a crystalline active pharmaceutical ingredient (API), avagacestat, containing two types of fluorine atoms and its API-polymer composite drug product. These results provide insight into the molecular structure, aid with assigning the carbon resonances, and probe API-polymer proximities in amorphous spray dried dispersions (SDD). This method has an advantage over the commonly used (1)H-(13)C HETCOR because of the large chemical shift dispersion in the fluorine dimension. In the present study, fluorine-carbon distances up to 8 Å were probed, giving insight into the API structure, crystal packing, and assignments. Most importantly, the study demonstrates a method for probing an intimate molecular level contact between an amorphous API and a polymer in an SDD, giving insights into molecular association and understanding of the role of the polymer in API stability (such as recrystallization, degradation, etc.) in such novel composite drug products.

Quinone-based stable isotope probing for assessment of 13C substrate-utilizing bacteria

NASA Astrophysics Data System (ADS)

Kunihiro, Tadao; Katayama, Arata; Demachi, Toyoko; Veuger, Bart; Boschker, Henricus T. S.; van Oevelen, Dick

2015-04-01

In this study, we attempted to establish quinone-stable-isotope probing (SIP) technique to link substrate-utilizing bacterial group to chemotaxonomic group in bacterial community. To identify metabolically active bacterial group in various environments, SIP techniques combined with biomarkers have been widely utilized as an attractive method for environmental study. Quantitative approaches of the SIP technique have unique advantage to assess substrate-incorporation into bacteria. As a most major quantitative approach, SIP technique based on phospholipid-derived fatty acids (PLFA) have been applied to simultaneously assess substrate-incorporation rate into bacteria and microbial community structure. This approach is powerful to estimate the incorporation rate because of the high sensitivity due to the detection by a gas chromatograph-combustion interface-isotope ratio mass spectrometer (GC-c-IRMS). However, its phylogenetic resolution is limited by specificity of a compound-specific marker. We focused on respiratory quinone as a biomarker. Our previous study found a good correlation between concentrations of bacteria-specific PLFAs and quinones over several orders of magnitude in various marine sediments, and the quinone method has a higher resolution (bacterial phylum level) for resolving differences in bacterial community composition more than that of bacterial PLFA. Therefore, respiratory quinones are potentially good biomarkers for quantitative approaches of the SIP technique. The LC-APCI-MS method as molecular-mass based detection method for quinone was developed and provides useful structural information for identifying quinone molecular species in environmental samples. LC-MS/MS on hybrid triple quadrupole/linear ion trap, which enables to simultaneously identify and quantify compounds in a single analysis, can detect high molecular compounds with their isotope ions. Use of LC-MS/MS allows us to develop quinone-SIP based on molecular mass differences due to 13C abundance in the quinone. In this study, we verified carbon stable isotope of quinone compared with bulk carbon stable isotope of bacterial culture. Results indicated a good correlation between carbon stable isotope of quinone compared with bulk carbon stable isotope. However, our measurement conditions for detection of quinone isotope-ions incurred underestimation of 13C abundance in the quinone. The quinone-SIP technique needs further optimization for measurement conditions of LC-MS/MS.

Towards a high sensitivity small animal PET system based on CZT detectors (Conference Presentation)

NASA Astrophysics Data System (ADS)

Abbaszadeh, Shiva; Levin, Craig

2017-03-01

Small animal positron emission tomography (PET) is a biological imaging technology that allows non-invasive interrogation of internal molecular and cellular processes and mechanisms of disease. New PET molecular probes with high specificity are under development to target, detect, visualize, and quantify subtle molecular and cellular processes associated with cancer, heart disease, and neurological disorders. However, the limited uptake of these targeted probes leads to significant reduction in signal. There is a need to advance the performance of small animal PET system technology to reach its full potential for molecular imaging. Our goal is to assemble a small animal PET system based on CZT detectors and to explore methods to enhance its photon sensitivity. In this work, we reconstruct an image from a phantom using a two-panel subsystem consisting of six CZT crystals in each panel. For image reconstruction, coincidence events with energy between 450 and 570 keV were included. We are developing an algorithm to improve sensitivity of the system by including multiple interaction events.

Noninvasive probes of mitochondrial molecular motors

NASA Astrophysics Data System (ADS)

Nawarathna, Dharmakeerthna; Claycomb, James

2005-03-01

We report on a noninvasive method of probing mitochondrial molecular motors using nonlinear dielectric spectroscopy. It has been found previously that enzymes in the plasma membrane, particularly H+ ATPase, result in a strong low frequency (less than 100 Hz) nonlinear harmonic response. In this study, we find evidence that molecular motors located in the inner membranes of mitochondria cause the generation of harmonics at relatively high frequencies (1 - 30 kHz). In particular, we find that potassium cyanide (KCN), a respiratory inhibitor that binds to cytochrome c oxidase and thus prevents transport of protons across the mitochondrial inner membrane, suppresses the harmonic response. We observe this behavior in yeast (S. cerevisiae), a eucaryote that typically contains about 300 mitochondria, and B. indicas, a procaryote believed to be related to the ancient ancestor of mitochondria. Our current modeling efforts are focusing on a Brownian ratchet model of the F0 unit of ATP synthase, a remarkable molecular turbine driven by the proton gradient across the mitochondrial inner membrane.

Novel 64Cu Labeled RGD2-BBN Heterotrimers for PET Imaging of Prostate Cancer.

PubMed

Lucente, Ermelinda; Liu, Hongguang; Liu, Yang; Hu, Xiang; Lacivita, Enza; Leopoldo, Marcello; Cheng, Zhen

2018-05-16

Bombesin receptor 2 (BB 2 ) and integrin α v β 3 receptor are privileged targets for molecular imaging of cancer because of their overexpression in a number of tumor tissues. The most recent developments in heterodimer-based radiopharmaceuticals concern BB 2 - and integrin α v β 3 -targeting compounds, consisting of bombesin (BBN) and cyclic arginine-glycine-aspartic acid peptides (RGD), connected through short length linkers. Molecular imaging probes based on RGD-BBN heterodimer design exhibit improved tumor targeting efficacy compared to the single-receptor targeting peptide monomers. However, their application in clinical study is restricted because of inefficient synthesis or unfavorable in vivo properties, which could depend on the short linker nature. Thus, the aim of the present study was to develop a RGD 2 -BBN heterotrimer, composed of (7-14)BBN-NH 2 peptide (BBN) linked to the E[ c(RGDyK)] 2 dimer peptide (RGD 2 ), bearing the new linker type [Pro-Gly] 12 . The heterodimer E[c(RGDyK)] 2 -PEG 3 -Glu-(Pro-Gly) 12 -BBN(7-14)-NH 2 (RGD 2 -PG 12 -BBN) was prepared through conventional solid phase synthesis, then conjugated with 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) or 1,4,7-triazacyclononane-1-glutaric acid-4,7-diacetic acid (NODA-GA). In 64 Cu labeling, the NODA-GA chelator showed superior radiochemical characteristics compared to DOTA (70% vs 40% yield, respectively). Both conjugates displayed dual targeting ability, showing good α v β 3 affinities and high BB 2 receptor affinities which, in the case of the NODA-GA conjugate, were in the same range as the best RGD-BBN heterodimer ligands reported to date ( K i = 24 nM). 64 Cu-DOTA and 64 Cu-NODA-GA probes were also found to be stable after 1 h incubation in mouse serum (>90%). In a microPET study in prostate cancer PC-3 xenograft mice, both probes showed low tumor uptake, probably due to poor pharmacokinetic properties in vivo. Overall, our study demonstrates that novel RGD-BBN heterodimer with long linker can be prepared and they preserve high binding affinities to BB 2 and integrin α v β 3 receptor binding ability. The present study represents a step forward in the design of effective heterodimer or heterotrimer probes for dual targeting.

Photoaffinity labeling in target- and binding-site identification

PubMed Central

Smith, Ewan; Collins, Ian

2015-01-01

Photoaffinity labeling (PAL) using a chemical probe to covalently bind its target in response to activation by light has become a frequently used tool in drug discovery for identifying new drug targets and molecular interactions, and for probing the location and structure of binding sites. Methods to identify the specific target proteins of hit molecules from phenotypic screens are highly valuable in early drug discovery. In this review, we summarize the principles of PAL including probe design and experimental techniques for in vitro and live cell investigations. We emphasize the need to optimize and validate probes and highlight examples of the successful application of PAL across multiple disease areas. PMID:25686004

Visual format for detection of Mycobacterium tuberculosis and M. bovis in clinical samples using molecular beacons.

PubMed

Kumar, Parameet; Nath, Kapili; Rath, Bimba; Sen, Manas K; Vishalakshi, Potharuju; Chauhan, Devender S; Katoch, Vishwa M; Singh, Sarman; Tyagi, Sanjay; Sreenivas, Vishnubhatla; Prasad, Hanumanthappa K

2009-09-01

A real-time polymerase chain reaction (PCR) assay for the direct identification of Mycobacterium tuberculosis and M. bovis using molecular beacons was developed. The assay was modified for use in regular thermal cyclers. Molecular beacons that were specific for M. tuberculosis (Tb-B) and M. bovis (Bo-B) were designed. The fluorescence of the target PCR product-molecular beacon probe complex was detected visually using a transilluminator. The results were then compared with those of conventional multiplex PCR (CM-PCR) assays and biochemical identification. The detection limit of Tb-B and Bo-B beacons was 500 fg and 50 fg by the visual format and real-time PCR assay, respectively, compared with 5 pg by CM-PCR assay. Pulmonary and extrapulmonary samples were examined. The agreement between culture and the two assays was very good in sputum samples and fair in extrapulmonary samples. The agreement between clinical diagnoses with the two assays was moderate in extrapulmonary samples. There was very good agreement between CM-PCR and visual format assays for all samples used in the study. Concordance in the identification of isolates by the visual, CM-PCR assay, and biochemical identification was seen. Hence, the use of molecular beacon detection of M. tuberculosis and M. bovis in clinical samples is feasible by setting up two asymmetric PCRs concurrently. The assay is sensitive, specific, simple to interpret, and takes less than 3 hours to complete.

Super-Earths, Warm-Neptunes, and Hot-Jupiters: Transmission Spectroscopy for Comparative Planetology

NASA Astrophysics Data System (ADS)

Fraine, Jonathan D.; Deming, Drake; Knutson, Heather; Jordán, Andrés

2014-11-01

We used the Kepler, Hubble, and Spitzer Space Telescopes to probe the diversity of exoplanetary atmospheres with transmission spectroscopy, constraining atomic and molecular absorption in Jupiter- and Neptune-sized exoplanets. The detections and non-detections of molecular species such as water, methane, and carbon monoxide lead to greater understanding of planet formation and evolution. Recent significant advances in both theoretical and observational discoveries from planets like HD189733b, HD209458b, GJ436, as well as our own work with HAT-P-11b and GJ1214b, have shown that the range of measurable atmospheric properties spans from clear, molecular absorption dominated worlds to opaque worlds, with cloudy, hazy, or high mean molecular weight atmospheres. Characterization of these significant non-detections allows us to infer the existence of cloud compositions at high altitudes, or mean molecular weights upwards of ~1000x solar. Neither scenario was expected from extrapolations of solar system analogs. We present here our published results from GJ1214b and HAT-P-11b, as well as our recent work on HAT-P-7b and HAT-P-13b. We search for evidence of atmospheric hazes and clouds, and place constraints on the relative abundance of water vapor, methane, and carbon monoxide-- in the case of cloud-free atmospheres. We conclude by discussing how our results compare to transmission spectra obtained for other similar planets, and use these combined data to develop a better understanding for the nature of these distant and alien worlds.

Visual Format for Detection of Mycobacterium tuberculosis and M. bovis in Clinical Samples Using Molecular Beacons

PubMed Central

Kumar, Parameet; Nath, Kapili; Rath, Bimba; Sen, Manas K.; Vishalakshi, Potharuju; Chauhan, Devender S.; Katoch, Vishwa M.; Singh, Sarman; Tyagi, Sanjay; Sreenivas, Vishnubhatla; Prasad, Hanumanthappa K.

2009-01-01

A real-time polymerase chain reaction (PCR) assay for the direct identification of Mycobacterium tuberculosis and M. bovis using molecular beacons was developed. The assay was modified for use in regular thermal cyclers. Molecular beacons that were specific for M. tuberculosis (Tb-B) and M. bovis (Bo-B) were designed. The fluorescence of the target PCR product-molecular beacon probe complex was detected visually using a transilluminator. The results were then compared with those of conventional multiplex PCR (CM-PCR) assays and biochemical identification. The detection limit of Tb-B and Bo-B beacons was 500 fg and 50 fg by the visual format and real-time PCR assay, respectively, compared with 5 pg by CM-PCR assay. Pulmonary and extrapulmonary samples were examined. The agreement between culture and the two assays was very good in sputum samples and fair in extrapulmonary samples. The agreement between clinical diagnoses with the two assays was moderate in extrapulmonary samples. There was very good agreement between CM-PCR and visual format assays for all samples used in the study. Concordance in the identification of isolates by the visual, CM-PCR assay, and biochemical identification was seen. Hence, the use of molecular beacon detection of M. tuberculosis and M. bovis in clinical samples is feasible by setting up two asymmetric PCRs concurrently. The assay is sensitive, specific, simple to interpret, and takes less than 3 hours to complete. PMID:19661384

In vivo detection of inducible nitric oxide synthase in rodent gliomas.

PubMed

Towner, Rheal A; Smith, Nataliya; Doblas, Sabrina; Garteiser, Philippe; Watanabe, Yasuko; He, Ting; Saunders, Debra; Herlea, Oana; Silasi-Mansat, Robert; Lupu, Florea

2010-03-01

Increased iNOS expression is often found in brain tumors, such as gliomas. The goal of this study was to develop and assess a novel molecular MRI (mMRI) probe for in vivo detection of iNOS in rodent models for gliomas (intracerebral implantation of rat C6 or RG2 cells or ethyl nitrosourea-induced glioma). The probe we used incorporated a Gd-DTPA (gadolinium(III) complex of diethylenetriamine-N,N,N',N'',N''-pentaacetate) backbone with albumin and biotin moieties and covalent binding of an anti-iNOS antibody (Ab) to albumin (anti-iNOS probe). We used mMRI with the anti-iNOS probe to detect in vivo iNOS levels in gliomas. Nonimmune normal rat IgG coupled to albumin-Gd-DTPA-biotin was used as a control nonspecific contrast agent. By targeting the biotin component of the anti-iNOS probe with streptavidin Cy3, fluorescence imaging confirmed the specificity of the probe for iNOS in glioma tissue. iNOS levels in glioma tumors were also confirmed via Western blots and immunohistochemistry. The presence of plasma membrane-associated iNOS in glioma cells was established by transmission electron microscopy and gold-labeled anti-iNOS Ab. The more aggressive RG2 glioma was not found to have higher levels of iNOS compared to C6. Differences in glioma vascularization and blood-brain barrier permeability between the C6 and the RG2 gliomas are discussed. In vivo assessment of iNOS levels associated with tumor development is quite feasible in heterogeneous tissues with mMRI. (c) 2009 Elsevier Inc. All rights reserved.

Optical imaging probes in oncology

PubMed Central

Martelli, Cristina; Dico, Alessia Lo; Diceglie, Cecilia; Lucignani, Giovanni; Ottobrini, Luisa

2016-01-01

Cancer is a complex disease, characterized by alteration of different physiological molecular processes and cellular features. Keeping this in mind, the possibility of early identification and detection of specific tumor biomarkers by non-invasive approaches could improve early diagnosis and patient management. Different molecular imaging procedures provide powerful tools for detection and non-invasive characterization of oncological lesions. Clinical studies are mainly based on the use of computed tomography, nuclear-based imaging techniques and magnetic resonance imaging. Preclinical imaging in small animal models entails the use of dedicated instruments, and beyond the already cited imaging techniques, it includes also optical imaging studies. Optical imaging strategies are based on the use of luminescent or fluorescent reporter genes or injectable fluorescent or luminescent probes that provide the possibility to study tumor features even by means of fluorescence and luminescence imaging. Currently, most of these probes are used only in animal models, but the possibility of applying some of them also in the clinics is under evaluation. The importance of tumor imaging, the ease of use of optical imaging instruments, the commercial availability of a wide range of probes as well as the continuous description of newly developed probes, demonstrate the significance of these applications. The aim of this review is providing a complete description of the possible optical imaging procedures available for the non-invasive assessment of tumor features in oncological murine models. In particular, the characteristics of both commercially available and newly developed probes will be outlined and discussed. PMID:27145373

Sequential Cross-Species Chromosome Painting among River Buffalo, Cattle, Sheep and Goat: A Useful Tool for Chromosome Abnormalities Diagnosis within the Family Bovidae

PubMed Central

Pauciullo, Alfredo; Perucatti, Angela; Cosenza, Gianfranco; Iannuzzi, Alessandra; Incarnato, Domenico; Genualdo, Viviana; Di Berardino, Dino; Iannuzzi, Leopoldo

2014-01-01

The main goal of this study was to develop a comparative multi-colour Zoo-FISH on domestic ruminants metaphases using a combination of whole chromosome and sub-chromosomal painting probes obtained from the river buffalo species (Bubalus bubalis, 2n = 50,XY). A total of 13 DNA probes were obtained through chromosome microdissection and DOP-PCR amplification, labelled with two fluorochromes and sequentially hybridized on river buffalo, cattle (Bos taurus, 2n = 60,XY), sheep (Ovis aries, 2n = 54,XY) and goat (Capra hircus, 2n = 60,XY) metaphases. The same set of paintings were then hybridized on bovine secondary oocytes to test their potential use for aneuploidy detection during in vitro maturation. FISH showed excellent specificity on metaphases and interphase nuclei of all the investigated species. Eight pairs of chromosomes were simultaneously identified in buffalo, whereas the same set of probes covered 13 out 30 chromosome pairs in the bovine and goat karyotypes and 40% of the sheep karyotype (11 out of 27 chromosome pairs). This result allowed development of the first comparative M-FISH karyotype within the domestic ruminants. The molecular resolution of complex karyotypes by FISH is particularly useful for the small chromosomes, whose similarity in the banding patterns makes their identification very difficult. The M-FISH karyotype also represents a practical tool for structural and numerical chromosome abnormalities diagnosis. In this regard, the successful hybridization on bovine secondary oocytes confirmed the potential use of this set of probes for the simultaneous identification on the same germ cell of 12 chromosome aneuploidies. This is a fundamental result for monitoring the reproductive health of the domestic animals in relation to management errors and/or environmental hazards. PMID:25330006

Detection of early primary colorectal cancer with upconversion luminescent NP-based molecular probes

NASA Astrophysics Data System (ADS)

Liu, Chunyan; Qi, Yifei; Qiao, Ruirui; Hou, Yi; Chan, Kaying; Li, Ziqian; Huang, Jiayi; Jing, Lihong; Du, Jun; Gao, Mingyuan

2016-06-01

Early detection and diagnosis of cancers is extremely beneficial for improving the survival rate of cancer patients and molecular imaging techniques are believed to be relevant for offering clinical solutions. Towards early cancer detection, we developed a primary animal colorectal cancer model and constructed a tumor-specific imaging probe by using biocompatible NaGdF4:Yb,Er@NaGdF4 upconversion luminescent NPs for establishing a sensitive early tumor imaging method. The primary animal tumor model, which can better mimic the human colorectal cancer, was built upon continual administration of 1,2-dimethylhydrazine in Kunming mice and the tumor development was carefully monitored through histopathological and immunohistochemical analyses to reveal the pathophysiological processes and molecular features of the cancer microenvironment. The upconversion imaging probe was constructed through covalent coupling of PEGylated core-shell NPs with folic acid whose receptor is highly expressed in the primary tumors. Upon 980 nm laser excitation, the primary colorectal tumors in the complex abdominal environment were sensitively imaged owing to the ultralow background of the upconversion luminescence and the high tumor-targeting specificity of the nanoprobe. We believe that the current studies provide a highly effective and potential approach for early colorectal cancer diagnosis and tumor surgical navigation.Early detection and diagnosis of cancers is extremely beneficial for improving the survival rate of cancer patients and molecular imaging techniques are believed to be relevant for offering clinical solutions. Towards early cancer detection, we developed a primary animal colorectal cancer model and constructed a tumor-specific imaging probe by using biocompatible NaGdF4:Yb,Er@NaGdF4 upconversion luminescent NPs for establishing a sensitive early tumor imaging method. The primary animal tumor model, which can better mimic the human colorectal cancer, was built upon continual administration of 1,2-dimethylhydrazine in Kunming mice and the tumor development was carefully monitored through histopathological and immunohistochemical analyses to reveal the pathophysiological processes and molecular features of the cancer microenvironment. The upconversion imaging probe was constructed through covalent coupling of PEGylated core-shell NPs with folic acid whose receptor is highly expressed in the primary tumors. Upon 980 nm laser excitation, the primary colorectal tumors in the complex abdominal environment were sensitively imaged owing to the ultralow background of the upconversion luminescence and the high tumor-targeting specificity of the nanoprobe. We believe that the current studies provide a highly effective and potential approach for early colorectal cancer diagnosis and tumor surgical navigation. Electronic supplementary information (ESI) available: (1) Molecular structure of Jeffamine-modified FA; (2) immunohistochemical analysis of FR expression in the colorectal tissue derived from mice treated with NaCl at different weeks; (3) biodistributions of probes of NP-FA and NP-IgG in the main organs of mice. See DOI: 10.1039/c5nr07858j

MOLECULAR PHYLOGENETIC AND BIOGEOCHEMICAL STUDIES OF SULFATE-REDUCING BACTERIA IN THE RHIZOSPHERE OF SPARTINA ALTERNIFLORA

EPA Science Inventory

The population composition and biogeochemistry of sulfate-reducing bacteria (SRB) in the rhizosphere of the marsh grass Spartina alterniflora was investigated over two growing seasons using molecular probing, enumerations of culturable SRB, and measurements of SO42- reduction rat...

Optical Probes for Neurobiological Sensing and Imaging.

PubMed

Kim, Eric H; Chin, Gregory; Rong, Guoxin; Poskanzer, Kira E; Clark, Heather A

2018-05-15

Fluorescent nanosensors and molecular probes are next-generation tools for imaging chemical signaling inside and between cells. Electrophysiology has long been considered the gold standard in elucidating neural dynamics with high temporal resolution and precision, particularly on the single-cell level. However, electrode-based techniques face challenges in illuminating the specific chemicals involved in neural cell activation with adequate spatial information. Measuring chemical dynamics is of fundamental importance to better understand synergistic interactions between neurons as well as interactions between neurons and non-neuronal cells. Over the past decade, significant technological advances in optical probes and imaging methods have enabled entirely new possibilities for studying neural cells and circuits at the chemical level. These optical imaging modalities have shown promise for combining chemical, temporal, and spatial information. This potential makes them ideal candidates to unravel the complex neural interactions at multiple scales in the brain, which could be complemented by traditional electrophysiological methods to obtain a full spatiotemporal picture of neurochemical dynamics. Despite the potential, only a handful of probe candidates have been utilized to provide detailed chemical information in the brain. To date, most live imaging and chemical mapping studies rely on fluorescent molecular indicators to report intracellular calcium (Ca 2+ ) dynamics, which correlates with neuronal activity. Methodological advances for monitoring a full array of chemicals in the brain with improved spatial, temporal, and chemical resolution will thus enable mapping of neurochemical circuits with finer precision. On the basis of numerous studies in this exciting field, we review the current efforts to develop and apply a palette of optical probes and nanosensors for chemical sensing in the brain. There is a strong impetus to further develop technologies capable of probing entire neurobiological units with high spatiotemporal resolution. Thus, we introduce selected applications for ion and neurotransmitter detection to investigate both neurons and non-neuronal brain cells. We focus on families of optical probes because of their ability to sense a wide array of molecules and convey spatial information with minimal damage to tissue. We start with a discussion of currently available molecular probes, highlight recent advances in genetically modified fluorescent probes for ions and small molecules, and end with the latest research in nanosensors for biological imaging. Customizable, nanoscale optical sensors that accurately and dynamically monitor the local environment with high spatiotemporal resolution could lead to not only new insights into the function of all cell types but also a broader understanding of how diverse neural signaling systems act in conjunction with neighboring cells in a spatially relevant manner.

Incorporation of a Bio-Active Reverse-Turn Heterocycle into a Peptide Template Using Solid-Phase Synthesis to Probe Melanocortin Receptor Selectivity and Ligand Conformations by 2D 1H NMR

PubMed Central

Singh, Anamika; Wilczynski, Andrzej; Holder, Jerry R.; Witek, Rachel M.; Dirain, Marvin L.; Xiang, Zhimin; Edison, Arthur S.; Haskell-Luevano, Carrie

2011-01-01

Using a solid-phase synthetic approach, a bioactive reverse turn heterocyclic was incorporated into a cyclic peptide template to probe melanocortin receptor potency and ligand structural conformations. The five melanocortin receptor isoforms (MC1R-MC5R) are G-protein coupled receptors (GPCRs) that are regulated by endogenous agonists and antagonists. This pathway is involved in pigmentation, weight, and energy homeostasis. Herein, we report novel analogues of the chimeric AGRP-melanocortin peptide template integrated with a small molecule moiety to probe the structural and functional consequences of the core His-Phe-Arg-Trp peptide domain using a reverse-turn heterocycle. A series of six compounds are reported that result in inactive to full agonists with nM potency. Biophysical structural analysis [2D 1H NMR and computer-assisted molecular modeling (CAMM)] were performed on selected analogues, resulting in the identification that these peptide-small molecule hybrids possessed increased flexibility and fewer discrete conformational families as compared to the reference peptide and result in a novel template for further structure-function studies. PMID:21306168

Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster

PubMed Central

He, Bing; Caudy, Amy; Parsons, Lance; Rosebrock, Adam; Pane, Attilio; Raj, Sandeep; Wieschaus, Eric

2012-01-01

Heterochromatin represents a significant portion of eukaryotic genomes and has essential structural and regulatory functions. Its molecular organization is largely unknown due to difficulties in sequencing through and assembling repetitive sequences enriched in the heterochromatin. Here we developed a novel strategy using chromosomal rearrangements and embryonic phenotypes to position unmapped Drosophila melanogaster heterochromatic sequence to specific chromosomal regions. By excluding sequences that can be mapped to the assembled euchromatic arms, we identified sequences that are specific to heterochromatin and used them to design heterochromatin specific probes (“H-probes”) for microarray. By comparative genomic hybridization (CGH) analyses of embryos deficient for each chromosome or chromosome arm, we were able to map most of our H-probes to specific chromosome arms. We also positioned sequences mapped to the second and X chromosomes to finer intervals by analyzing smaller deletions with breakpoints in heterochromatin. Using this approach, we were able to map >40% (13.9 Mb) of the previously unmapped heterochromatin sequences assembled by the whole-genome sequencing effort on arm U and arm Uextra to specific locations. We also identified and mapped 110 kb of novel heterochromatic sequences. Subsequent analyses revealed that sequences located within different heterochromatic regions have distinct properties, such as sequence composition, degree of repetitiveness, and level of underreplication in polytenized tissues. Surprisingly, although heterochromatin is generally considered to be transcriptionally silent, we detected region-specific temporal patterns of transcription in heterochromatin during oogenesis and early embryonic development. Our study provides a useful approach to elucidate the molecular organization and function of heterochromatin and reveals region-specific variation of heterochromatin. PMID:22745230

Turbulence in molecular clouds - A new diagnostic tool to probe their origin

NASA Technical Reports Server (NTRS)

Canuto, V. M.; Battaglia, A.

1985-01-01

A method is presented to uncover the instability responsible for the type of turbulence observed in molecular clouds and the value of the physical parameters of the 'placental medium' from which turbulence originated. The method utilizes the observational relation between velocities and sizes of molecular clouds, together with a recent model for large-scale turbulence (constructed by Canuto and Goldman, 1985).

Lymph Node Metastases Optical Molecular Diagnostic and Radiation Therapy

DTIC Science & Technology

2017-03-01

because most imaging is based upon structures and not molecular functions. The one tool commonly used for metastases imaging is nuclear medicine...imaging, which is that micro metastases cannot be visualized at a relevant stage., largely because most imaging is based upon structures and not...evaluate the limits on structural , metabolic and immunologic probes for molecular imaging, and (4) to complete studies on metastatic breast cancer

Probing Electronic and Thermoelectric Properties of Single Molecule Junctions

NASA Astrophysics Data System (ADS)

Widawsky, Jonathan R.

In an effort to further understand electronic and thermoelectric phenomenon at the nanometer scale, we have studied the transport properties of single molecule junctions. To carry out these transport measurements, we use the scanning tunneling microscope-break junction (STM-BJ) technique, which involves the repeated formation and breakage of a metal point contact in an environment of the target molecule. Using this technique, we are able to create gaps that can trap the molecules, allowing us to sequentially and reproducibly create a large number of junctions. By applying a small bias across the junction, we can measure its conductance and learn about the transport mechanisms at the nanoscale. The experimental work presented here directly probes the transmission properties of single molecules through the systematic measurement of junction conductance (at low and high bias) and thermopower. We present measurements on a variety of molecular families and study how conductance depends on the character of the linkage (metal-molecule bond) and the nature of the molecular backbone. We start by describing a novel way to construct single molecule junctions by covalently connecting the molecular backbone to the electrodes. This eliminates the use of linking substituents, and as a result, the junction conductance increases substantially. Then, we compare transport across silicon chains (silanes) and saturated carbon chains (alkanes) while keeping the linkers the same and find a stark difference in their electronic transport properties. We extend our studies of molecular junctions by looking at two additional aspects of quantum transport -- molecular thermopower and molecular current-voltage characteristics. Each of these additional parameters gives us further insight into transport properties at the nanoscale. Evaluating the junction thermopower allows us to determine the nature of charge carriers in the system and we demonstrate this by contrasting the measurement of amine-terminated and pyridine-terminated molecules (which exhibit hole transport and electron transport, respectively). We also report the thermopower of the highly conducting, covalently bound molecular junctions that we have recently been able to form, and learn that, because of their unique transport properties, the junction power factors, GS2, are extremely high. Finally, we discuss the measurement of molecular current-voltage curves and consider the electronic and physical effects of applying a large bias to the system. We conclude with a summary of the work discussed and an outlook on related scientific studies.

The association of low-molecular-weight hydrophobic compounds with native casein micelles in bovine milk.

PubMed

Cheema, M; Mohan, M S; Campagna, S R; Jurat-Fuentes, J L; Harte, F M

2015-08-01

The agreed biological function of the casein micelles in milk is to carry minerals (calcium, magnesium, and phosphorus) from mother to young along with amino acids for growth and development. Recently, native and modified casein micelles were used as encapsulating and delivery agents for various hydrophobic low-molecular-weight probes. The ability of modified casein micelles to bind certain probes may derive from the binding affinity of native casein micelles. Hence, a study with milk from single cows was conducted to further elucidate the association of hydrophobic molecules into native casein micelles and further understand their biological function. Hydrophobic and hydrophilic extraction followed by ultraperformance liquid chromatography-high resolution mass spectrometry analysis were performed over protein fractions obtained from size exclusion fractionation of raw skim milk. Hydrophobic compounds, including phosphatidylcholine, lyso-phosphatidylcholine, phosphatidylethanolamine, and sphingomyelin, showed strong association exclusively to casein micelles as compared with whey proteins, whereas hydrophilic compounds did not display any preference for their association among milk proteins. Further analysis using liquid chromatography-tandem mass spectrometry detected 42 compounds associated solely with the casein-micelles fraction. Mass fragments in tandem mass spectrometry identified 4 of these compounds as phosphatidylcholine with fatty acid composition of 16:0/18:1, 14:0/16:0, 16:0/16:0, and 18:1/18:0. These results support that transporting low-molecular-weight hydrophobic molecules is also a biological function of the casein micelles in milk. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Next generation of optical diagnostics for bladder cancer using probe-based confocal laser endomicroscopy

NASA Astrophysics Data System (ADS)

Liu, Jen-Jane; Chang, Timothy C.; Pan, Ying; Hsiao, Shelly T.; Mach, Kathleen E.; Jensen, Kristin C.; Liao, Joseph C.

2012-02-01

Real-time imaging with confocal laser endomicroscopy (CLE) probes that fit in standard endoscopes has emerged as a clinically feasible technology for optical biopsy of bladder cancer. Confocal images of normal, inflammatory, and neoplastic urothelium obtained with intravesical fluorescein can be differentiated by morphologic characteristics. We compiled a confocal atlas of the urinary tract using these diagnostic criteria to be used in a prospective diagnostic accuracy study. Patients scheduled to undergo transurethral resection of bladder tumor underwent white light cystoscopy (WLC), followed by CLE, and histologic confirmation of resected tissue. Areas that appeared normal by WLC were imaged and biopsied as controls. We imaged and prospectively analyzed 135 areas in 57 patients. We show that CLE improves the diagnostic accuracy of WLC for diagnosing benign tissue, low and high grade cancer. Interobserver studies showed a moderate level of agreement by urologists and nonclinical researchers. Despite morphologic differences between inflammation and cancer, real-time differentiation can still be challenging. Identification of bladder cancer-specific contrast agents could provide molecular specificity to CLE. By using fluorescently-labeled antibodies or peptides that bind to proteins expressed in bladder cancer, we have identified putative molecular contrast agents for targeted imaging with CLE. We describe one candidate agent - anti-CD47 - that was instilled into bladder specimens. The tumor and normal urothelium were imaged with CLE, with increased fluorescent signal demonstrated in areas of tumor compared to normal areas. Thus, cancer-specificity can be achieved using molecular contrast agents ex vivo in conjunction with CLE.

Probing the hydrogen equilibrium and kinetics in zeolite imidazolate frameworks via molecular dynamics and quasi-elastic neutron scattering experiments.

PubMed

Pantatosaki, Evangelia; Jobic, Hervé; Kolokolov, Daniil I; Karmakar, Shilpi; Biniwale, Rajesh; Papadopoulos, George K

2013-01-21

The problem of simulating processes involving equilibria and dynamics of guest sorbates within zeolitic imidazolate frameworks (ZIF) by means of molecular dynamics (MD) computer experiments is of growing importance because of the promising role of ZIFs as molecular "traps" for clean energy applications. A key issue for validating such an atomistic modeling attempt is the possibility of comparing the MD results, with real experiments being able to capture analogous space and time scales to the ones pertained to the computer experiments. In the present study, this prerequisite is fulfilled through the quasi-elastic neutron scattering technique (QENS) for measuring self-diffusivity, by elaborating the incoherent scattering signal of hydrogen nuclei. QENS and MD experiments were performed in parallel to probe the hydrogen motion, for the first time in ZIF members. The predicted and measured dynamics behaviors show considerable concentration variation of the hydrogen self-diffusion coefficient in the two topologically different ZIF pore networks of this study, the ZIF-3 and ZIF-8. Modeling options such as the flexibility of the entire matrix versus a rigid framework version, the mobility of the imidazolate ligand, and the inclusion of quantum mechanical effects in the potential functions were examined in detail for the sorption thermodynamics and kinetics of hydrogen and also of deuterium, by employing MD combined with Widom averaging towards studying phase equilibria. The latter methodology ensures a rigorous and efficient way for post-processing the dynamics trajectory, thereby avoiding stochastic moves via Monte Carlo simulation, over the large number of configurational degrees of freedom a nonrigid framework encompasses.

Molecular Gas Heating Mechanisms, and Star Formation Feedback in Merger/Starbursts: NGC 6240 and Arp 193 as Case Studies

NASA Astrophysics Data System (ADS)

Papadopoulos, Padelis P.; Zhang, Zhi-Yu; Xilouris, E. M.; Weiss, Axel; van der Werf, Paul; Israel, F. P.; Greve, T. R.; Isaak, Kate G.; Gao, Y.

2014-06-01

We used the SPIRE/FTS instrument aboard the Herschel Space Observatory to obtain the Spectral Line Energy Distributions (SLEDs) of CO from J = 4-3 to J = 13-12 of Arp 193 and NGC 6240, two classical merger/starbursts selected from our molecular line survey of local Luminous Infrared Galaxies (L IR >= 1011 L ⊙). The high-J CO SLEDs are then combined with ground-based low-J CO, 13CO, HCN, HCO+, CS line data and used to probe the thermal and dynamical states of their large molecular gas reservoirs. We find the two CO SLEDs strongly diverging from J = 4-3 onward, with NGC 6240 having a much higher CO line excitation than Arp 193, despite their similar low-J CO SLEDs and L FIR/L CO, 1 - 0, L HCN/L CO (J = 1-0) ratios (proxies of star formation efficiency and dense gas mass fraction). In Arp 193, one of the three most extreme starbursts in the local universe, the molecular SLEDs indicate a small amount (~5%-15%) of dense gas (n >= 104 cm-3) unlike NGC 6240 where most of the molecular gas (~60%-70%) is dense (n ~ (104-105) cm-3). Strong star-formation feedback can drive this disparity in their dense gas mass fractions, and also induce extreme thermal and dynamical states for the molecular gas. In NGC 6240, and to a lesser degree in Arp 193, we find large molecular gas masses whose thermal states cannot be maintained by FUV photons from Photon-Dominated Regions. We argue that this may happen often in metal-rich merger/starbursts, strongly altering the initial conditions of star formation. ALMA can now directly probe these conditions across cosmic epoch, and even probe their deeply dust-enshrouded outcome, the stellar initial mass function averaged over galactic evolution.

Molecular frame photoemission by a comb of elliptical high-order harmonics: a sensitive probe of both photodynamics and harmonic complete polarization state.

PubMed

Veyrinas, K; Gruson, V; Weber, S J; Barreau, L; Ruchon, T; Hergott, J-F; Houver, J-C; Lucchese, R R; Salières, P; Dowek, D

2016-12-16

Due to the intimate anisotropic interaction between an XUV light field and a molecule resulting in photoionization (PI), molecular frame photoelectron angular distributions (MFPADs) are most sensitive probes of both electronic/nuclear dynamics and the polarization state of the ionizing light field. Consequently, they encode the complex dipole matrix elements describing the dynamics of the PI transition, as well as the three normalized Stokes parameters s 1 , s 2 , s 3 characterizing the complete polarization state of the light, operating as molecular polarimetry. The remarkable development of advanced light sources delivering attosecond XUV pulses opens the perspective to visualize the primary steps of photochemical dynamics in time-resolved studies, at the natural attosecond to few femtosecond time-scales of electron dynamics and fast nuclear motion. It is thus timely to investigate the feasibility of measurement of MFPADs when PI is induced e.g., by an attosecond pulse train (APT) corresponding to a comb of discrete high-order harmonics. In the work presented here, we report MFPAD studies based on coincident electron-ion 3D momentum imaging in the context of ultrafast molecular dynamics investigated at the PLFA facility (CEA-SLIC), with two perspectives: (i) using APTs generated in atoms/molecules as a source for MFPAD-resolved PI studies, and (ii) taking advantage of molecular polarimetry to perform a complete polarization analysis of the harmonic emission of molecules, a major challenge of high harmonic spectroscopy. Recent results illustrating both aspects are reported for APTs generated in unaligned SF 6 molecules by an elliptically polarized infrared driving field. The observed fingerprints of the elliptically polarized harmonics include the first direct determination of the complete s 1 , s 2 , s 3 Stokes vector, equivalent to (ψ, ε, P), the orientation and the signed ellipticity of the polarization ellipse, and the degree of polarization P. They are compared to so far incomplete results of XUV optical polarimetry. We finally discuss the comparison between the outcomes of photoionization and high harmonic spectroscopy for the description of molecular photodynamics.

Results from the irradiation of stainless steel and copper by 23 MeV γ-quanta in the atmosphere of molecular deuterium at a pressure of 2 kbar

NASA Astrophysics Data System (ADS)

Didyk, A. Yu.; Wisniewski, R.

2014-05-01

Metal samples were arranged inside a "finger-type" high-pressure chamber (DHPC-FT) filled by deuterium. They were two aluminum rods, a copper rod, two specimens of homogeneous YMn2 alloy, and a stainless steel wire. The pressure of molecular deuterium in DHPC-FT was about 2 kbar. The samples were irradiated by braking γ-quanta at a threshold energy of 23 MeV. All the samples were studied using scanning electron microscopy (SEM) and X-ray (roentgen) microelement probe analysis (RMPA). Considerable changes in the surface structure and elemental composition were found for the samples of copper, aluminum, YMn2 alloy, and stainless steel. Unusual results were analyzed in detail and compared with the earlier data.

Polyketide intermediate mimics as probes for revealing cryptic stereochemistry of ketoreductase domains.

PubMed

Li, Yang; Fiers, William D; Bernard, Steffen M; Smith, Janet L; Aldrich, Courtney C; Fecik, Robert A

2014-12-19

Among natural product families, polyketides have shown the most promise for combinatorial biosynthesis of natural product-like libraries. Though recent research in the area has provided many mechanistic revelations, a basic-level understanding of kinetic and substrate tolerability is still needed before the full potential of combinatorial biosynthesis can be realized. We have developed a novel set of chemical probes for the study of ketoreductase domains of polyketide synthases. This chemical tool-based approach was validated using the ketoreductase of pikromycin module 2 (PikKR2) as a model system. Triketide substrate mimics 12 and 13 were designed to increase stability (incorporating a nonhydrolyzable thioether linkage) and minimize nonessential functionality (truncating the phosphopantetheinyl arm). PikKR2 reduction product identities as well as steady-state kinetic parameters were determined by a combination of LC-MS/MS analysis of synthetic standards and a NADPH consumption assay. The d-hydroxyl product is consistent with bioinformatic analysis and results from a complementary biochemical and molecular biological approach. When compared to widely employed substrates in previous studies, diketide 63 and trans-decalone 64, substrates 12 and 13 showed 2-10 fold lower K(M) values (2.4 ± 0.8 and 7.8 ± 2.7 mM, respectively), indicating molecular recognition of intermediate-like substrates. Due to an abundance of the nonreducable enol-tautomer, the k(cat) values were attenuated by as much as 15-336 fold relative to known substrates. This study reveals the high stereoselectivity of PikKR2 in the face of gross substrate permutation, highlighting the utility of a chemical probe-based approach in the study of polyketide ketoreductases.

Longitudinal molecular characterization of endoscopic specimens from colorectal lesions

PubMed Central

Minarikova, Petra; Benesova, Lucie; Halkova, Tereza; Belsanova, Barbora; Suchanek, Stepan; Cyrany, Jiri; Tuckova, Inna; Bures, Jan; Zavoral, Miroslav; Minarik, Marek

2016-01-01

AIM: To compare molecular profiles of proximal colon, distal colon and rectum in large adenomas, early and late carcinomas. To assess feasibility of testing directed at molecular markers from this study in routine clinical practice. METHODS: A prospective 3-year study has resulted in the acquisition of samples from 159 large adenomas and 138 carcinomas along with associated clinical parameters including localization, grade and histological type for adenomas and localization and stage for carcinomas. A complex molecular phenotyping has been performed using multiplex ligation-dependent probe amplification technique for the evaluation of CpG-island methylator phenotype (CIMP), PCR fragment analysis for detection of microsatellite instability and denaturing capillary electrophoresis for sensitive detection of somatic mutations in KRAS, BRAF, TP53 and APC genes. RESULTS: Molecular types according to previously introduced Jass classification have been evaluated for large adenomas and early and late carcinomas. An increase in CIMP+ type, eventually accompanied with KRAS mutations, was notable between large adenomas and early carcinomas. As expected, the longitudinal observations revealed a correlation of the CIMP+/BRAF+ type with proximal location. CONCLUSION: Prospective molecular classification of tissue specimens is feasible in routine endoscopy practice. Increased frequency of some molecular types corresponds to the developmental stages of colorectal tumors. As expected, a clear distinction is notable for tumors located in proximal colon supposedly arising from the serrated (methylation) pathway. PMID:27239120

Cd(2+) Triggered the FRET "ON": A New Molecular Switch for the Ratiometric Detection of Cd(2+) with Live-Cell Imaging and Bound X-ray Structure.

PubMed

Aich, Krishnendu; Goswami, Shyamaprosad; Das, Sangita; Mukhopadhyay, Chitrangada Das; Quah, Ching Kheng; Fun, Hoong-Kun

2015-08-03

On the basis of the Förster resonance energy transfer mechanism between rhodamine and quinoline-benzothiazole conjugated dyad, a new colorimetric as well as fluorescence ratiometric probe was synthesized for the selective detection of Cd(2+). The complex formation of the probe with Cd(2+) was confirmed through Cd(2+)-bound single-crystal structure. Capability of the probe as imaging agent to detect the cellular uptake of Cd(2+) was demonstrated here using living RAW cells.

High Resolution PET Imaging Probe for the Detection, Molecular Characterization, and Treatment Monitoring of Prostate cancer

DTIC Science & Technology

2011-07-01

impact on overall probe performance, including spatial resolution, energy resolution and timing resolution. We will show that 1 mm3 voxels will...ring, description of a strategy to remove scattered events, followed by characterization of impact of timing properties of the probe. In summary, the...described by the total distance d¼d1+d2 and a¼ d1=ðd1þd2Þ. We also want to account for impact angles, y1 and y2, defined versus line perpendicular to

Sequential Excitation Preparation of Molecular Energy Levels with Special Structural and Chemical Properties.

DTIC Science & Technology

1986-01-06

D.E. Reisner, and P.H. Vaccaro, pp. 393-404 in Lasers as Reactants and Probes in Chemistry, (eds. W.M. Jackson and A.B. Harvey) Howard University Press...as Reactants and Probes in Chemistry, Howard University (May 1982). 4. J.L. Kinsey, "An Outsider’s View of the Spectroscopy of Polyatomic Systems...Kinsey, C. Kittrell, D.E. Reisner, and P.H. Vaccaro, pp. 393-404 in Lasers as Reactants and Probes in Chemistry (eds. W.M. Jackson and A.B. Harvey), Howard

Phosphor Scanner For Imaging X-Ray Diffraction

NASA Technical Reports Server (NTRS)

Carter, Daniel C.; Hecht, Diana L.; Witherow, William K.

1992-01-01

Improved optoelectronic scanning apparatus generates digitized image of x-ray image recorded in phosphor. Scanning fiber-optic probe supplies laser light stimulating luminescence in areas of phosphor exposed to x rays. Luminescence passes through probe and fiber to integrating sphere and photomultiplier. Sensitivity and resolution exceed previously available scanners. Intended for use in x-ray crystallography, medical radiography, and molecular biology.

Optical gain in an optically driven three-level ? system in atomic Rb vapor

NASA Astrophysics Data System (ADS)

Ballmann, C. W.; Yakovlev, V. V.

2018-06-01

In this work, we report experimentally achieved optical gain of a weak probe beam in a three-level ? system in a low density Rubidium vapor cell driven by a single pump beam. The maximum measured gain of the probe beam was about 0.12%. This work could lead to new approaches for enhancing molecular spectroscopy applications.

Cysteamine-based cell-permeable Zn(2+)-specific molecular bioimaging materials: from animal to plant cells.

PubMed

Sinha, Sougata; Dey, Gourab; Kumar, Sunil; Mathew, Jomon; Mukherjee, Trinetra; Mukherjee, Subhrakanti; Ghosh, Subrata

2013-11-27

Structure-interaction/fluorescence relationship studies led to the development of a small chemical library of Zn(2+)-specific cysteamine-based molecular probes. The probe L5 with higher excitation/emission wavelengths, which absorbs in the visible region and emits in the green, was chosen as a model imaging material for biological studies. After successful imaging of intracellular zinc in four different kinds of cells including living organisms, plant, and animal cells, in vivo imaging potential of L5 was evaluated using plant systems. In vivo imaging of translocation of zinc through the stem of a small herb with a transparent stem, Peperomia pellucida, confirmed the stability of L5 inside biological systems and the suitability of L5 for real-time analysis. Similarly, fluorescence imaging of zinc in gram sprouts revealed the efficacy of the probe in the detection and localization of zinc in cereal crops. This imaging technique will help in knowing the efficiency of various techniques used for zinc enrichment of cereal crops. Computational analyses were carried out to better understand the structure, the formation of probe-Zn(2+) complexes, and the emission properties of these complexes.

Molecular imaging reveals elevated VEGFR-2 expression in retinal capillaries in diabetes: a novel biomarker for early diagnosis

PubMed Central

Sun, Dawei; Nakao, Shintaro; Xie, Fang; Zandi, Souska; Bagheri, Abouzar; Kanavi, Mozhgan Rezaei; Samiei, Shahram; Soheili, Zahra-Soheila; Frimmel, Sonja; Zhang, Zhongyu; Ablonczy, Zsolt; Ahmadieh, Hamid; Hafezi-Moghadam, Ali

2014-01-01

Diabetic retinopathy (DR) is a microvascular complication of diabetes and a leading cause of vision loss. Biomarkers and methods for early diagnosis of DR are urgently needed. Using a new molecular imaging approach, we show up to 94% higher accumulation of custom designed imaging probes against vascular endothelial growth factor receptor 2 (VEGFR-2) in retinal and choroidal vessels of diabetic animals (P<0.01), compared to normal controls. More than 80% of the VEGFR-2 in the diabetic retina was in the capillaries, compared to 47% in normal controls (P<0.01). Angiography in rabbit retinas revealed microvascular capillaries to be the location for VEGF-A-induced leakage, as expressed by significantly higher rate of fluorophore spreading with VEGF-A injection when compared to vehicle control (26±2 vs. 3±1 μm/s, P<0.05). Immunohistochemistry showed VEGFR-2 expression in capillaries of diabetic animals but not in normal controls. Macular vessels from diabetic patients (n=7) showed significantly more VEGFR-2 compared to nondiabetic controls (n=5) or peripheral retinal regions of the same retinas (P<0.01 in both cases). Here we introduce a new approach for early diagnosis of DR and VEGFR-2 as a molecular marker. VEGFR-2 could become a key diagnostic target, one that might help to prevent retinal vascular leakage and proliferation in diabetic patients.—Sun, D., Nakao, S., Xie, F., Zandi, S., Bagheri, A., Kanavi, M. R., Samiei, S., Soheili, Z.-S., Frimmel, S., Zhang, Z., Ablonczy, Z., Ahmadieh, H., Hafezi-Moghadam, A. Molecular imaging reveals elevated VEGFR-2 expression in retinal capillaries in diabetes: a novel biomarker for early diagnosis. PMID:24903276

Mesoscale Polymer Dissolution Probed by Raman Spectroscopy and Molecular Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, Tsun-Mei; Xantheas, Sotiris S.; Vasdekis, Andreas E.

2016-10-13

The diffusion of various solvents into a polystyrene (PS) matrix was probed experimentally by monitoring the temporal profiles of the Raman spectra and theoretically from molecular dynamics (MD) simulations of the binary system. The simulation results assist in providing a fundamental, molecular level connection between the mixing/dissolution processes and the difference = solvent – PS in the values of the Hildebrand parameter () between the two components of the binary systems: solvents having similar values of with PS (small ) exhibit fast diffusion into the polymer matrix, whereas the diffusion slows down considerably when the ’s are different (large ).more » To this end, the Hildebrand parameter was identified as a useful descriptor that governs the process of mixing in polymer – solvent binary systems. The experiments also provide insight into further refinements of the models specific to non-Fickian diffusion phenomena that need to be used in the simulations.« less

Probing C-O bond activation on gas-phase transition metal clusters: Infrared multiple photon dissociation spectroscopy of Fe, Ru, Re, and W cluster CO complexes

NASA Astrophysics Data System (ADS)

Lyon, Jonathan T.; Gruene, Philipp; Fielicke, André; Meijer, Gerard; Rayner, David M.

2009-11-01

The binding of carbon monoxide to iron, ruthenium, rhenium, and tungsten clusters is studied by means of infrared multiple photon dissociation spectroscopy. The CO stretching mode is used to probe the interaction of the CO molecule with the metal clusters and thereby the activation of the C-O bond. CO is found to adsorb molecularly to atop positions on iron clusters. On ruthenium and rhenium clusters it also binds molecularly. In the case of ruthenium, binding is predominantly to atop sites, however higher coordinated CO binding is also observed for both metals and becomes prevalent for rhenium clusters containing more than nine atoms. Tungsten clusters exhibit a clear size dependence for molecular versus dissociative CO binding. This behavior denotes the crossover to the purely dissociative CO binding on the earlier transition metals such as tantalum.

Simulation of field-induced molecular dissociation in atom-probe tomography: Identification of a neutral emission channel

NASA Astrophysics Data System (ADS)

Zanuttini, David; Blum, Ivan; Rigutti, Lorenzo; Vurpillot, François; Douady, Julie; Jacquet, Emmanuelle; Anglade, Pierre-Matthieu; Gervais, Benoit

2017-06-01

We investigate the dynamics of dicationic metal-oxide molecules under large electric-field conditions, on the basis of ab initio calculations coupled to molecular dynamics. Applied to the case of ZnO2 + in the field of atom probe tomography (APT), our simulation reveals the dissociation into three distinct exit channels. The proportions of these channels depend critically on the field strength and on the initial molecular orientation with respect to the field. For typical field strength used in APT experiments, an efficient dissociation channel leads to emission of neutral oxygen atoms, which escape detection. The calculated composition biases and their dependence on the field strength show remarkable consistency with recent APT experiments on ZnO crystals. Our work shows that bond breaking in strong static fields may lead to significant neutral atom production, and therefore to severe elemental composition biases in measurements.

Simultaneous all-optical determination of molecular concentration and extinction coefficient.

PubMed

Cho, Byungmoon; Tiwari, Vivek; Jonas, David M

2013-06-04

Absolute molecular number concentration and extinction coefficient are simultaneously determined from linear and nonlinear spectroscopic measurements. This method is based on measurements of absolute femtosecond pump-probe signals. Accounting for pulse propagation, we present a closed form expression for molecular number concentration in terms of absorbance, fluorescence, absolute pump-probe signal, and laser pulse parameters (pulse energy, spectrum, and spatial intensity profile); all quantities are measured optically. As in gravimetric and coulometric determinations of concentration, no standard samples are needed for calibration. The extinction coefficient can then be determined from the absorbance spectrum and the concentration. For fluorescein in basic methanol, the optically determined molar concentrations and extinction coefficients match gravimetric determinations to within 10% for concentrations from 0.032 to 0.540 mM, corresponding to absorbance from 0.06 to 1. In principle, this photonumeric method is extensible to transient chemical species for which other methods are not available.

Smallest fullerene-like clusters in two-probe device junctions: first principle study

NASA Astrophysics Data System (ADS)

Kaur, Milanpreet; Sawhney, Ravinder Singh; Engles, Derick

2017-07-01

First principle calculations based on density functional theory are realised to investigate the electron transport of the smallest fullerene-like clusters as two-probe junction devices. The junction devices are constructed by mechanically controlled break junction techniques to ensure the maximum stability of the Be20, B20 and N20 cluster molecular junctions. We investigate the density of states, transmission spectrum, molecular orbitals, current and differential conductance characteristics at discrete bias voltages to gain insight about the various transport phenomena occurring in these nano-junctions. The results show that B20 molecule when stringed to gold electrodes works as an ideal nano-device similar to the pure C20 device and is more symmetric in its characteristic nature. However, in N20 molecular device, the conduction is negligible due to the higher atomic interactions within N20 molecule, despite the fact that it is constructed with penta-valent atoms.

Super-quenched Molecular Probe Based on Aggregation-Induced Emission and Photoinduced Electron Transfer Mechanisms for Formaldehyde Detection in Human Serum.

PubMed

Yang, Haitao; Wang, Fujia; Zheng, Jilin; Lin, Hao; Liu, Bin; Tang, Yi-Da; Zhang, Chong-Jing

2018-06-04

Energy transfer between fluorescent dyes and quenchers is widely used in the design of light-up probes. Although dual quenchers are more effective in offering lower background signals and higher turn-on ratios than one quencher, such probes are less explored in practice as they require both quenchers to be within the proximity of the fluorescent core. In this contribution, we utilized intramolecular motion and photoinduced electron transfer (PET) as quenching mechanisms to build super-quenched light-up probes based on fluorogens with aggregation-induced emission. The optimized light-up probe possesses negligible background and is able to detect not only free formaldehyde (FA) but also polymeric FA, with an unprecedented turn-on ratio of >4900. We envision that this novel dual quenching strategy will help to develop various light-up probes for analyte sensing. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Broad spectrum microarray for fingerprint-based bacterial species identification

PubMed Central

2010-01-01

Background Microarrays are powerful tools for DNA-based molecular diagnostics and identification of pathogens. Most target a limited range of organisms and are based on only one or a very few genes for specific identification. Such microarrays are limited to organisms for which specific probes are available, and often have difficulty discriminating closely related taxa. We have developed an alternative broad-spectrum microarray that employs hybridisation fingerprints generated by high-density anonymous markers distributed over the entire genome for identification based on comparison to a reference database. Results A high-density microarray carrying 95,000 unique 13-mer probes was designed. Optimized methods were developed to deliver reproducible hybridisation patterns that enabled confident discrimination of bacteria at the species, subspecies, and strain levels. High correlation coefficients were achieved between replicates. A sub-selection of 12,071 probes, determined by ANOVA and class prediction analysis, enabled the discrimination of all samples in our panel. Mismatch probe hybridisation was observed but was found to have no effect on the discriminatory capacity of our system. Conclusions These results indicate the potential of our genome chip for reliable identification of a wide range of bacterial taxa at the subspecies level without laborious prior sequencing and probe design. With its high resolution capacity, our proof-of-principle chip demonstrates great potential as a tool for molecular diagnostics of broad taxonomic groups. PMID:20163710

A Metabolic Probe-Enabled Strategy Reveals Uptake and Protein Targets of Polyunsaturated Aldehydes in the Diatom Phaeodactylum tricornutum

PubMed Central

Wolfram, Stefanie; Wielsch, Natalie; Hupfer, Yvonne; Mönch, Bettina; Lu-Walther, Hui-Wen; Heintzmann, Rainer; Werz, Oliver; Svatoš, Aleš; Pohnert, Georg

2015-01-01

Diatoms are unicellular algae of crucial importance as they belong to the main primary producers in aquatic ecosystems. Several diatom species produce polyunsaturated aldehydes (PUAs) that have been made responsible for chemically mediated interactions in the plankton. PUA-effects include chemical defense by reducing the reproductive success of grazing copepods, allelochemical activity by interfering with the growth of competing phytoplankton and cell to cell signaling. We applied a PUA-derived molecular probe, based on the biologically highly active 2,4-decadienal, with the aim to reveal protein targets of PUAs and affected metabolic pathways. By using fluorescence microscopy, we observed a substantial uptake of the PUA probe into cells of the diatom Phaeodactylum tricornutum in comparison to the uptake of a structurally closely related control probe based on a saturated aldehyde. The specific uptake motivated a chemoproteomic approach to generate a qualitative inventory of proteins covalently targeted by the α,β,γ,δ-unsaturated aldehyde structure element. Activity-based protein profiling revealed selective covalent modification of target proteins by the PUA probe. Analysis of the labeled proteins gave insights into putative affected molecular functions and biological processes such as photosynthesis including ATP generation and catalytic activity in the Calvin cycle or the pentose phosphate pathway. The mechanism of action of PUAs involves covalent reactions with proteins that may result in protein dysfunction and interference of involved pathways. PMID:26496085

Novel electronic ferroelectricity in an organic charge-order insulator investigated with terahertz-pump optical-probe spectroscopy

PubMed Central

Yamakawa, H.; Miyamoto, T.; Morimoto, T.; Yada, H.; Kinoshita, Y.; Sotome, M.; Kida, N.; Yamamoto, K.; Iwano, K.; Matsumoto, Y.; Watanabe, S.; Shimoi, Y.; Suda, M.; Yamamoto, H. M.; Mori, H.; Okamoto, H.

2016-01-01

In electronic-type ferroelectrics, where dipole moments produced by the variations of electron configurations are aligned, the polarization is expected to be rapidly controlled by electric fields. Such a feature can be used for high-speed electric-switching and memory devices. Electronic-type ferroelectrics include charge degrees of freedom, so that they are sometimes conductive, complicating dielectric measurements. This makes difficult the exploration of electronic-type ferroelectrics and the understanding of their ferroelectric nature. Here, we show unambiguous evidence for electronic ferroelectricity in the charge-order (CO) phase of a prototypical ET-based molecular compound, α-(ET)2I3 (ET:bis(ethylenedithio)tetrathiafulvalene), using a terahertz pulse as an external electric field. Terahertz-pump second-harmonic-generation(SHG)-probe and optical-reflectivity-probe spectroscopy reveal that the ferroelectric polarization originates from intermolecular charge transfers and is inclined 27° from the horizontal CO stripe. These features are qualitatively reproduced by the density-functional-theory calculation. After sub-picosecond polarization modulation by terahertz fields, prominent oscillations appear in the reflectivity but not in the SHG-probe results, suggesting that the CO is coupled with molecular displacements, while the ferroelectricity is electronic in nature. The results presented here demonstrate that terahertz-pump optical-probe spectroscopy is a powerful tool not only for rapidly controlling polarizations, but also for clarifying the mechanisms of ferroelectricity. PMID:26864779

Identifying mechanism-of-action targets for drugs and probes

PubMed Central

Gregori-Puigjané, Elisabet; Setola, Vincent; Hert, Jérôme; Crews, Brenda A.; Irwin, John J.; Lounkine, Eugen; Marnett, Lawrence; Roth, Bryan L.; Shoichet, Brian K.

2012-01-01

Notwithstanding their key roles in therapy and as biological probes, 7% of approved drugs are purported to have no known primary target, and up to 18% lack a well-defined mechanism of action. Using a chemoinformatics approach, we sought to “de-orphanize” drugs that lack primary targets. Surprisingly, targets could be easily predicted for many: Whereas these targets were not known to us nor to the common databases, most could be confirmed by literature search, leaving only 13 Food and Drug Administration—approved drugs with unknown targets; the number of drugs without molecular targets likely is far fewer than reported. The number of worldwide drugs without reasonable molecular targets similarly dropped, from 352 (25%) to 44 (4%). Nevertheless, there remained at least seven drugs for which reasonable mechanism-of-action targets were unknown but could be predicted, including the antitussives clemastine, cloperastine, and nepinalone; the antiemetic benzquinamide; the muscle relaxant cyclobenzaprine; the analgesic nefopam; and the immunomodulator lobenzarit. For each, predicted targets were confirmed experimentally, with affinities within their physiological concentration ranges. Turning this question on its head, we next asked which drugs were specific enough to act as chemical probes. Over 100 drugs met the standard criteria for probes, and 40 did so by more stringent criteria. A chemical information approach to drug-target association can guide therapeutic development and reveal applications to probe biology, a focus of much current interest. PMID:22711801

Novel electronic ferroelectricity in an organic charge-order insulator investigated with terahertz-pump optical-probe spectroscopy.

PubMed

Yamakawa, H; Miyamoto, T; Morimoto, T; Yada, H; Kinoshita, Y; Sotome, M; Kida, N; Yamamoto, K; Iwano, K; Matsumoto, Y; Watanabe, S; Shimoi, Y; Suda, M; Yamamoto, H M; Mori, H; Okamoto, H

2016-02-11

In electronic-type ferroelectrics, where dipole moments produced by the variations of electron configurations are aligned, the polarization is expected to be rapidly controlled by electric fields. Such a feature can be used for high-speed electric-switching and memory devices. Electronic-type ferroelectrics include charge degrees of freedom, so that they are sometimes conductive, complicating dielectric measurements. This makes difficult the exploration of electronic-type ferroelectrics and the understanding of their ferroelectric nature. Here, we show unambiguous evidence for electronic ferroelectricity in the charge-order (CO) phase of a prototypical ET-based molecular compound, α-(ET)2I3 (ET:bis(ethylenedithio)tetrathiafulvalene), using a terahertz pulse as an external electric field. Terahertz-pump second-harmonic-generation(SHG)-probe and optical-reflectivity-probe spectroscopy reveal that the ferroelectric polarization originates from intermolecular charge transfers and is inclined 27° from the horizontal CO stripe. These features are qualitatively reproduced by the density-functional-theory calculation. After sub-picosecond polarization modulation by terahertz fields, prominent oscillations appear in the reflectivity but not in the SHG-probe results, suggesting that the CO is coupled with molecular displacements, while the ferroelectricity is electronic in nature. The results presented here demonstrate that terahertz-pump optical-probe spectroscopy is a powerful tool not only for rapidly controlling polarizations, but also for clarifying the mechanisms of ferroelectricity.

Development of a Photo-Cross-Linkable Diaminoquinazoline Inhibitor for Target Identification in Plasmodium falciparum.

PubMed

Lubin, Alexandra S; Rueda-Zubiaurre, Ainoa; Matthews, Holly; Baumann, Hella; Fisher, Fabio R; Morales-Sanfrutos, Julia; Hadavizadeh, Kate S; Nardella, Flore; Tate, Edward W; Baum, Jake; Scherf, Artur; Fuchter, Matthew J

2018-04-13

Diaminoquinazolines represent a privileged scaffold for antimalarial discovery, including use as putative Plasmodium histone lysine methyltransferase inhibitors. Despite this, robust evidence for their molecular targets is lacking. Here we report the design and development of a small-molecule photo-cross-linkable probe to investigate the targets of our diaminoquinazoline series. We demonstrate the effectiveness of our designed probe for photoaffinity labeling of Plasmodium lysates and identify similarities between the target profiles of the probe and the representative diaminoquinazoline BIX-01294. Initial pull-down proteomics experiments identified 104 proteins from different classes, many of which are essential, highlighting the suitability of the developed probe as a valuable tool for target identification in Plasmodium falciparum.

Photoinduced molecular chirality probed by ultrafast resonant X-ray spectroscopy

DOE PAGES

Rouxel, Jérémy R.; Kowalewski, Markus; Mukamel, Shaul

2017-07-01

Recently developed circularly polarized X-ray light sources can probe the ultrafast chiral electronic and nuclear dynamics through spatially localized resonant core transitions. Here, we present simulations of time-resolved circular dichroism signals given by the difference of left and right circularly polarized X-ray probe transmission following an excitation by a circularly polarized optical pump with the variable time delay. Application is made to formamide which is achiral in the ground state and assumes two chiral geometries upon optical excitation to the first valence excited state. Probes resonant with various K-edges (C, N, and O) provide different local windows onto the paritymore » breaking geometry change thus revealing the enantiomer asymmetry.« less

Selective interactions of trivalent cations Fe³⁺, Al³⁺ and Cr³⁺ turn on fluorescence in a naphthalimide based single molecular probe.

PubMed

Janakipriya, Subramaniyan; Chereddy, Narendra Reddy; Korrapati, Purnasai; Thennarasu, Sathiah; Mandal, Asit Baran

2016-01-15

Synthesis and fluorescence turn-on behavior of a naphthalimide based probe is described. Selective interactions of trivalent cations Fe(3+), Al(3+) or Cr(3+) with probe 1 inhibit the PET operating in the probe, and thereby, permit the detection of these trivalent cations present in aqueous samples and live cells. Failure of other trivalent cations (Eu(3+), Gd(3+) and Nb(3+)) to inhibit the PET process in 1 demonstrates the role of chelating ring size vis-à-vis ionic radius in the selective recognition of specific metal ions. Copyright © 2015 Elsevier B.V. All rights reserved.

Photoinduced molecular chirality probed by ultrafast resonant X-ray spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rouxel, Jérémy R.; Kowalewski, Markus; Mukamel, Shaul

Recently developed circularly polarized X-ray light sources can probe the ultrafast chiral electronic and nuclear dynamics through spatially localized resonant core transitions. Here, we present simulations of time-resolved circular dichroism signals given by the difference of left and right circularly polarized X-ray probe transmission following an excitation by a circularly polarized optical pump with the variable time delay. Application is made to formamide which is achiral in the ground state and assumes two chiral geometries upon optical excitation to the first valence excited state. Probes resonant with various K-edges (C, N, and O) provide different local windows onto the paritymore » breaking geometry change thus revealing the enantiomer asymmetry.« less

Metabolism of Endosulfan-Alpha by Human Liver Microsomes and its Utility as a Simultaneous In Vitro Probe for CYP2B6 and CYP3A4

DTIC Science & Technology

2006-03-30

METABOLISM OF ENDOSULFAN-ALPHA BY HUMAN LIVER MICROSOMES AND ITS UTILITY AS A SIMULTANEOUS IN VITRO PROBE FOR CYP2B6 AND CYP3A4 Richard C.T. Casabar...MICROSOMES AND ITS UTILITY AS A SIMULTANEOUS IN VITRO PROBE FOR CYP2B6 AND CYP3A4 Corresponding Author: Randy L. Rose Department of Environmental and Molecular...ALPHA BY HUMAN LIVER MICROSOMES AND ITS UTILITY AS A SIMULTANEOUS IN VITRO PROBE FOR CYP2B6 AND CYP3A4 . 6. AUTHOR(S) CAPT CASABAR RICHARD C 7

Development of Functional Fluorescent Molecular Probes for the Detection of Biological Substances

PubMed Central

Suzuki, Yoshio; Yokoyama, Kenji

2015-01-01

This review is confined to sensors that use fluorescence to transmit biochemical information. Fluorescence is, by far, the most frequently exploited phenomenon for chemical sensors and biosensors. Parameters that define the application of such sensors include intensity, decay time, anisotropy, quenching efficiency, and luminescence energy transfer. To achieve selective (bio)molecular recognition based on these fluorescence phenomena, various fluorescent elements such as small organic molecules, enzymes, antibodies, and oligonucleotides have been designed and synthesized over the past decades. This review describes the immense variety of fluorescent probes that have been designed for the recognitions of ions, small and large molecules, and their biological applications in terms of intracellular fluorescent imaging techniques. PMID:26095660

Non-invasive optical modulation of local vascular permeability

NASA Astrophysics Data System (ADS)

Choi, Myunghwan; Choi, Chulhee

2011-03-01

For a systemically administered drug to act, it first needs to cross the vascular wall. This step represents a bottleneck for drug development, especially in the brain or retina, where tight junctions between endothelial cells form physiological barriers. Here, we demonstrate that femtosecond pulsed laser irradiation focused on the blood vessel wall induces transient permeabilization of plasma. Nonlinear absorption of the pulsed laser enabled the noninvasive modulation of vascular permeability with high spatial selectivity in three dimensions. By combining this method with systemic injection, we could locally deliver molecular probes in various tissues, such as brain cortex, meninges, ear, striated muscle, and bone. We suggest this method as a novel delivery tool for molecular probes or drugs.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuramochi, Hikaru; Takeuchi, Satoshi; Tahara, Tahei, E-mail: tahei@riken.jp

We describe details of the setup for time-resolved impulsive stimulated Raman spectroscopy (TR-ISRS). In this method, snapshot molecular vibrational spectra of the photoreaction transients are captured via time-domain Raman probing using ultrashort pulses. Our instrument features transform-limited sub-7-fs pulses to impulsively excite and probe coherent nuclear wavepacket motions, allowing us to observe vibrational fingerprints of transient species from the terahertz to 3000-cm{sup −1} region with high sensitivity. Key optical components for the best spectroscopic performance are discussed. The TR-ISRS measurements for the excited states of diphenylacetylene in cyclohexane are demonstrated, highlighting the capability of our setup to track femtosecond dynamicsmore » of all the Raman-active fundamental molecular vibrations.« less

Molecular level studies on interfacial hydration of zwitterionic and other antifouling polymers in situ.

PubMed

Leng, Chuan; Sun, Shuwen; Zhang, Kexin; Jiang, Shaoyi; Chen, Zhan

2016-08-01

Antifouling polymers have wide applications in biomedical engineering and marine industry. Recently, zwitterionic materials have been reported as promising candidates for antifouling applications, while strong hydration is believed to be the key antifouling mechanism. Zwitterionic materials can be designed with various molecular structures, which affect their hydration and antifouling performance. Although strong hydration has been proposed to occur at the material surfaces, probing the solid material/water interfaces is challenging with traditional analytical techniques. Here in this review, we will review our studies on surface hydration of zwitterionic materials and other antifouling materials by using sum frequency generation (SFG) vibrational spectroscopy, which provides molecular understanding of the water structures at various material surfaces. The materials studied include zwitterionic polymer brushes with different molecular structures, amphiphilic polymers with zwitterionic groups, uncharged hydrophilic polymer brushes, amphiphilic polypeptoids, and widely used antifouling material poly(ethylene glycol). We will compare the differences among zwitterionic materials with various molecular structures as well as the differences between antifouling materials and fouling surfaces of control samples. We will also discuss the effects of pH and biological molecules like proteins on the surface hydration of the zwitterionic materials. Using SFG spectroscopy, we have measured the hydration layers of antifouling materials and found that strong hydrogen bonds are key to the formation of strong hydration layers preventing protein fouling at the polymer interfaces. Antifouling polymers have wide applications in biomedical engineering and marine industry. Recently, zwitterionic materials have been reported as promising candidates for antifouling applications, while strong hydration is believed to be the key antifouling mechanism. However, zwitterionic materials can be designed with various molecular structures, which affect their hydration and antifouling performance. Moreover, although strong hydration has been proposed to occur at the material surfaces, probing the solid material/water interfaces is challenging with traditional analytical techniques. Here in this manuscript, we will review our studies on surface hydration of zwitterionic materials and other antifouling materials by using sum frequency generation (SFG) vibrational spectroscopy, which provides molecular understanding of the water structures at various material surfaces. The materials studied include zwitterionic polymer brushes with different molecular structures, amphiphilic polymers with zwitterionic groups, uncharged hydrophilic polymer brushes, amphiphilic polypeptoids, and widely used antifouling material poly(ethylene glycol). We will compare the differences among zwitterionic materials with various molecular structures as well as the differences between antifouling materials and fouling surfaces of control samples. We will also discuss the effects of pH and biological molecules like proteins on the surface hydration of the zwitterionic materials. All the SFG results indicate that strongly hydrogen-bonded water at the materials' surfaces (strong surface hydration) is closely correlated to the good antifouling properties of the materials. This review will be widely interested by readers of Acta Biomaterialia and will impact many different research fields in chemistry, materials, engineering, and beyond. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

OCaPPI-Db: an oligonucleotide probe database for pathogen identification through hybridization capture.

PubMed

Gasc, Cyrielle; Constantin, Antony; Jaziri, Faouzi; Peyret, Pierre

2017-01-01

The detection and identification of bacterial pathogens involved in acts of bio- and agroterrorism are essential to avoid pathogen dispersal in the environment and propagation within the population. Conventional molecular methods, such as PCR amplification, DNA microarrays or shotgun sequencing, are subject to various limitations when assessing environmental samples, which can lead to inaccurate findings. We developed a hybridization capture strategy that uses a set of oligonucleotide probes to target and enrich biomarkers of interest in environmental samples. Here, we present Oligonucleotide Capture Probes for Pathogen Identification Database (OCaPPI-Db), an online capture probe database containing a set of 1,685 oligonucleotide probes allowing for the detection and identification of 30 biothreat agents up to the species level. This probe set can be used in its entirety as a comprehensive diagnostic tool or can be restricted to a set of probes targeting a specific pathogen or virulence factor according to the user's needs. : http://ocappidb.uca.works. © The Author(s) 2017. Published by Oxford University Press.

Sensitive determination of endogenous hydroxyl radical in live cell by a BODIPY based fluorescent probe.

PubMed

Lei, Kepeng; Sun, Mingtai; Du, Libo; Zhang, Xiaojie; Yu, Huan; Wang, Suhua; Hayat, Tasawar; Alsaedi, Ahmed

2017-08-01

The sensitive and selective fluorescence probe for hydroxyl radical analysis is of significance because hydroxyl radical plays key roles in many physiological and pathological processes. In this work, a novel organic fluorescence molecular probe OHP for hydroxyl radical is synthesized by a two-step route. The probe employs 4-bora-3a,4a-diaza-s-indacene (difluoroboron dipyrromethene, BODIPY) as the fluorophore and possesses relatively high fluorescence quantum yields (77.14%). Hydroxyl radical can rapidly react with the probe and quench the fluorescence in a good linear relationship (R 2 =0.9967). The limit of detection is determined to be as low as 11nM. In addition, it has been demonstrated that the probe has a good stability against pH and light illumination, low cytotoxicity and high biocompatibility. Cell culture experimental results show that the probe OHP is sensitive and selective for imaging and tracking endogenous hydroxyl radical in live cells. Copyright © 2017 Elsevier B.V. All rights reserved.

SU-E-T-610: Phosphor-Based Fiber Optic Probes for Proton Beam Characterization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Darafsheh, A; Soldner, A; Liu, H

2015-06-15

Purpose: To investigate feasibility of using fiber optics probes with rare-earth-based phosphor tips for proton beam radiation dosimetry. We designed and fabricated a fiber probe with submillimeter resolution (<0.5 mm3) based on TbF3 phosphors and evaluated its performance for measurement of proton beam including profiles and range. Methods: The fiber optic probe with TbF3 phosphor tip, embedded in tissue-mimicking phantoms was irradiated with double scattering proton beam with energy of 180 MeV. Luminescence spectroscopy was performed by a CCD-coupled spectrograph to analyze the emission spectra of the fiber tip. In order to measure the spatial beam profile and percentage depthmore » dose, we used singular value decomposition method to spectrally separate the phosphors ionoluminescence signal from the background Cerenkov radiation signal. Results: The spectra of the TbF3 fiber probe showed characteristic ionoluminescence emission peaks at 489, 542, 586, and 620 nm. By using singular value decomposition we found the contribution of the ionoluminescence signal to measure the percentage depth dose in phantoms and compared that with measurements performed with ion chamber. We observed quenching effect at the spread out Bragg peak region, manifested as under-responding of the signal, due to the high LET of the beam. However, the beam profiles were not dramatically affected by the quenching effect. Conclusion: We have evaluated the performance of a fiber optic probe with submillimeter resolution for proton beam dosimetry. We demonstrated feasibility of spectral separation of the Cerenkov radiation from the collected signal. Such fiber probes can be used for measurements of proton beams profile and range. The experimental apparatus and spectroscopy method developed in this work provide a robust platform for characterization of proton-irradiated nanophosphor particles for ultralow fluence photodynamic therapy or molecular imaging applications.« less

Development of a new bioactivatable fluorescent probe for quantification of apolipoprotein A-I proteolytic degradation in vitro and in vivo.

PubMed

Maafi, Foued; Li, Baoqiang; Gebhard, Catherine; Brodeur, Mathieu R; Nachar, Walid; Villeneuve, Louis; Lesage, Frédéric; Rhainds, David; Rhéaume, Eric; Tardif, Jean-Claude

2017-03-01

The potential benefits of high-density lipoproteins (HDL) against atherosclerosis are attributed to its major protein component, apolipoprotein A-I (apoA-I). Most of the apoA-I in the vascular wall appears to be in its lipid-poor form. The latter, however, is subjected to degradation by proteases localized in atherosclerotic plaques, which, in turn, has been shown to negatively impact its atheroprotective functions. Here, we report the development and in vivo use of a bioactivatable near-infrared full-length apoA-I-Cy5.5 fluorescent probe for the assessment of apoA-I-degrading proteolytic activities. Fluorescence quenching was obtained by saturation of Cy5.5 fluorophore molecules on apoA-I protein. ApoA-I cleavage led to near-infrared fluorescence enhancement. In vitro proteolysis of the apoA-I probe by a variety of proteases including serine, cysteine, and metalloproteases resulted in an up to 11-fold increase in fluorescence (n = 5, p ≤ 0.05). We detected activation of the probe in atherosclerotic mice aorta sections using in situ zymography and showed that broad-spectrum protease inhibitors protected the probe from degradation, resulting in decreased fluorescence (-54%, n = 6 per group, p ≤ 0.0001). In vivo, the injected probe showed stronger fluorescence emission in the aorta of human apoB transgenic Ldlr - /- atherosclerotic mice (ATX) as compared to wild-type mice. In vivo observations were confirmed by ex vivo aorta imaging quantification where a 10-fold increase in fluorescent signal in ATX mice (p ≤ 0.05 vs. control mice) was observed. The use of this probe in different applications may help to assess new molecular mechanisms of atherosclerosis and may improve current HDL-based therapies by enhancing apoA-I functionality. Copyright © 2017 Elsevier B.V. All rights reserved.

Ultrafast High Harmonic, Soft X-Ray Probing of Molecular Dynamics

DTIC Science & Technology

2013-04-30

590 L/s scroll pump and a titanium sublimation pump . A TOF-PES has been designed and constructed to analyze the energy of the photoelectrons...are studied using the quasi-continuous vacuum ultraviolet light of the Advanced Light Source at Lawrence Berkeley National Laboratory. The molecular...34), the method of high order harmonic generation of ultrashort vacuum ultraviolet pulses was used to investigate molecular photodissociation, ultrafast

Large-Area, Ensemble Molecular Electronics: Motivation and Challenges.

PubMed

Vilan, Ayelet; Aswal, Dinesh; Cahen, David

2017-03-08

We review charge transport across molecular monolayers, which is central to molecular electronics (MolEl), using large-area junctions (NmJ). We strive to provide a wide conceptual overview of three main subtopics. First, a broad introduction places NmJ in perspective to related fields of research and to single-molecule junctions (1mJ) in addition to a brief historical account. As charge transport presents an ultrasensitive probe for the electronic perfection of interfaces, in the second part ways to form both the monolayer and the contacts are described to construct reliable, defect-free interfaces. The last part is dedicated to understanding and analyses of current-voltage (I-V) traces across molecular junctions. Notwithstanding the original motivation of MolEl, I-V traces are often not very sensitive to molecular details and then provide a poor probe for chemical information. Instead, we focus on how to analyze the net electrical performance of molecular junctions, from a functional device perspective. Finally, we point to creation of a built-in electric field as a key to achieve functionality, including nonlinear current-voltage characteristics that originate in the molecules or their contacts to the electrodes. This review is complemented by a another review that covers metal-molecule-semiconductor junctions and their unique hybrid effects.

Reproducibility of the cutoff probe for the measurement of electron density

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, D. W.; Oh, W. Y.; You, S. J., E-mail: sjyou@cnu.ac.kr

2016-06-15

Since a plasma processing control based on plasma diagnostics attracted considerable attention in industry, the reproducibility of the diagnostics using in this application has become a great interest. Because the cutoff probe is one of the potential candidates for this application, knowing the reproducibility of the cutoff probe measurement becomes quit important in the cutoff probe application research. To test the reproducibility of the cutoff probe measurement, in this paper, a comparative study among the different cutoff probe measurements was performed. The comparative study revealed remarkable result: the cutoff probe has a great reproducibility for the electron density measurement, i.e.,more » there are little differences among measurements by different probes made by different experimenters. The discussion including the reason for the result was addressed via this paper by using a basic measurement principle of cutoff probe and a comparative experiment with Langmuir probe.« less

Molecular imprinted polymer-coated optical fiber sensor for the identification of low molecular weight molecules.

PubMed

Lépinay, Sandrine; Ianoul, Anatoli; Albert, Jacques

2014-10-01

A biomimetic optical probe for detecting low molecular weight molecules (maltol, 3-hydroxy-2-methyl-4H-pyran-4-one, molecular weight of 126.11 g/mol), was designed, fabricated, and characterized. The sensor couples a molecular imprinted polymer (MIP) and the Bragg grating refractometry technology into an optical fiber. The probe is fabricated first by inscribing tilted grating planes in the core of the fiber, and then by photopolymerization to immobilize a maltol imprinted MIP on the fiber cladding surface over the Bragg grating. The sensor response to the presence of maltol in different media is obtained by spectral interrogation of the fiber transmission signal. The results showed that the limit of detection of the sensor reached 1 ng/mL in pure water with a sensitivity of 6.3 × 10(8)pm/M. The selectivity of the sensor against other compounds and its reusability were also studied experimentally. Finally, the unambiguous detection of concentrations as little as 10nM of maltol in complex media (real food samples) by the MIP-coated tilted fiber Bragg grating sensor was demonstrated. Copyright © 2014 Elsevier B.V. All rights reserved.

Red Fluorescent Line Emission from Hydrogen Molecules in Diffuse Molecular Clouds

NASA Technical Reports Server (NTRS)

Neufeld, David A.; Spaans, Marco

1996-01-01

We have modeled the fluorescent pumping of electronic and vibrational emissions of molecular hydrogen (H2) within diffuse molecular clouds that are illuminated by ultraviolet continuum radiation. Fluorescent line intensities are predicted for transitions at ultraviolet, infrared, and red visible wavelengths as functions of the gas density, the visual extinction through the cloud, and the intensity of the incident UV continuum radiation. The observed intensity in each fluorescent transition is roughly proportional to the integrated rate of H2 photodissociation along the line of sight. Although the most luminous fluorescent emissions detectable from ground-based observatories lie at near-infrared wavelengths, we argue that the lower sky brightness at visible wavelengths makes the red fluorescent transitions a particularly sensitive probe. Fabry-Perot spectrographs of the type that have been designed to observe very faint diffuse Ha emissions are soon expected to yield sensitivities that will be adequate to detect H2 vibrational emissions from molecular clouds that are exposed to ultraviolet radiation no stronger than the mean radiation field within the Galaxy. Observations of red H2 fluorescent emission together with cospatial 21 cm H I observations could serve as a valuable probe of the gas density in diffuse molecular clouds.

Investigating buried polymer interfaces using sum frequency generation vibrational spectroscopy

PubMed Central

Chen, Zhan

2010-01-01

This paper reviews recent progress in the studies of buried polymer interfaces using sum frequency generation (SFG) vibrational spectroscopy. Both buried solid/liquid and solid/solid interfaces involving polymeric materials are discussed. SFG studies of polymer/water interfaces show that different polymers exhibit varied surface restructuring behavior in water, indicating the importance of probing polymer/water interfaces in situ. SFG has also been applied to the investigation of interfaces between polymers and other liquids. It has been found that molecular interactions at such polymer/liquid interfaces dictate interfacial polymer structures. The molecular structures of silane molecules, which are widely used as adhesion promoters, have been investigated using SFG at buried polymer/silane and polymer/polymer interfaces, providing molecular-level understanding of polymer adhesion promotion. The molecular structures of polymer/solid interfaces have been examined using SFG with several different experimental geometries. These results have provided molecular-level information about polymer friction, adhesion, interfacial chemical reactions, interfacial electronic properties, and the structure of layer-by-layer deposited polymers. Such research has demonstrated that SFG is a powerful tool to probe buried interfaces involving polymeric materials, which are difficult to study by conventional surface sensitive analytical techniques. PMID:21113334

Comparing Cognitive Interviewing and Online Probing: Do They Find Similar Results?

ERIC Educational Resources Information Center

Meitinger, Katharina; Behr, Dorothée

2016-01-01

This study compares the application of probing techniques in cognitive interviewing (CI) and online probing (OP). Even though the probing is similar, the methods differ regarding typical mode setting, sample size, level of interactivity, and goals. We analyzed probing answers to the International Social Survey Programme item battery on specific…

Preparation and quality test of superparamagnetic iron oxide labeled antisense oligodeoxynucleotide probe: a preliminary study.

PubMed

Wen, Ming; Li, Bibo; Ouyang, Yu; Luo, Yi; Li, Shaolin

2009-06-01

Molecular imaging of tumor antisense gene techniques have been applied to the study of magnetic resonance (MR) gene imaging associated with malignant tumors. In this study, we designed, synthesized, and tested a novel molecular probe, in which the antisense oligodeoxynucleotide (ASODN) was labeled with superparamagnetic iron oxide (SPIO), and its efficiency was examined by in vitro MR imaging after SK-Br-3 mammary carcinoma cell lines (oncocytes) transfection. The SPIO-labeled ASODN probe was prepared through SPIO conjugated to ASODN using a chemical cross linking method. Its morphology and size were detected by atomic force microscope, size distribution were detected by laser granulometer, the conjugating rate and biological activity were determined by high performance liquid chromatography, and the stability was determined by polyacrylamide gel electrophoresis. After that, the probes were transfected into the SK-Br-3 oncocytes, cellular iron uptake was analyzed qualitatively at light and electron microscopy and was quantified at atomic absorption spectrometry, and the signal change of the transfected cells was observed and measured using MR imaging. The morphology of the SPIO-labeled ASODN probe was mostly spherical with well-distributed scattering, and the diameters were between 25 and 40 nm (95%) by atomic force microscope and laser granulometer, the conjugating rate of the probe was 99%. Moreover, this probe kept its activity under physiological conditions and could conjugate with antisense oligodeoxynucleotide. In addition, light microscopy revealed an intracellular uptake of iron oxides in the cytosol and electron microscopic studies revealed a lysosomal deposition of iron oxides in the transfected SK-Br-3 oncocytes by antisense probes, some of them gathered stacks, and the iron content of the group of transfected SK-Br-3 oncocytes by antisense probe is significantly higher (18.37 +/- 0.42 pg) than other contrast groups, the MR imaging showed that transfected SK-Br-3 oncocytes by antisense probe had the lowest signal of all. The SPIO-labeled ASODN probe shows unique features including well-distributed spherical morphology, high conjugating rate and loading efficiency, and the signal intensity of SPIO-labeled ASODN-transfected SK-Br-3 oncocytes is reduced in MR imaging. These results indicate that the SPIO-labeled ASODN probe is potentially useful as a MR targeting contrast enhancing agent to specifically diagnose tumors which had over-expression of the c-erbB2 oncogene at an early stage.

Precise Orientation of a Single C60 Molecule on the Tip of a Scanning Probe Microscope

NASA Astrophysics Data System (ADS)

Chiutu, C.; Sweetman, A. M.; Lakin, A. J.; Stannard, A.; Jarvis, S.; Kantorovich, L.; Dunn, J. L.; Moriarty, P.

2012-06-01

We show that the precise orientation of a C60 molecule which terminates the tip of a scanning probe microscope can be determined with atomic precision from submolecular contrast images of the fullerene cage. A comparison of experimental scanning tunneling microscopy data with images simulated using computationally inexpensive Hückel theory provides a robust method of identifying molecular rotation and tilt at the end of the probe microscope tip. Noncontact atomic force microscopy resolves the atoms of the C60 cage closest to the surface for a range of molecular orientations at tip-sample separations where the molecule-substrate interaction potential is weakly attractive. Measurements of the C60C60 pair potential acquired using a fullerene-terminated tip are in excellent agreement with theoretical predictions based on a pairwise summation of the van der Waals interactions between C atoms in each cage, i.e., the Girifalco potential [L. Girifalco, J. Phys. Chem. 95, 5370 (1991)JPCHAX0022-365410.1021/j100167a002].

Towards non-invasive diagnostic imaging of early-stage Alzheimer's disease

NASA Astrophysics Data System (ADS)

Viola, Kirsten L.; Sbarboro, James; Sureka, Ruchi; de, Mrinmoy; Bicca, Maíra A.; Wang, Jane; Vasavada, Shaleen; Satpathy, Sreyesh; Wu, Summer; Joshi, Hrushikesh; Velasco, Pauline T.; Macrenaris, Keith; Waters, E. Alex; Lu, Chang; Phan, Joseph; Lacor, Pascale; Prasad, Pottumarthi; Dravid, Vinayak P.; Klein, William L.

2015-01-01

One way to image the molecular pathology in Alzheimer's disease is by positron emission tomography using probes that target amyloid fibrils. However, these fibrils are not closely linked to the development of the disease. It is now thought that early-stage biomarkers that instigate memory loss are composed of Aβ oligomers. Here, we report a sensitive molecular magnetic resonance imaging contrast probe that is specific for Aβ oligomers. We attach oligomer-specific antibodies onto magnetic nanostructures and show that the complex is stable and binds to Aβ oligomers on cells and brain tissues to give a magnetic resonance imaging signal. When intranasally administered to an Alzheimer's disease mouse model, the probe readily reached hippocampal Aβ oligomers. In isolated samples of human brain tissue, we observed a magnetic resonance imaging signal that distinguished Alzheimer's disease from controls. Such nanostructures that target neurotoxic Aβ oligomers are potentially useful for evaluating the efficacy of new drugs and ultimately for early-stage Alzheimer's disease diagnosis and disease management.

Two-Photon Optical Properties of Near-Infrared Dyes at 1.55 microns Excitation

PubMed Central

Berezin, Mikhail; Zhan, Chun; Lee, Hyeran; Joo, Chulmin; Akers, Walter; Yazdanfar, Siavash; Achilefu, Samuel

2011-01-01

Two-photon (2P) optical properties of cyanine dyes were evaluated using a 2P fluorescence spectrophotometer with 1.55 μm excitation. We report the 2P characteristics of common NIR polymethine dyes, including their 2P action cross-sections and the 2P excited fluorescence lifetime. One of the dyes, DTTC showed the highest 2P action cross-section (~103 ± 19 GM) and relatively high 2P excited fluorescence lifetime and can be used as a scaffold for the synthesis of 2P molecular imaging probes. The 2P action cross-section of DTTC and the lifetime were also highly sensitive to the solvent polarity, providing other additional parameters for its use in optical imaging and the mechanism for probing environmental factors Overall, this study demonstrated the quantitative measurement of 2P properties of NIR dyes and established the foundation for designing molecular probes for 2P imaging applications in the NIR region. PMID:21866928

Controlling the femtosecond laser-driven transformation of dicyclopentadiene into cyclopentadiene

PubMed Central

Goswami, Tapas; Das, Dipak K.; Goswami, Debabrata

2013-01-01

Dynamics of the chemical transformation of dicyclopentadiene into cyclopentadiene in a supersonic molecular beam is elucidated using femtosecond time-resolved degenerate pump–probe mass spectrometry. Control of this ultrafast chemical reaction is achieved by using linearly chirped frequency modulated pulses. We show that negatively chirped femtosecond laser pulses enhance the cyclopentadiene photoproduct yield by an order of magnitude as compared to that of the unmodulated or the positively chirped pulses. This demonstrates that the phase structure of femtosecond laser pulse plays an important role in determining the outcome of a chemical reaction. PMID:24098059

Rapid spectro-polarimetry to probe molecular symmetry in multiplex coherent anti-Stokes Raman scattering.

PubMed

Würthwein, Thomas; Brinkmann, Maximilian; Hellwig, Tim; Fallnich, Carsten

2017-11-21

We present the simultaneous detection of the spectrum and the complete polarization state of a multiplex coherent anti-Stokes Raman scattering signal with a fast division-of-amplitude spectro-polarimeter. The spectro-polarimeter is based on a commercial imaging spectrograph, a birefringent wedge prism, and a segmented polarizer. Compared to the standard rotating-retarder fixed-analyzer spectro-polarimeter, only a single measurement is required and an up to 21-fold reduced acquisition time is shown. The measured Stokes parameters allow us to differentiate between vibrational symmetries and to determine the depolarization ratio ρ by data post-processing.

C3H2 observations as a diagnostic probe for molecular clouds

NASA Technical Reports Server (NTRS)

Avery, L. W.

1986-01-01

Recently the three-membered ring molecule, cyclopropenylidene, C3H2, has been identified in the laboratory and detected in molecular clouds by Thaddeus, Vrtilek and Gottlieb (1985). This molecule is wide-spread throughout the Galaxy and has been detected in 25 separate sources including cold dust clouds, circumstellar envelopes, HII regions, and the spiral arms observed against the Cas supernova remnant. In order to evaluate the potential of C3H2 as a diagnostic probe for molecular clouds, and to attempt to identify the most useful transitions, statistical equilibrium calculations were carried out for the lowest 24 levels of the ortho species and the lowest 10 levels of the para species. Many of the sources observed by Matthews and Irvine (1985) show evidence of being optically thick in the 1(10)-1(01) line. Consequently, the effects of radiative trapping should be incorporated into the equilibrium calculations. This was done using the Large Velocity Gradient approximation for a spherical cloud of uniform density. Some results of the calculations for T(K)=10K are given. Figures are presented which show contours of the logarithm of the ratio of peak line brightness temperatures for ortho-para pairs of lines at similar frequencies. It appears that the widespread nature of C3H2, the relatively large strength of its spectral lines, and their sensitivity to density and molecular abundance combine to make this a useful molecule for probing physical conditions in molecular clouds. The 1(10)-1(01) and 2(20)-2(11) K-band lines may be especially useful in this regard because of the ease with which they are observed and their unusual density-dependent emission/absorption properties.

Microscopic Analysis of Corn Fiber Using Corn Starch- and Cellulose-Specific Molecular Probes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Porter, S. E.; Donohoe, B. S.; Beery, K. E.

Ethanol is the primary liquid transportation fuel produced from renewable feedstocks in the United States today. The majority of corn grain, the primary feedstock for ethanol production, has been historically processed in wet mills yielding products such as gluten feed, gluten meal, starch, and germ. Starch extracted from the grain is used to produce ethanol in saccharification and fermentation steps; however the extraction of starch is not 100% efficient. To better understand starch extraction during the wet milling process, we have developed fluorescent probes that can be used to visually localize starch and cellulose in samples using confocal microscopy. Thesemore » probes are based on the binding specificities of two types of carbohydrate binding modules (CBMs), which are small substrate-specific protein domains derived from carbohydrate degrading enzymes. CBMs were fused, using molecular cloning techniques, to a green fluorescent protein (GFP) or to the red fluorescent protein DsRed (RFP). Using these engineered probes, we found that the binding of the starch-specific probe correlates with starch content in corn fiber samples. We also demonstrate that there is starch internally localized in the endosperm that may contribute to the high starch content in corn fiber. We also surprisingly found that the cellulose-specific probe did not bind to most corn fiber samples, but only to corn fiber that had been hydrolyzed using a thermochemical process that removes the residual starch and much of the hemicellulose. Our findings should be of interest to those working to increase the efficiency of the corn grain to ethanol process.« less

A new class of fast-response and highly selective fluorescent probes for visualizing peroxynitrite in live cells, subcellular organelles, and kidney tissue of diabetic rats.

PubMed

Miao, Junfeng; Huo, Yingying; Liu, Qian; Li, Zhe; Shi, Heping; Shi, Yawei; Guo, Wei

2016-11-01

Peroxynitrite (ONOO(-)) is an extremely powerful oxidant in biological systems, and can react with a wide variety of molecular targets including proteins, lipids, and nucleic acids, eventually resulting in a series of disease states such as diabetes, Alzheimer's disease, cancer, arthritis, autoimmune, and other disorders. In this work, we present a new class of ONOO(-) fluorescent probes by exploiting the ONOO(-)-triggered N-oxidation and N-nitrosation reactions of aromatic tertiary amine for the first time. The as-obtained fluorescent probe A2 could detect ONOO(-) with quite fast fluorescence off-on response (within seconds), ultrasensitivity (detection limit: <2 nM), and excellent selectivity over a series of biologically relevant reactive oxygen species as well as metal cations. With the probe, the endogenous ONOO(-) in activated RAW264.7 murine macrophage, EA.hy926 endothelial cells after oxygen glucose deprivation and reoxygenation (OGD/RO), and kidney tissue of diabetic rats has been successfully visualized. Based on the molecular platform of A2, we further develop its mitochondria- and lysosome-targetable fluorescent probes Mito-A2 and Lyso-A2 by installing the corresponding targeting groups to alkoxy unit of A2, and confirm their abilities to image ONOO(-) in mitochondria and lysosomes, respectively, by co-localization assays. It is greatly expected that these probes can serve as useful imaging tools for clarifying the distribution and pathophysiological functions of ONOO(-) in cells, subcellular organelles, and animal tissues. Copyright © 2016 Elsevier Ltd. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prabhakaran, Venkateshkumar; Johnson, Grant E.; Wang, Bingbing

Molecular-level understanding of electrochemical processes occurring at electrode-electrolyte interfaces (EEI) is key to the rational development of high-performance and sustainable electrochemical technologies. This article reports the development and first application of solid-state in situ electrochemical probes to study redox and catalytic processes occurring at well-defined EEI generated using soft-landing of mass- and charge-selected cluster ions (SL). In situ electrochemical probes with excellent mass transfer properties are fabricated using carefully-designed nanoporous ionic liquid membranes. SL enables deposition of pure active species that are not obtainable with other techniques onto electrode surfaces with precise control over charge state, composition, and kinetic energy.more » SL is, therefore, a unique tool for studying fundamental processes occurring at EEI. For the first time using an aprotic electrochemical probe, the effect of charge state (PMo12O403-/2-) and the contribution of building blocks of Keggin polyoxometalate (POM) clusters to redox processes are characterized by populating EEI with novel POM anions generated by electrospray ionization and gas phase dissociation. Additionally, a proton conducting electrochemical probe has been developed to characterize the reactive electrochemistry (oxygen reduction activity) of bare Pt clusters (Pt40 ~1 nm diameter), thus demonstrating the capability of the probe for studying reactions in controlled gaseous environments. The newly developed in situ electrochemical probes combined with ion SL provide a versatile method to characterize the EEI in solid-state redox systems and reactive electrochemistry at precisely-defined conditions. This capability will advance molecular-level understanding of processes occurring at EEI that are critical to many energy-related technologies.« less

Ultrafast Structural Dynamics in Combustion Relevant Model Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weber, Peter M.

2014-03-31

The research project explored the time resolved structural dynamics of important model reaction system using an array of novel methods that were developed specifically for this purpose. They include time resolved electron diffraction, time resolved relativistic electron diffraction, and time resolved Rydberg fingerprint spectroscopy. Toward the end of the funding period, we also developed time-resolved x-ray diffraction, which uses ultrafast x-ray pulses at LCLS. Those experiments are just now blossoming, as the funding period expired. In the following, the time resolved Rydberg Fingerprint Spectroscopy is discussed in some detail, as it has been a very productive method. The binding energymore » of an electron in a Rydberg state, that is, the energy difference between the Rydberg level and the ground state of the molecular ion, has been found to be a uniquely powerful tool to characterize the molecular structure. To rationalize the structure sensitivity we invoke a picture from electron diffraction: when it passes the molecular ion core, the Rydberg electron experiences a phase shift compared to an electron in a hydrogen atom. This phase shift requires an adjustment of the binding energy of the electron, which is measurable. As in electron diffraction, the phase shift depends on the molecular, geometrical structure, so that a measurement of the electron binding energy can be interpreted as a measurement of the molecule’s structure. Building on this insight, we have developed a structurally sensitive spectroscopy: the molecule is first elevated to the Rydberg state, and the binding energy is then measured using photoelectron spectroscopy. The molecule’s structure is read out as the binding energy spectrum. Since the photoionization can be done with ultrafast laser pulses, the technique is inherently capable of a time resolution in the femtosecond regime. For the purpose of identifying the structures of molecules during chemical reactions, and for the analysis of molecular species in the hot environments of combustion processes, there are several features that make the Rydberg ionization spectroscopy uniquely useful. First, the Rydberg electron’s orbit is quite large and covers the entire molecule for most molecular structures of combustion interest. Secondly, the ionization does not change vibrational quantum numbers, so that even complicated and large molecules can be observed with fairly well resolved spectra. In fact, the spectroscopy is blind to vibrational excitation of the molecule. This has the interesting consequence for the study of chemical dynamics, where the molecules are invariably very energetic, that the molecular structures are observed unobstructed by the vibrational congestion that dominates other spectroscopies. This implies also that, as a tool to probe the time-dependent structural dynamics of chemically interesting molecules, Rydberg spectroscopy may well be better suited than electron or x-ray diffraction. With recent progress in calculating Rydberg binding energy spectra, we are approaching the point where the method can be evolved into a structure determination method. To implement the Rydberg ionization spectroscopy we use a molecular beam based, time-resolved pump-probe multi-photon ionization/photoelectron scheme in which a first laser pulse excites the molecule to a Rydberg state, and a probe pulse ionizes the molecule. A time-of-flight detector measures the kinetic energy spectrum of the photoelectrons. The photoelectron spectrum directly provides the binding energy of the electron, and thereby reveals the molecule’s time-dependent structural fingerprint. Only the duration of the laser pulses limits the time resolution. With a new laser system, we have now reached time resolutions better than 100 fs, although very deep UV wavelengths (down to 190 nm) have slightly longer instrument functions. The structural dynamics of molecules in Rydberg-excited states is obtained by delaying the probe ionization photon from the pump photon; the structural dynamics of molecules in their ground state or excited valence states is measured by inducing the dynamics using a near UV laser pulse, and employing a multi-photon ionization scheme via the Rydberg states as a probe process. Thus, the technique is capable of measuring the reaction dynamics in any electronic state of neutral molecules.« less

[Future perspectives for diagnostic imaging in urology: from anatomic and functional to molecular imaging].

PubMed

Macis, Giuseppe; Di Giovanni, Silvia; Di Franco, Davide; Bonomo, Lorenzo

2013-01-01

The future approach of diagnostic imaging in urology follows the technological progress, which made the visualization of in vivo molecular processes possible. From anatomo-morphological diagnostic imaging and through functional imaging molecular radiology is reached. Based on molecular probes, imaging is aimed at assessing the in vivo molecular processes, their physiology and function at cellular level. The future imaging will investigate the complex tumor functioning as metabolism, aerobic glycolysis in particular, angiogenesis, cell proliferation, metastatic potential, hypoxia, apoptosis and receptors expressed by neoplastic cells. Methods for performing molecular radiology are CT, MRI, PET-CT, PET-MRI, SPECT and optical imaging. Molecular ultrasound combines technological advancement with targeted contrast media based on microbubbles, this allowing the selective registration of microbubble signal while that of stationary tissues is suppressed. An experimental study was carried out where the ultrasound molecular probe BR55 strictly bound to prostate tumor results in strong enhancement in the early phase after contrast, this contrast being maintained in the late phase. This late enhancement is markedly significant for the detection of prostatic cancer foci and to guide the biopsy sampling. The 124I-cG250 molecular antibody which is strictly linked to cellular carbonic anhydrase IX of clear cell renal carcinoma, allows the acquisition of diagnostic PET images of clear cell renal carcinoma without biopsy. This WG-250 (RENCAREX) antibody was used as a therapy in metastatic clear cell renal carcinoma. Future advancements and applications will result in early cancer diagnosis, personalized therapy that will be specific according to the molecular features of cancer and leading to the development of catheter-based multichannel molecular imaging devices for cystoscopy-based molecular imaging diagnosis and intervention.