A tool for rapid screening of direct DNA agents using reaction rates and relative interaction potency: towards screening environmental contaminants for hazard.

PubMed

Gavina, Jennilee M A; Rubab, Mamoona; Zhang, Huijuan; Zhu, Jiping; Nong, Andy; Feng, Yong-Lai

2011-11-01

DNA damage represents a potential biomarker for determining the exposure risk to chemicals and may provide early warning data for identifying chemical hazards to human health. Here, we have demonstrated a simple chromatography-based method that can be used to rapidly screen for the presence of chemical hazards as well as to determine parameters relevant to hazard assessment. In this proof-of-principle study, a simple in vitro system was used to determine the interaction of pollutants and probable carcinogens, phenyl glycidyl ether (PGE), tetrachlorohydroquinone (Cl(4)HQ), methylmethane sulfonate (MMS), styrene-7,8-oxide (SO), and benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (BPDE), a metabolite of benzo[a]pyrene (B[a]P), with single- and double-stranded DNA probes. Differences in potency and reaction kinetics were studied for chemical and DNA type. A relative interaction potency equivalency (PEQ) of a chemical was determined by ratio of interaction potency of a chemical to BPDE as the reference chemical in the reaction with single- and double-stranded oligodeoxynucleotides. PEQs were found to be BPDE > PGE > SO > MMS > Cl(4)HQ for single-stranded oligodeoxynucleotides while they were found to be BPDE > PGE > Cl(4)HQ > MMS > SO for double-stranded oligodeoxynucleotides. Kinetics evaluation revealed that BPDE reacted with both DNA probes at a significantly faster rate, as compared to the remaining test chemicals. Equilibrium was reached within an hour for BPDE, but required a minimum of 48 h for the remaining chemicals. First-order rate constants were (1.61 ± 0.2) × 10(-3) s(-1) and (3.18 ± 0.4) × 10(-4) s(-1) for reaction of BPDE with double- and single-stranded DNA, respectively. The remaining chemicals possessed rate constants from 2 to 13 × 10(-6) s(-1) with a relative kinetic order for reaction with DNA of BPDE ≫ MMS > SO > PGE > Cl(4)HQ for ds-DNA and BPDE ≫ SO ≈ Cl(4)HQ ≈ MMS > PGE for ss-DNA. We further found that the reaction potency, defined by dose-response between chemical pollutants and DNA, depends on the form of DNA present for reaction. Noteworthy, we found that relative PEQ did not follow the same kinetic trends. However, our preliminary findings suggest that reaction kinetics, in combination with relative interaction potency, may be a significant parameter that can be used to evaluate the hazard level of environmental pollutants.

C-fos mediates antipsychotic-induced neurotensin gene expression in the rodent striatum.

PubMed

Robertson, G S; Tetzlaff, W; Bedard, A; St-Jean, M; Wigle, N

1995-07-01

The ubiquitous inducibility of the immediate-early gene c-fos in the central nervous system has led to the search for downstream genes which are regulated by its product, Fos. Recent evidence suggests that c-fos induction by a single injection of the classical antipsychotic haloperidol may contribute to the subsequent increase in neurotensin gene expression in the rodent striatum. Consistent with this proposal, in the present study haloperidol-induced Fos-like immunoreactivity and neurotensin/neuromedin N messenger RNA were found to be expressed by the same population of striatal neurons. Moreover, inhibition of haloperidol-induced c-fos expression by intrastriatal injection of antisense phosphorothioate oligodeoxynucleotides complimentary either to bases 109-126 or 127-144 of c-fos attenuated the subsequent increase in neurotensin/neuromedin N messenger RNA. However, injection of a sense phosphorothioate oligodeoxynucleotide corresponding to bases 127-144 of c-fos did not reduce haloperidol-induced c-fos or neurotensin/neuromedin N expression. Furthermore, constitutive expression of Jun-like immunoreactivity in the striatum was not reduced by either the sense or antisense phosphorothioate oligodeoxynucleotides. Similarly, the sense and antisense phosphorothioate oligodeoxynucleotide failed to reduce proenkephalin messenger RNA, which is located in the same striatal neurons that express haloperidol-induced neurotensin/neuromedin N messenger RNA, which is located in the same striatal neurons that express haloperidol-induced neurotensin/neuromedin N messenger RNA. Lastly, haloperidol-induced increases in nerve growth factor I-A-, JunB- and FosB-like immunoreactivity and fosB messenger RNA were not decreased by intrastriatal injection of either the sense or antisense phosphorothioate oligodeoxynucleotides. These results indicate that the antisense phosphorothioate oligodeoxynucleotides attenuated haloperidol-induced neurotensin/neuromedin N expression by selectively reducing c-fos expression and emphasize the potential importance of immediate-early gene induction in the mechanism of action of this antipsychotic drug.

Studies into the microbial spectrum of apical periodontitis.

PubMed

Brauner, A W; Conrads, G

1995-09-01

This study examined the variety of obligate and facultative anaerobic bacterial species recovered from cases of acute apical periodontitis. A total of 19 root canal samples and 24 periapical granuloma samples were taken from patients suffering pain and discomfort. Bacteria were identified by applying the following techniques: culturing on various media, Gram-staining and using commercially available biochemical test strips. In addition, Prevotella intermedia and Porphyromonas endodontalis were differentiated on a molecular genetic level using species-specific oligodeoxynucleotide probes. The most frequently identified bacteria were Prevotella intermedia, Bifidobacterium spp., Streptococcus sanguis, Streptococcus milleri-group and Bacteroides spp. Obligate anaerobes occurred at a rate of 82.3%, and the average number of isolates was 6.4 per sample.

Disruption of Msx-1 and Msx-2 reveals roles for these genes in craniofacial, eye, and axial development.

PubMed

Foerst-Potts, L; Sadler, T W

1997-05-01

In mouse embryos, the muscle segment homeobox genes, Msx-1 and Msx-2 are expressed during critical stages of neural tube, neural crest, and craniofacial development, suggesting that these genes play important roles in organogenesis and cell differentiation. Although the patterns of expression are intriguing, little is known about the function of these genes in vertebrate embryonic development. Therefore, the expression of both genes, separately and together, was disrupted using antisense oligodeoxynucleotides and whole embryo culture techniques. Antisense attenuation of Msx-1 during early stages of neurulation produced hypoplasia of the maxillary, mandibular, and frontonasal prominences, eye anomalies, and somite and neural tube abnormalities. Eye defects consisted of enlarged optic vesicles, which may ultimately result in micropthalmia similar to that observed in Small eye mice homozygous for mutations in the Pax-6 gene. Histological sections and SEM analysis revealed a thinning of the neuroepithelium in the diencephalon and optic vesicle and mesenchymal deficiencies in the craniofacial region. Injections of Msx-2 antisense oligodeoxynucleotides produced similar malformations as those targeting Msx-1, with the exception that there was an increase in number and severity of neural tube and somite defects. Embryos injected with the combination of Msx-1 + Msx-2 antisense oligodeoxynucleotides showed no novel abnormalities, suggesting that the genes do not operate in a redundant manner.

Gold nanocluster-based vaccines for dual-delivery of antigens and immunostimulatory oligonucleotides

NASA Astrophysics Data System (ADS)

Tao, Yu; Zhang, Yan; Ju, Enguo; Ren, Hui; Ren, Jinsong

2015-07-01

We here report a facile one-pot synthesis of fluorescent gold nanoclusters (AuNCs) via the peptide biomineralization method, which can elicit specific immunological responses. The as-prepared peptide-protected AuNCs (peptide-AuNCs) display strong red fluorescence, and more importantly, as compared to the peptide alone, the immune stimulatory ability of the resulting peptide-AuNCs can not only be retained, but can also be efficaciously enhanced. Moreover, through a dual-delivery of antigen peptides and cytosine-phosphate-guanine (CpG) oligodeoxynucleotides (ODNs), the as-prepared peptide-AuNC-CpG conjugates can also act as smart self-vaccines to assist in the generation of high immunostimulatory activity, and be applied as a probe for intracellular imaging. Both in vitro and in vivo studies provide strong evidence that the AuNC-based vaccines may be utilized as safe and efficient immunostimulatory agents that are able to prevent and/or treat a variety of ailments.We here report a facile one-pot synthesis of fluorescent gold nanoclusters (AuNCs) via the peptide biomineralization method, which can elicit specific immunological responses. The as-prepared peptide-protected AuNCs (peptide-AuNCs) display strong red fluorescence, and more importantly, as compared to the peptide alone, the immune stimulatory ability of the resulting peptide-AuNCs can not only be retained, but can also be efficaciously enhanced. Moreover, through a dual-delivery of antigen peptides and cytosine-phosphate-guanine (CpG) oligodeoxynucleotides (ODNs), the as-prepared peptide-AuNC-CpG conjugates can also act as smart self-vaccines to assist in the generation of high immunostimulatory activity, and be applied as a probe for intracellular imaging. Both in vitro and in vivo studies provide strong evidence that the AuNC-based vaccines may be utilized as safe and efficient immunostimulatory agents that are able to prevent and/or treat a variety of ailments. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr02240a

75 FR 60761 - Government-Owned Inventions; Availability for Licensing

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-01

... cells conjugated to a K-type CpG oligodeoxynucleotide (ODN) to a subject. Methods for treating a tumor... therapeutically effective amount of apoptotic tumor cells conjugated to a K-type CpG oligodeoxynucleotide (ODN) to... the prevention of cancer and other indications Use of CpG oligonucleotides for prophylaxis and/or...

Growth inhibition of N1E-115 mouse neuroblastoma cells by c-myc or N-myc antisense oligodeoxynucleotides causes limited differentiation but is not coupled to neurite formation.

PubMed

Larcher, J C; Basseville, M; Vayssiere, J L; Cordeau-Lossouarn, L; Croizat, B; Gros, F

1992-06-30

Antisense oligodeoxynucleotides were found to be stable in the culture medium containing fetal calf serum (heat-inactivated 30 minutes at 65 degrees C) and in cells. Antisense oligomer treatment causes cessation of mitoses, but does not lead to morphological differentiation. Under antisense conditions, we have observed an increase in the amount of two neurospecific protein, namely peripherin and gamma-enolase. Comparison of the results obtained with chemical inducers and antisense oligodeoxynucleotides allows us to postulate three phases in N1E-115 differentiation: the first correspond to the arrest of mitosis, the second to the expression of a limited neuronal program, and the third to the morphological and electrophysiological differentiation.

Breast imaging technology: Recent advances in imaging endogenous or transferred gene expression utilizing radionuclide technologies in living subjects - applications to breast cancer

PubMed Central

Berger, Frank; Sam Gambhir, Sanjiv

2001-01-01

A variety of imaging technologies is being investigated as tools for studying gene expression in living subjects. Two technologies that use radiolabeled isotopes are single photon emission computed tomography (SPECT) and positron emission tomography (PET). A relatively high sensitivity, a full quantitative tomographic capability, and the ability to extend small animal imaging assays directly into human applications characterize radionuclide approaches. Various radiolabeled probes (tracers) can be synthesized to target specific molecules present in breast cancer cells. These include antibodies or ligands to target cell surface receptors, substrates for intracellular enzymes, antisense oligodeoxynucleotide probes for targeting mRNA, probes for targeting intracellular receptors, and probes for genes transferred into the cell. We briefly discuss each of these imaging approaches and focus in detail on imaging reporter genes. In a PET reporter gene system for in vivo reporter gene imaging, the protein products of the reporter genes sequester positron emitting reporter probes. PET subsequently measures the PET reporter gene dependent sequestration of the PET reporter probe in living animals. We describe and review reporter gene approaches using the herpes simplex type 1 virus thymidine kinase and the dopamine type 2 receptor genes. Application of the reporter gene approach to animal models for breast cancer is discussed. Prospects for future applications of the transgene imaging technology in human gene therapy are also discussed. Both SPECT and PET provide unique opportunities to study animal models of breast cancer with direct application to human imaging. Continued development of new technology, probes and assays should help in the better understanding of basic breast cancer biology and in the improved management of breast cancer patients. PMID:11250742

Dendritic Cell-Based Immunotherapy of Breast Cancer: Modulation by CpG DNA

DTIC Science & Technology

2005-09-01

tumor-associated antigens and bacterial DNA oligodeoxynucleotides containing unmethylated CpG sequences (CpG DNA) further augment the immune priming...associated antigens by cytotoxic T lymphocytes, and bacterial DNA oligodeoxy- nucleotides containing unmethylated CpG sequences (CpG DNA) can further...further amplify their immunostimulatory capacity and bacterial DNA oligodeoxynucleotides (ODN) containing unmethylated CpG sequences (CpG DNA) provide such

Phylogenetic perspective and the search for life on earth and elsewhere

NASA Technical Reports Server (NTRS)

Pace, Norman R.

1989-01-01

Any search for microbial life on Mars cannot rely upon cultivation of indigenous organisms. Only a minority of even terrestrial organisms that are observed in mixed, naturally-occurring microbial populations can be cultivated in the laboratory. Consequently, methods are being developed for analyzing the phylogenetic affiliations of the constituents of natural microbial populations without the need for their cultivation. This is more than an exercise in taxonomy, for the extent of phylogenetic relatedness between unknown and known organisms is some measure of the extent of their biochemical commonalities. In one approach, total DNA is isolated from natural microbial populations and 16S rRNA genes are shotgun cloned for rapid sequence determinations and phylogenetic analyses. A second approach employs oligodeoxynucleotide hybridization probes that bind to phylogenetic group-specific sequences in 16S rRNA. Since each actively growing cell contains about 104 ribosomes, the binding of the diagnostic probes to single cells can be visualized by radioactivity or fluorescence. The application of these methods and the use of in situ cultivation techniques is illustrated using submarine hydrothermal vent communities. Recommendations are made regarding planning toward future Mars missions.

Intercalation of aflatoxin B sub 1 in two oligodeoxynucleotide adducts: Comparative sup 1 H NMR analysis of d(ATC sup AFB GAT)ter dot d(ATCGAT) and d(AT sup ATB GCAT) sub 2

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

Gopalakrishnan, S.; Harris, T.M.; Stone, M.P.

8,9-Dihydro-8-(N7-guanyl-(d(ATCGAT)))-9-hydroxyaflatoxin B{sub 1}{center dot}d(ATCGAT) and 8,9-dihydro-8-(N7-guanyl-(d(ATGCAT)))-9-hydroxyafltoxin B{sub 1}{center dot}8,9-dihydro-8-(N7-guanyl-(d(ATGCAT)))-9-hydroxyaflatoxin B{sub 1} were prepared by direct addition of aflatoxin B{sub 1} 8,9-expoxide to d(ATCGAT){sub 2} and d(ATGCAT){sub 2}, respectively. {sup 1}H NOE experiments, nonselective {sup 1}H T{sub 1} relaxation measurements, and {sup 1}H chemical shift perturbations demonstrate that in both modified oligodeoxynucleotides the aflatoxin moiety is intercalated above the 5{prime}-face of the modified guanine. The oligodeoxynucleotides remain right-handed, and perturbation of the B-DNA structure is localized adjacent to the adducted guanine. Aflatoxin-oligodeoxynucleotide {sup 1}H NOEs are observed between aflatoxin and the 5{prime}-neighbor base pair and include both the major groove andmore » the minor groove. The protons at C8 and C9 of the aflatoxin terminal furan ring exhibit slower spin-lattice relaxation as compared to other oligodeoxynucleotide protons, which supports the conclusion that they face into the major groove. Increased shielding is observed for aflatoxin protons. The difference in reaction stoichiometry is consistent with an intercalated transition-state complex between aflatoxin B{sub 1} 8,9-epoxide and B-DNA. Intercalation provides excellent positioning for nucleophilic attack by guanine N7 on aflatoxin B{sub 1} 8,9-epoxide, which probably accounts for the observed efficiency of adduct formation despite the relatively low DNA binding affinity observed for aflatoxin B{sub 1}.« less

Microenvironmental Effect of 2'-O-(1-Pyrenylmethyl)uridine Modified Fluorescent Oligonucleotide Probes on Sensitive and Selective Detection of Target RNA.

PubMed

Imincan, Gülnur; Pei, Fen; Yu, Lijia; Jin, Hongwei; Zhang, Liangren; Yang, Xiaoda; Zhang, Lihe; Tang, XinJing

2016-04-19

2'-O-(1-Pyrenylmethyl)uridine modified oligoribonucleotides provide highly sensitive pyrene fluorescent probes for detecting specific nucleotide mutation of RNA targets. To develop more stable and cost-effective oligonucleotide probes, we investigated the local microenvironmental effects of nearby nucleobases on pyrene fluorescence in duplexes of RNAs and 2'-O-(1-pyrenylmethyl)uridine modified oligonucleotides. By incorporation of deoxyribonucleotides, ribonucleotides, 2'-MeO-nucleotides and 2'-F-nucleotides at both sides of 2'-O-(1-pyrenylmethyl)uridine (U(p)) in oligodeoxynucleotide probes, we synthesized a series of pyrene modified oligonucleotide probes. Their pyrene fluorescence emission spectra indicated that only two proximal nucleotides have a substantial effect on the pyrene fluorescence properties of these oligonucleotide probes hybridized with target RNA with an order of fluorescence sensitivity of 2'-F-nucleotides > 2'-MeO-nucleotides > ribonucleotides ≫ deoxyribonucleotides. While based on circular dichroism spectra, overall helix conformations (either A- or B-form) of the duplexes have marginal effects on the sensitivity of the probes. Instead, the local substitution reflected the propensity of the nucleotide sugar ring to adopt North type conformation and, accordingly, shifted their helix geometry toward a more A-type like conformation in local microenvironments. Thus, higher enhancement of pyrene fluorescence emission favored local A-type helix structures and more polar and hydrophobic environments (F > MeO > OH at 2' substitution) of duplex minor grooves of probes with the target RNA. Further dynamic simulation revealed that local microenvironmental effect of 2'-F-nucleotides or ribonucleotides was enough for pyrene moiety to move out of nucleobases to the minor groove of duplexes; in addition, 2'-F-nucleotide had less effect on π-stack of pyrene-modified uridine with upstream and downstream nucleobases. The present oligonucleotide probes successfully distinguished target RNA from single-mutated RNA analyte during an in vitro assay of RNA synthesis.

Immunostimulation by cytosine-phosphate-guanine oligodeoxynucleotides in combination with IL-2 can improve the success rate of karyotype analysis in chronic lymphocytic leukaemia.

PubMed

Lin, Xiaolan; Chen, Jiadi; Huang, Huifang

2016-07-01

To assess whether immunostimulatory cytosine-phosphate-guanine oligodeoxynucleotides (CpG-ODN) combined with interleukin-2 (IL-2) improves the number of mitotic metaphases and the detection rate of chromosomal abnormalities in chronic lymphocytic leukaemia (CLL). Bone marrow specimens were collected from 36 patients with CLL. CLL cells were cultured with CpG-ODN type DSP30 plus IL-2 for 72 h, following which R-banding analysis was conducted. Conventional culture without the immunostimulant served as the control group. The incidence of genetic abnormalities was measured by fluorescence in situ hybridisation (FISH) using a panel of five specific probes: D13S25 (13q14.3), RB1 (13q14), P53 (17p13), ATM (11q22.3) and CSP12 (trisomy 12, +12). In the control group, chromosome analysis achieved a success rate of only 22.2, and 11.1% of abnormal karyotypes were detected. After immunostimulation with DSP30 plus IL-2, chromosome analysis achieved a success rate of up to 91.6, and 41.6% of abnormal karyotypes were detected. FISH analysis detected 77.7% of abnormalities. FISH combined with CpG-ODN DSP30 plus IL-2 improved the detection rate of chromosomal abnormalities in CLL to 83.3%. CpG-ODN DSP30 combined with IL-2 is effective in improving the detection rate of chromosomal abnormalities in CLL cells. This combination with FISH analysis is conducive to increasing the detection rate of genetic abnormalities in CLL.

Oxidative generation of guanine radicals by carbonate radicals and their reactions with nitrogen dioxide to form site specific 5-guanidino-4-nitroimidazole lesions in oligodeoxynucleotides.

PubMed

Joffe, Avrum; Mock, Steven; Yun, Byeong Hwa; Kolbanovskiy, Alexander; Geacintov, Nicholas E; Shafirovich, Vladimir

2003-08-01

A simple photochemical approach is described for synthesizing site specific, stable 5-guanidino-4-nitroimidazole (NIm) adducts in single- and double-stranded oligodeoxynucleotides containing single and multiple guanine residues. The DNA sequences employed, 5'-d(ACC CG(1)C G(2)TC CG(3)C G(4)CC) and 5'-d(ACC CG(1)C G(2)TC C), were a portion of exon 5 of the p53 tumor suppressor gene, including the codons 157 (G(2)) and 158 (G(3)) mutation hot spots in the former sequence with four Gs and the codon 157 (G(2)) mutation hot spot in the latter sequence with two Gs. The nitration of oligodeoxynucleotides was initiated by the selective photodissociation of persulfate anions to sulfate radicals induced by UV laser pulses (308 nm). In aqueous solutions, of bicarbonate and nitrite anions, the sulfate radicals generate carbonate anion radicals and nitrogen dioxide radicals by one electron oxidation of the respective anions. The guanine residue in the oligodeoxynucleotide is oxidized by the carbonate anion radical to form the neutral guanine radical. While the nitrogen dioxide radicals do not react with any of the intact DNA bases, they readily combine with the guanine radicals at either the C8 or the C5 positions. The C8 addition generates the well-known 8-nitroguanine (8-nitro-G) lesions, whereas the C5 attack produces unstable adducts, which rapidly decompose to NIm lesions. The maximum yields of the nitro products (NIm + 8-nitro-G) were typically in the range of 20-40%, depending on the number of guanine residues in the sequence. The ratio of the NIm to 8-nitro-G lesions gradually decreases from 3.4 in the model compound, 2',3',5'-tri-O-acetylguanosine, to 2.1-2.6 in the single-stranded oligodeoxynucleotides and to 0.8-1.1 in the duplexes. The adduct of the 5'-d(ACC CG(1)C G(2)TC C) oligodeoxynucleotide containing the NIm lesion in codon 157 (G(2)) was isolated in HPLC-pure form. The integrity of this adduct was established by a detailed analysis of exonuclease digestion ladders by matrix-assisted laser desorption ionization with time-of-flight detection MS techniques.

Double-stranded RNA transcribed from vector-based oligodeoxynucleotide acts as transcription factor decoy

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

Xiao, Xiao; Gang, Yi; Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi’an 710038, Shaanxi Province

2015-02-06

Highlights: • A shRNA vector based transcription factor decoy, VB-ODN, was designed. • VB-ODN for NF-κB inhibited cell viability in HEK293 cells. • VB-ODN inhibited expression of downstream genes of target transcription factors. • VB-ODN may enhance nuclear entry ratio for its feasibility of virus production. - Abstract: In this study, we designed a short hairpin RNA vector-based oligodeoxynucleotide (VB-ODN) carrying transcription factor (TF) consensus sequence which could function as a decoy to block TF activity. Specifically, VB-ODN for Nuclear factor-κB (NF-κB) could inhibit cell viability and decrease downstream gene expression in HEK293 cells without affecting expression of NF-κB itself.more » The specific binding between VB-ODN produced double-stranded RNA and NF-κB was evidenced by electrophoretic mobility shift assay. Moreover, similar VB-ODNs designed for three other TFs also inhibit their downstream gene expression but not that of themselves. Our study provides a new design of decoy for blocking TF activity.« less

Aggregate Formation of Oligonucleotides that Assist Molecular Imaging for Tracking of the Oxygen Status in Tumor Tissue.

PubMed

Yoshihara, Kazuki; Takagi, Kohei; Son, Aoi; Kurihara, Ryohsuke; Tanabe, Kazuhito

2017-08-17

The use of DNA aggregates could be a promising strategy for the molecular imaging of biological functions. Herein, phosphorescent oligodeoxynucleotides were designed with the aim of visualizing oxygen fluctuation in tumor cells. DNA-ruthenium conjugates (DRCs) that consisted of oligodeoxynucleotides, a phosphorescent ruthenium complex, a pyrene unit for high oxygen responsiveness, and a nitroimidazole unit as a tumor-targeting unit were prepared. In general, oligonucleotides have low cell permeability because of their own negative charges; however, the DRC formed aggregates in aqueous solution due to the hydrophobic pyrene and nitroimidazole groups, and smoothly penetrated the cellular membrane to accumulate in tumor cells in a hypoxia-selective manner. The oxygen-dependent phosphorescence of DRC in cells was also observed. In vivo experiments revealed that aggregates of DRC accumulated in hypoxic tumor tissue that was transplanted into the left leg of mice, and showed that oxygen fluctuations in tumor tissue could be monitored by tracking of the phosphorescence emission of DRC. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Determination of the order of substrate addition to MspI DNA methyltransferase using a novel mechanism-based inhibitor.

PubMed Central

Taylor, C; Ford, K; Connolly, B A; Hornby, D P

1993-01-01

The cloning and overexpression of the MspI DNA methyltransferase as a functional fusion with glutathione S-transferase is described. The fusion enzyme retains full biological activity and has been used to investigate the interaction of substrates and inhibitors with MspI DNA methyltransferase. The fusion enzyme has been purified to homogeneity in a single step on GSH-agarose and is free from contaminating exonuclease activity. The enzyme can be photolabelled with S-adenosyl-L-methionine and the level of incorporation of label is enhanced by the presence of a nonspecific DNA duplex. In the presence of a cognate oligodeoxynucleotide, no photolabelling was observed since methyl transfer occurs instead. The inclusion of a mechanism-based inhibitor of C-5 deoxycytidine DNA methylation (an oligodeoxynucleotide containing the base 2-pyrimidinone-1-beta-D-2'-deoxyribofuranoside in the position of the deoxycytidine to which methyl addition occurs), which is thought to form a covalent interaction with the reactive cysteine of such enzymes, led to an enhancement of S-adenosyl-L-methionine photolabelling which suggests that, in contrast with results obtained with EcoRII DNA methyltransferase [Som and Friedman (1991) J. Biol. Chem. 266, 2937-2945], methylcysteine is not the photolabelled product. The implications of the results obtained with this mechanism-based inhibitor are discussed with respect to other C-5-specific DNA methyltransferases. Gel-retardation assays in the presence of cognate oligodeoxynucleotides that contain the reactive pyrimidinone base in place of the deoxycytidine target base are described. These demonstrate that most probably a stable covalent bond is formed between the methyltransferase and this oligodeoxynucleotide. However, the alternative of extremely tight non-covalent binding cannot be rigorously excluded. Furthermore, the results from these experiments indicate that the reaction mechanism proceeds in a manner similar to that of HhaI DNA methyltransferase with sequence-specific DNA binding being followed by addition of S-adenosyl-L-methionine and concomitant isomerization of the ternary complex leading to methyl transfer. S-Adenosyl-L-homocysteine appears to inhibit the reaction pathway as a result of either competition with the methyl donor and potentiation of a high-affinity interaction between the enzyme and DNA in an abortive ternary complex or through an allosteric interaction. Images Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Figure 10 Figure 11 Figure 12 Figure 13 Figure 14 PMID:8484730

Effects of probiotics, probiotic DNA and the CpG oligodeoxynucleotides on ovalbumin-sensitized Brown-Norway rats via TLR9/NF-κB pathway.

PubMed

Zhong, Yan; Huang, Juan; Tang, Wenjing; Chen, Bing; Cai, Wei

2012-10-01

The aim of the study was to investigate the effect of living probiotics, probiotic DNA and the synthetic oligodeoxynucleotides containing CpG motifs (CpG-ODN) on both immune response and intestinal barrier function in ovalbumin-sensitized rat and the underlying mechanisms. Brown-Norway rats were orally sensitized with ovalbumin, and living probiotics, probiotic DNA extraction, synthetic CpG-ODN or non-CpG ODN control was administered. In the living probiotics, probiotic DNA and CpG-ODN groups, the allergic response was significantly inhibited, the Th1/Th2 cytokine balance was shifted away from Th2 side, the percentage of CD4(+) CD25(+high) Treg cells was increased, and the intestinal barrier function was improved. The levels of toll-like receptor (TLR) 9 mRNA and nuclear factor (NF)-κB activity, as well as the IκB-α phosphorylation (p-IκB-α) was significantly increased in these three intervention groups compared with the OVA-positive group, whereas no such effects were found in the non-CpG ODN control group. These data show that the probiotic genomic DNA and the synthetic CpG-ODN was comparable with living probiotics in preventing food allergic response by immune modulation and intestinal barrier function enhancement, and the activation of TLR9/NF-κB signal pathway might be involved in this process. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Direct production of mouse disease models by embryo microinjection of TALENs and oligodeoxynucleotides

PubMed Central

Wefers, Benedikt; Meyer, Melanie; Ortiz, Oskar; Hrabé de Angelis, Martin; Hansen, Jens; Wurst, Wolfgang; Kühn, Ralf

2013-01-01

The study of genetic disease mechanisms relies mostly on targeted mouse mutants that are derived from engineered embryonic stem (ES) cells. Nevertheless, the establishment of mutant ES cells is laborious and time-consuming, restricting the study of the increasing number of human disease mutations discovered by high-throughput genomic analysis. Here, we present an advanced approach for the production of mouse disease models by microinjection of transcription activator-like effector nucleases (TALENs) and synthetic oligodeoxynucleotides into one-cell embryos. Within 2 d of embryo injection, we created and corrected chocolate missense mutations in the small GTPase RAB38; a regulator of intracellular vesicle trafficking and phenotypic model of Hermansky-Pudlak syndrome. Because ES cell cultures and targeting vectors are not required, this technology enables instant germline modifications, making heterozygous mutants available within 18 wk. The key features of direct mutagenesis by TALENs and oligodeoxynucleotides, minimal effort and high speed, catalyze the generation of future in vivo models for the study of human disease mechanisms and interventions. PMID:23426636

Associations of Methanotrophs With the Roots and Rhizomes of Aquatic Vegetation

NASA Technical Reports Server (NTRS)

King, Gary M.

1994-01-01

Results of an in vitro assay revealed that root-associated methane consumption was a common attribute or diverse emergent wetland macrophytes from a variety of habitats. Maximum potential uptake rates (V(sub maxp)) varied between about 1 and 10 micro mol g/ (dry weight) h, with no obvious correlation between rate and gross morphological characteristics of the plants. The V(sub maxp) corresponded to about 2 x 10(exp 18) to 2 x 10(exp 9) methanotrophs g/ (dry weight), assuming that root-associated methanotrophs have cell-specific activities comparable to those of known isolates. V(sub maxp) varied seasonally for an aquatic grass, Calamogrostis canadensis, and for the cattail, Typha latifolia, with highest rates in late summer. V(sub maxp) was well correlated with ambient temperature for C. canadensis but weakly correlated for T. Wifolia. The seasonal changes in V(sub maxp), as well as inferences from apparent half-saturation constants for methane uptake (K(sub app); generally 3 to 6 micro M), indicated that oxygen availability might be more important than methane as a rate determinant. In addition, roots incubated under anoxic conditions showed little or no postanoxia aerobic methane consumption, indicating that root-associated metbanotrophic populations might not tolerate variable oxygen availability. Hybridization of oligodeoxynucleotide probes specific for group 1 or group 2 methylotrophs also varied seasonally. The group 2-specific probe consistently hybridized to a greater extent than the group 1 probe, and the relative amount of group 2 probe hybridization to C. canadensis root extracts was positively correlated with V(sub maxp).

Generation of Knock-in Mouse by Genome Editing.

PubMed

Fujii, Wataru

2017-01-01

Knock-in mice are useful for evaluating endogenous gene expressions and functions in vivo. Instead of the conventional gene-targeting method using embryonic stem cells, an exogenous DNA sequence can be inserted into the target locus in the zygote using genome editing technology. In this chapter, I describe the generation of epitope-tagged mice using engineered endonuclease and single-stranded oligodeoxynucleotide through the mouse zygote as an example of how to generate a knock-in mouse by genome editing.

A Simple Procedure for Constructing 5'-Amino-Terminated Oligodeoxynucleotides in Aqueous Solution

NASA Technical Reports Server (NTRS)

Bruick, Richard K.; Koppitz, Marcus; Joyce, Gerald F.; Orgel, Leslie E.

1997-01-01

A rapid method for the synthesis of oligodeoxynucleotides (ODNs) terminated by 5'-amino-5'-deoxythymidine is described. A 3'-phosphorylated ODN (the donor) is incubated in aqueous solution with 5'-amino- 5'-deoxythymidine in the presence of N-(3-dimethylaminopropyl)-)N'-ethylcarbodiimide hydrochloride (EDC), extending the donor by one residue via a phosphoramidate bond. Template- directed ligation of the extended donor and an acceptor ODN, followed by acid hydrolysis, yields the acceptor ODN extended by a single 5'-amino-5'-deoxythymidine residue at its 5'terminus.

Synthesis of peptide nucleic acids containing pyridazine derivatives as cytosine and thymine analogs, and their duplexes with complementary oligodeoxynucleotides.

PubMed

Tomori, Takahito; Miyatake, Yuya; Sato, Yuta; Kanamori, Takashi; Masaki, Yoshiaki; Ohkubo, Akihiro; Sekine, Mitsuo; Seio, Kohji

2015-03-20

Synthesis of peptide nucleic acids (PNAs) is reported with new pyridazine-type nucleobases: 3-aminopyridazine (aPz) and 1-aminophthalazine (aPh) as cytosine analogs, and pyridazin-3-one (Pz(O)) and phthalazin-1-one (Ph(O)) as thymine analogs. The PNAs having an aPz or a Pz(O) formed duplexes with each complementary oligodeoxynucleotide forming a base pair with G or A, respectively, as evaluated by using UV melting analyses and circular dichroism (CD) spectra.

Immunostimulatory Oligodeoxynucleotides Containing the CpG Motif are Effective as Immune Adjuvants in Tumor Antigen Immunization

NASA Astrophysics Data System (ADS)

Weiner, George J.; Liu, Hsin-Ming; Wooldridge, James E.; Dahle, Christopher E.; Krieg, Arthur M.

1997-09-01

Recent advances in our understanding of the immune response are allowing for the logical design of new approaches to cancer immunization. One area of interest is the development of new immune adjuvants. Immunostimulatory oligodeoxynucleotides containing the CpG motif (CpG ODN) can induce production of a wide variety of cytokines and activate B cells, monocytes, dendritic cells, and NK cells. Using the 38C13 B cell lymphoma model, we assessed whether CpG ODN can function as immune adjuvants in tumor antigen immunization. The idiotype served as the tumor antigen. Select CpG ODN were as effective as complete Freund's adjuvant at inducing an antigen-specific antibody response but were associated with less toxicity. These CpG ODN induced a higher titer of antigen-specific IgG2a than did complete Freund's adjuvant, suggesting an enhanced TH1 response. Mice immunized with CpG ODN as an adjuvant were protected from tumor challenge to a degree similar to that seen in mice immunized with complete Freund's adjuvant. We conclude that CpG ODN are effective as immune adjuvants and are attractive as part of a tumor immunization strategy.

Synthetic Oligodeoxynucleotides (ODN) Containing Suppressive TTAGGG Motifs Inhibit AIM2 Inflammasome Activation

PubMed Central

Kaminski, John J.; Schattgen, Stefan A.; Tzeng, Te-Chen; Bode, Christian; Klinman, Dennis M.; Fitzgerald, Katherine A.

2013-01-01

Synthetic oligodeoxynucleotides comprised of the immunosuppressive motif TTAGGG block TLR9 signaling, prevent STAT1 and STAT4 phosphorylation and attenuate a variety of inflammatory responses in vivo. Here, we demonstrate that such suppressive oligodeoxynucleotides (sup ODN) abrogate activation of cytosolic nucleic acid sensing pathways. Pretreatment of dendritic cells and macrophages with the suppressive ODN-A151 abrogated type I IFN, TNFα and ISG induction in response to cytosolic dsDNA. In addition, A151 abrogated caspase-1-dependent IL-1β and IL-18 maturation in dendritic cells stimulated with dsDNA and murine cytomegalovirus (MCMV). Inhibition was dependent on A151’s phosphorothioate backbone while substitution of the guanosine residues for adenosine negatively affected potency. A151 mediates these effects by binding to AIM2 in a manner that is competitive with immune-stimulatory DNA and as a consequence prevents AIM2 inflammasome complex formation. Collectively, these findings reveal a new route by which suppressive ODNs modulate the immune system and unveil novel applications for suppressive ODNs in the treatment of infectious and autoimmune diseases. PMID:23986531

Zebularine: A Novel DNL Methylation Inhibitor that Forms a Covalent Complex with DNA Methyltransferases

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

Zhou, L.; Cheng, X; Connolly, B

2009-01-01

Mechanism-based inhibitors of enzymes, which mimic reactive intermediates in the reaction pathway, have been deployed extensively in the analysis of metabolic pathways and as candidate drugs. The inhibition of cytosine-[C5]-specific DNA methyltransferases (C5 MTases) by oligodeoxynucleotides containing 5-azadeoxycytidine (AzadC) and 5-fluorodeoxycytidine (FdC) provides a well-documented example of mechanism-based inhibition of enzymes central to nucleic acid metabolism. Here, we describe the interaction between the C5 MTase from Haemophilus haemolyticus (M.HhaI) and an oligodeoxynucleotide duplex containing 2-H pyrimidinone, an analogue often referred to as zebularine and known to give rise to high-affinity complexes with MTases. X-ray crystallography has demonstrated the formation ofmore » a covalent bond between M.HhaI and the 2-H pyrimidinone-containing oligodeoxynucleotide. This observation enables a comparison between the mechanisms of action of 2-H pyrimidinone with other mechanism-based inhibitors such as FdC. This novel complex provides a molecular explanation for the mechanism of action of the anti-cancer drug zebularine.« less

Structure of the circumsporozoite protein gene in 18 strains of Plasmodium falciparum.

PubMed

Weber, J L; Hockmeyer, W T

1985-06-01

Using the cloned circumsporozoite (CS) protein gene of a Brazilian strain of Plasmodium falciparum as probe, we have analyzed the structure of the CS protein gene from 17 other Asian, African, Central and South American parasite strains by nucleic acid hybridization. Each strain appears to have one CS protein gene which hybridizes readily to the Brazilian strain probe. The 5' and 3' thirds of the genes are invariant in size in all 18 strains whereas the central third containing the 12 base pair tandem repeats varies in size over a range of about 100 base pairs. Several differences were found in the locations of Sau3A sites in the genes. The Sau3A sites are significant because each of the minority Asn-Val-Asp-Pro repeats in the cloned gene has a Sau3A site. DNA melting of hybrids revealed a high degree of homology between the sequences of the cloned gene and genes from an Asian strain and an African strain. A 14 base oligodeoxynucleotide with a sequence from the central repeat region hybridized to all strains tested. We conclude that the CS protein gene is highly conserved among strains of P. falciparum and that malaria vaccine development with the CS protein is unlikely to be complicated by strain variation.

Activation of human B cells by phosphorothioate oligodeoxynucleotides.

PubMed Central

Liang, H; Nishioka, Y; Reich, C F; Pisetsky, D S; Lipsky, P E

1996-01-01

To investigate the potential of DNA to elicit immune responses in man, we examined the capacity of a variety of oligodeoxynucleotides (ODNs) to stimulate highly purified T cell-depleted human peripheral blood B cells. Among 47 ODNs of various sequences tested, 12 phosphorothioate oligodeoxynucleotides (sODNs) induced marked B cell proliferation and Ig production. IL-2 augmented both proliferation and production of IgM, IgG, and IgA, as well as IgM anti-DNA antibodies, but was not necessary for B cell stimulation. Similarly, T cells enhanced stimulation, but were not necessary for B cell activation. After stimulation with the active sODNs, more than 95% of B cells expressed CD25 and CD86. In addition, B cells stimulated with sODNs expressed all six of the major immunoglobulin VH gene families. These results indicate that the human B cell response to sODN is polyclonal. Active sODN coupled to Sepharose beads stimulated B cells as effectively as the free sODN, suggesting that stimulation resulted from engagement of surface receptors. These data indicate that sODNs can directly induce polyclonal activation of human B cells in a T cell-independent manner by engaging as yet unknown B cell surface receptors. PMID:8787674

Encapsulation of c-myc antisense oligodeoxynucleotides in lipid particles improves antitumoral efficacy in vivo in a human melanoma line.

PubMed

Leonetti, C; Biroccio, A; Benassi, B; Stringaro, A; Stoppacciaro, A; Semple, S C; Zupi, G

2001-06-01

Phosphorothioate c-myc antisense oligodeoxynucleotides [S]ODNs (free INX-6295) were encapsulated in a new liposome formulation and the antitumor activity was compared to the unencapsulated antisense in a human melanoma xenograft. The systemic administration of INX-6295 encapsulated in stabilized antisense lipid particles (SALP INX-6295) improved plasma AUC (area under the plasma concentration-time curve) and initial half-life of free INX-6295, resulting in a significant enhancement in tumor accumulation and improvement in tumor distribution of antisense oligodeoxynucleotides. Animals treated with SALP INX-6295 exhibited a prolonged reduction of c-myc expression, reduced tumor growth and increased mice survival. When administered in combination with cisplatin (DDP), SALP INX-6295 produced a complete tumor regression in approximately 30% of treated mice, which persisted for at least 60 days following the first cycle of treatment. Finally, the median survival of mice treated with DDP/SALP INX-6295 increased by 105% compared to 84% for animals treated with the combination DDP/free INX-6295. These data indicate that the biological activity and the therapeutic efficacy of c-myc antisense therapy may be improved when these agents are administered in lipid-based delivery systems.

Immunization of Aged Mice with a Pneumococcal Conjugate Vaccine Combined with an Unmethylated CpG-Containing Oligodeoxynucleotide Restores Defective Immunoglobulin G Antipolysaccharide Responses and Specific CD4+-T-Cell Priming to Young Adult Levels

DTIC Science & Technology

2006-04-01

aged and young adult mice made comparable levels of proinflammatory cytokines in response to CpG-ODN, although cells from aged mice secreted higher...sepsis, is significantly elevated in the elderly relative to young adults (37, 60). Defective innate immunity including diminished neutrophil and...young adult recipients (15). Exposure to inflammatory cy- tokines in vivo could restore the defective CD4-T-cell function in aged mice (20). Pn

Distinct Effects of Monophosphoryl Lipid A, Oligodeoxynucleotide CpG, and Combination Adjuvants on Modulating Innate and Adaptive Immune Responses to Influenza Vaccination.

PubMed

Ko, Eun-Ju; Lee, Young-Tae; Lee, Youri; Kim, Ki-Hye; Kang, Sang-Moo

2017-10-01

Monophosphoryl lipid A (MPL) and oligodeoxynucleotide CpG are toll-like receptor (TLR) 4 and 9 agonist, respectively. Here, we investigated the effects of MPL, CpG, and combination adjuvants on stimulating in vitro dendritic cells (DCs), in vivo innate and adaptive immune responses, and protective efficacy of influenza vaccination. Combination of MPL and CpG was found to exhibit distinct effects on stimulating DCs in vitro to secrete IL-12p70 and tumor necrosis factor (TNF)-α and proliferate allogeneic CD8 T cells. Prime immunization of mice with inactivated split influenza vaccine in the presence of low dose MPL+CpG adjuvants increased the induction of virus-specific IgG and IgG2a isotype antibodies. MPL and CpG adjuvants contribute to improving the efficacy of prime influenza vaccination against lethal influenza challenge as determined by body weight monitoring, lung function, viral titers, and histology. A combination of MPL and CpG adjuvants was effective in improving vaccine efficacy as well as in reducing inflammatory immune responses locally and in inducing cellular immune responses upon lethal influenza virus challenge. This study demonstrates unique adjuvant effects of MPL, CpG, and combination adjuvants on modulating innate and adaptive immune responses to influenza prime vaccination.

Polyethyleneimine-functionalized boron nitride nanospheres as efficient carriers for enhancing the immunostimulatory effect of CpG oligodeoxynucleotides

PubMed Central

Zhang, Huijie; Feng, Shini; Yan, Ting; Zhi, Chunyi; Gao, Xiao-Dong; Hanagata, Nobutaka

2015-01-01

CpG oligodeoxynucleotides (ODNs) stimulate innate and adaptive immune responses. Thus, these molecules are promising therapeutic agents and vaccine adjuvants against various diseases. In this study, we developed a novel CpG ODNs delivery system based on polyethyleneimine (PEI)-functionalized boron nitride nanospheres (BNNS). PEI was coated on the surface of BNNS via electrostatic interactions. The prepared BNNS–PEI complexes had positive zeta potential and exhibited enhanced dispersity and stability in aqueous solution. In vitro cytotoxicity assays revealed that the BNNS–PEI complexes with concentrations up to 100 μg/mL exhibited no obvious cytotoxicity. Furthermore, the positively charged surface of the BNNS–PEI complexes greatly improved the loading capacity and cellular uptake efficiency of CpG ODNs. Class B CpG ODNs loaded on the BNNS–PEI complexes enhanced the production of interleukin-6 and tumor necrosis factor-α from peripheral blood mononuclear cells compared with CpG ODNs directly loaded on BNNS. Contrary to the free CpG ODNs or CpG ODNs directly loaded on BNNS, class B CpG ODNs loaded on the BNNS–PEI complexes induced interferon-α simultaneously. PEI coating may have changed the physical form of class B CpG ODNs on BNNS, which further affected their interaction with Toll-like receptor 9 and induced interferon-α. Therefore, BNNS–PEI complexes can be used to enhance the immunostimulatory effect and therapeutic activity of CpG ODNs and the treatment of diseases requiring interleukin-6, tumor necrosis factor-α, and interferon-α. PMID:26346655

Polyethyleneimine-functionalized boron nitride nanospheres as efficient carriers for enhancing the immunostimulatory effect of CpG oligodeoxynucleotides.

PubMed

Zhang, Huijie; Feng, Shini; Yan, Ting; Zhi, Chunyi; Gao, Xiao-Dong; Hanagata, Nobutaka

2015-01-01

CpG oligodeoxynucleotides (ODNs) stimulate innate and adaptive immune responses. Thus, these molecules are promising therapeutic agents and vaccine adjuvants against various diseases. In this study, we developed a novel CpG ODNs delivery system based on polyethyleneimine (PEI)-functionalized boron nitride nanospheres (BNNS). PEI was coated on the surface of BNNS via electrostatic interactions. The prepared BNNS-PEI complexes had positive zeta potential and exhibited enhanced dispersity and stability in aqueous solution. In vitro cytotoxicity assays revealed that the BNNS-PEI complexes with concentrations up to 100 μg/mL exhibited no obvious cytotoxicity. Furthermore, the positively charged surface of the BNNS-PEI complexes greatly improved the loading capacity and cellular uptake efficiency of CpG ODNs. Class B CpG ODNs loaded on the BNNS-PEI complexes enhanced the production of interleukin-6 and tumor necrosis factor-α from peripheral blood mononuclear cells compared with CpG ODNs directly loaded on BNNS. Contrary to the free CpG ODNs or CpG ODNs directly loaded on BNNS, class B CpG ODNs loaded on the BNNS-PEI complexes induced interferon-α simultaneously. PEI coating may have changed the physical form of class B CpG ODNs on BNNS, which further affected their interaction with Toll-like receptor 9 and induced interferon-α. Therefore, BNNS-PEI complexes can be used to enhance the immunostimulatory effect and therapeutic activity of CpG ODNs and the treatment of diseases requiring interleukin-6, tumor necrosis factor-α, and interferon-α.

[The influence of HOXB2 anti-sense oligodeoxynucleotides on the proliferation and expression of human umbilical vein endothelial cells].

PubMed

Zhang, X; Liu, X; Liu, L

2001-12-01

To explore the effects of HOXB2 anti-sense oligodeoxynucleotides (asodn) on the proliferation and the expression of human umbilical vein endothelial cells (HUVECs). Various concentrations of HOXB2 ASODN modified by thiophosphate were transfected into HUVECs by liposome mediation. MTT and RT-PCR methods were employed to determine the influence of different concentrations of ASODN on endothelial proliferation and the expression level of HOXB2 mRNA. After the transfection of HOXB2 ASODN, the endothelial proliferation was inhibited in dose-dependent manner. Simultaneously, the expression level of HOXB2 mRNA decreased significantly. HOXB2 might play important roles in the proliferation of endothelial cells.

Caged circular antisense oligonucleotides for photomodulation of RNA digestion and gene expression in cells

PubMed Central

Wu, Li; Wang, Yuan; Wu, Junzhou; Lv, Cong; Wang, Jie; Tang, Xinjing

2013-01-01

We synthesized three 20mer caged circular antisense oligodeoxynucleotides (R20, R20B2 and R20B4) with a photocleavable linker and an amide bond linker between two 10mer oligodeoxynucleotides. With these caged circular antisense oligodeoxynucleotides, RNA-binding affinity and its digestion by ribonuclease H were readily photomodulated. RNA cleavage rates were upregulated ∼43-, 25- and 15-fold for R20, R20B2 and R20B4, respectively, upon light activation in vitro. R20B2 and R20B4 with 2- or 4-nt gaps in the target RNA lost their ability to bind the target RNA even though a small amount of RNA digestion was still observed. The loss of binding ability indicated promising gene photoregulation through a non-enzymatic strategy. To test this strategy, three caged circular antisense oligonucleotides (PS1, PS2 and PS3) with 2′-OMe RNA and phosphorothioate modifications were synthesized to target GFP expression. Upon light activation, photomodulation of target hybridization and GFP expression in cells was successfully achieved with PS1, PS2 and PS3. These caged circular antisense oligonucleotides show promising applications of photomodulating gene expression through both ribonuclease H and non-enzyme involved antisense strategies. PMID:23104375

Development of a time-resolved fluorometric method for observing hybridization in living cells using fluorescence resonance energy transfer.

PubMed Central

Tsuji, A; Sato, Y; Hirano, M; Suga, T; Koshimoto, H; Taguchi, T; Ohsuka, S

2001-01-01

We previously showed that a specific kind of mRNA (c-fos) was detected in a living cell under a microscope by introducing two fluorescently labeled oligodeoxynucleotides, each labeled with donor or acceptor, into the cytoplasm, making them hybridize to adjacent locations on c-fos mRNA, and taking images of fluorescence resonance energy transfer (FRET) (A. Tsuji, H. Koshimoto, Y. Sato, M. Hirano. Y. Sei-Iida, S. Kondo, and K. Ishibashi, 2000, Biophys. J. 78:3260-3274). On the formed hybrid, the distance between donor and acceptor becomes close and FRET occurs. To observe small numbers of mRNA in living cells using this method, it is required that FRET fluorescence of hybrid must be distinguished from fluorescence of excess amounts of non-hybridizing probes and from cell autofluorescence. To meet these requirements, we developed a time-resolved method using acceptor fluorescence decays. When a combination of a donor having longer fluorescence lifetime and an acceptor having shorter lifetime is used, the measured fluorescence decays of acceptors under FRET becomes slower than the acceptor fluorescence decay with direct excitation. A combination of Bodipy493/503 and Cy5 was selected as donor and acceptor. When the formed hybrid had a configuration where the target RNA has no single-strand part between the two fluorophores, the acceptor fluorescence of hybrid had a sufficiently longer delay to detect fluorescence of hybrid in the presence of excess amounts of non-hybridizing probes. Spatial separation of 10-12 bases between two fluorophores on the hybrid is also required. The decay is also much slower than cell autofluorescence, and smaller numbers of hybrid were detected with less interference of cell autofluorescence in the cytoplasm of living cells under a time-resolved fluorescence microscope with a time-gated function equipped camera. The present method will be useful when observing induced expressions of mRNA in living cells. PMID:11423432

Isolation and characterization of full-length cDNA clones coding for cholinesterase from fetal human tissues

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

Prody, C.A.; Zevin-Sonkin, D.; Gnatt, A.

1987-06-01

To study the primary structure and regulation of human cholinesterases, oligodeoxynucleotide probes were prepared according to a consensus peptide sequence present in the active site of both human serum pseudocholinesterase and Torpedo electric organ true acetylcholinesterase. Using these probes, the authors isolated several cDNA clones from lambdagt10 libraries of fetal brain and liver origins. These include 2.4-kilobase cDNA clones that code for a polypeptide containing a putative signal peptide and the N-terminal, active site, and C-terminal peptides of human BtChoEase, suggesting that they code either for BtChoEase itself or for a very similar but distinct fetal form of cholinesterase. Inmore » RNA blots of poly(A)/sup +/ RNA from the cholinesterase-producing fetal brain and liver, these cDNAs hybridized with a single 2.5-kilobase band. Blot hybridization to human genomic DNA revealed that these fetal BtChoEase cDNA clones hybridize with DNA fragments of the total length of 17.5 kilobases, and signal intensities indicated that these sequences are not present in many copies. Both the cDNA-encoded protein and its nucleotide sequence display striking homology to parallel sequences published for Torpedo AcChoEase. These finding demonstrate extensive homologies between the fetal BtChoEase encoded by these clones and other cholinesterases of various forms and species.« less

The cel3 gene of Agaricus bisporus codes for a modular cellulase and is transcriptionally regulated by the carbon source.

PubMed Central

Chow, C M; Yagüe, E; Raguz, S; Wood, D A; Thurston, C F

1994-01-01

A 52-kDa protein, CEL3, has been separated from the culture filtrate of Agaricus bisporus during growth on cellulose. A PCR-derived probe was made, with a degenerate oligodeoxynucleotide derived from the amino acid sequence of a CEL3 CNBr cleavage product and was used to select cel3 cDNA clones from an A. bisporus cDNA library. Two allelic cDNAs were isolated. They showed 98.8% identity of their nucleotide sequences. The deduced amino acid sequence and domain architecture of CEL3 showed a high degree of similarity to those of cellobiohydrolase II of Trichoderma reesei. Functional expression of cel3 cDNA in Saccharomyces cerevisiae was achieved by placing it under the control of a constitutive promoter and fusing it to the yeast invertase signal sequence. Recombinant CEL3 secreted by yeast showed enzymatic activity towards crystalline cellulose. At long reaction times, CEL3 was also able to degrade carboxymethyl cellulose. Northern (RNA) analysis showed that cel3 gene expression was induced by cellulose and repressed by glucose, fructose, 2-deoxyglucose, and lactose. Glycerol, mannitol, sorbitol, and maltose were neutral carbon sources. Nuclear run-on analysis showed that the rate of synthesis of cel3 mRNA in cellulose-grown cultures was 13 times higher than that in glucose-grown cultures. A low basal rate of cel3 mRNA synthesis was observed in the nuclei isolated from glucose-grown mycelia. Images PMID:8085821

Effect of anti-sense oligodeoxynucleotides homeobox B2 on the proliferation and expression of primary human umbilical vein endothelial cells.

PubMed

Liu, Xusheng; Zhang, Xiaoqi

2002-02-01

To explore the effect of homeobox B2 (HOXB2) anti sense oligodeoxynucleotides (asodn) on the proliferation and expression of primary human umbilical vein endothelial cells (HUVECs). Various concentrations of HOXB2 asodn modified by thiophosphate transfected the induction of liposome into HUVECs. MTT a nd RT-PCR methods were employed to determine the effect of different conc ent rations of asodn on the endothelial proliferation and the expression level of HOXB2 mRNA. After the transfection of HOXB2 asodn, the endothelial proliferation was inhibited in a dose-dependent fashion. Simultaneously, the expression of HOXB2 mRNA decreased significantly. HOXB2 plays an important role in the proliferation of endothelia.

CpG oligodeoxynucleotides containing GACGTT motifs enhance the immune responses elicited by a goose parvovirus vaccine in ducks.

PubMed

Lee, Jai-Wei; Lin, Yu-Ming; Yen, Ting-Ying; Yang, Wen-Jen; Chu, Chun-Yen

2010-11-23

Recombinant parvovirus VP2 (rVP2) was formulated with different types of adjuvant, including aluminum adjuvant and CpG oligodeoxynucleotides (ODNs), and the immunological responses after vaccination in ducks were examined. In comparison with the control group, production of rVP2-specific antibodies, expression of cytokines in peripheral blood mononuclear cells (PBMC) stimulated by rVP2, and percentage of CD4(+)/CD8(+) cells in PBMC were significantly increased in ducks immunized with rVP2 formulated with CpG ODNs containing 3 copies of GACGTT motif. CpG ODNs with GACGTT motifs might be used to improve the efficacy of vaccines for ducks. Copyright © 2010 Elsevier Ltd. All rights reserved.

Distinct Effects of Monophosphoryl Lipid A, Oligodeoxynucleotide CpG, and Combination Adjuvants on Modulating Innate and Adaptive Immune Responses to Influenza Vaccination

PubMed Central

Ko, Eun-Ju; Lee, Young-Tae; Lee, Youri; Kim, Ki-Hye

2017-01-01

Monophosphoryl lipid A (MPL) and oligodeoxynucleotide CpG are toll-like receptor (TLR) 4 and 9 agonist, respectively. Here, we investigated the effects of MPL, CpG, and combination adjuvants on stimulating in vitro dendritic cells (DCs), in vivo innate and adaptive immune responses, and protective efficacy of influenza vaccination. Combination of MPL and CpG was found to exhibit distinct effects on stimulating DCs in vitro to secrete IL-12p70 and tumor necrosis factor (TNF)-α and proliferate allogeneic CD8 T cells. Prime immunization of mice with inactivated split influenza vaccine in the presence of low dose MPL+CpG adjuvants increased the induction of virus-specific IgG and IgG2a isotype antibodies. MPL and CpG adjuvants contribute to improving the efficacy of prime influenza vaccination against lethal influenza challenge as determined by body weight monitoring, lung function, viral titers, and histology. A combination of MPL and CpG adjuvants was effective in improving vaccine efficacy as well as in reducing inflammatory immune responses locally and in inducing cellular immune responses upon lethal influenza virus challenge. This study demonstrates unique adjuvant effects of MPL, CpG, and combination adjuvants on modulating innate and adaptive immune responses to influenza prime vaccination. PMID:29093654

Interactions of the EcoRV restriction endonuclease with fluorescent oligodeoxynucleotides.

PubMed

Erskine, S G; Halford, S E

1995-05-19

A self-complementary dodecadeoxyribonucleotide that contains the recognition sequence for the R.EcoRV ENase was synthesised with a primary amino group at its 5' terminus. The 5' amino function was labeled with the fluorescent dye 5-[dimethylamino] napthalene-1-sulfonyl chloride. The labeled oligodeoxyribonucleotide in its duplex form was shown to be a suitable substrate for kinetic studies on the ENase and that no significant dye-DNA or dye-protein interactions occurred. Finally, the binding of R.EcoRV to the labeled DNA was followed by detecting the fluorescence resonance energy transfer between the tryptophans of the protein and the fluorescent labels of the DNA.

Isolation and characterization of full-length cDNA clones coding for cholinesterase from fetal human tissues.

PubMed Central

Prody, C A; Zevin-Sonkin, D; Gnatt, A; Goldberg, O; Soreq, H

1987-01-01

To study the primary structure and regulation of human cholinesterases, oligodeoxynucleotide probes were prepared according to a consensus peptide sequence present in the active site of both human serum pseudocholinesterase (BtChoEase; EC 3.1.1.8) and Torpedo electric organ "true" acetylcholinesterase (AcChoEase; EC 3.1.1.7). Using these probes, we isolated several cDNA clones from lambda gt10 libraries of fetal brain and liver origins. These include 2.4-kilobase cDNA clones that code for a polypeptide containing a putative signal peptide and the N-terminal, active site, and C-terminal peptides of human BtChoEase, suggesting that they code either for BtChoEase itself or for a very similar but distinct fetal form of cholinesterase. In RNA blots of poly(A)+ RNA from the cholinesterase-producing fetal brain and liver, these cDNAs hybridized with a single 2.5-kilobase band. Blot hybridization to human genomic DNA revealed that these fetal BtChoEase cDNA clones hybridize with DNA fragments of the total length of 17.5 kilobases, and signal intensities indicated that these sequences are not present in many copies. Both the cDNA-encoded protein and its nucleotide sequence display striking homology to parallel sequences published for Torpedo AcChoEase. These findings demonstrate extensive homologies between the fetal BtChoEase encoded by these clones and other cholinesterases of various forms and species. Images PMID:3035536

Intermolecular ‘cross-torque’: the N4-cytosine propargyl residue is rotated to the ‘CH’-edge as a result of Watson–Crick interaction

PubMed Central

Domingo, Olwen; Hellmuth, Isabell; Jäschke, Andres; Kreutz, Christoph; Helm, Mark

2015-01-01

Propargyl groups are attractive functional groups for labeling purposes, as they allow CuAAC-mediated bioconjugation. Their size minimally exceeds that of a methyl group, the latter being frequent in natural nucleotide modifications. To understand under which circumstances propargyl-containing oligodeoxynucleotides preserve base pairing, we focused on the exocyclic amine of cytidine. Residues attached to the exocyclic N4 may orient away from or toward the Watson–Crick face, ensuing dramatic alteration of base pairing properties. ROESY-NMR experiments suggest a uniform orientation toward the Watson–Crick face of N4-propargyl residues in derivatives of both deoxycytidine and 5-methyl-deoxycytidine. In oligodeoxynucleotides, however, UV-melting indicated that N4-propargyl-deoxycytidine undergoes standard base pairing. This implies a rotation of the propargyl moiety toward the ‘CH’-edge as a result of base pairing on the Watson–Crick face. In oligonucleotides containing the corresponding 5-methyl-deoxycytidine derivative, dramatically reduced melting temperatures indicate impaired Watson–Crick base pairing. This was attributed to a steric clash of the propargyl moiety with the 5-methyl group, which prevents back rotation to the ‘CH’-edge, consequently preventing Watson–Crick geometry. Our results emphasize the tendency of an opposing nucleic acid strand to mechanically rotate single N4-substituents to make way for Watson–Crick base pairing, providing no steric hindrance is present on the ‘CH’-edge. PMID:25934805

A limited CpG-containing oligodeoxynucleotide therapy regimen induces sustained suppression of allergic airway inflammation in mice

PubMed Central

Kozy, Heather M.; Lum, Jeremy A.; Sweetwood, Rosemary; Chu, Mabel; Cunningham, Cameron R.; Salamon, Hugh; Lloyd, Clare M.; Coffman, Robert L.; Hessel, Edith M.

2015-01-01

Background CpG-containing oligodeoxynucleotides (CpG-ODN) are potent inhibitors of Th2-mediated allergic airway disease in sensitized mice challenged with allergen. A single treatment has transient effects but a limited series of treatments has potential to achieve clinically meaningful sustained inhibition of allergic airway disease. Objective To optimize the treatment regimen and determine the mechanisms of action in mice of an inhaled form of CpG-ODN being developed for human asthma treatment. Methods A limited series of weekly intranasal 1018 ISS (CpG-ODN; B-class) treatments were given to ragweed allergen-sensitized mice chronically exposed to allergen during and after the 1018 ISS treatment regimen. Treatment effects were evaluated by measuring effect on lung Th2 cytokines and eosinophilia as well as lung dendritic cell function and T cell responses. Results Twelve intranasal 1018 ISS treatments induced significant suppression of BAL eosinophilia and IL-4, IL-5, and IL-13 levels and suppression was maintained through 13 weekly ragweed exposures administered after treatment cessation. At least 5 treatments were required for lasting Th2 suppression. CpG-ODN induced moderate Th1 responses but Th2 suppression did not require IFN-γ. Th2 suppression was associated with induction of a regulatory T cell response. Conclusion A short series of CpG-ODN treatments results in sustained suppression of allergic lung inflammation induced by a clinically relevant allergen. PMID:24464743

Amelioration of collagen-induced arthritis using antigen-loaded dendritic cells modified with NF-κB decoy oligodeoxynucleotides

PubMed Central

Jiang, Hongmei; Hu, Henggui; Zhang, Yali; Yue, Ping; Ning, Lichang; Zhou, Yan; Shi, Ping; Yuan, Rui

2017-01-01

Dendritic cells (DCs) play an important role in the initiation of autoimmunity in rheumatoid arthritis (RA); therefore, the use of DCs needs to be explored to develop new therapeutic approaches for RA. Here, we investigated the therapeutic effect of bovine type II collagen (BIIC)-loaded DCs modified with NF-κB decoy oligodeoxynucleotides (ODNs) on collagen-induced arthritis (CIA) in rats and explored the underlying mechanisms. DCs treated with BIIC and NF-κB decoy ODNs exhibited features of immature DCs with low levels of costimulatory molecule (CD80 and CD86) expression. The development of arthritis in rats with CIA injected with BIIC + NF-κB decoy ODN-propagated DCs (BIIC–decoy DCs) was significantly ameliorated compared to that in rats injected with BIIC-propagated DCs or phosphate-buffered saline. We also found that the BIIC–decoy DCs exerted antiarthritis effects by inhibiting self-lymphocyte proliferative response and suppressing IFN-γ and anti-BIIC antibody production and inducing IL-10 antibody production. Additionally, antihuman serum antibodies were successfully produced in the rats treated with BIIC–decoy DCs but not in those treated with NF-κB decoy ODN-propagated DCs; moreover, the BIIC–decoy DCs did not affect immune function in the normal rats. These findings suggested that NF-κB decoy ODN-modified DCs loaded with a specific antigen might offer a practical method for the treatment of human RA. PMID:29075103

TLR9-ERK-mTOR signaling is critical for autophagic cell death induced by CpG oligodeoxynucleotide 107 combined with irradiation in glioma cells

PubMed Central

Li, Xiaoli; Cen, Yanyan; Cai, Yongqing; Liu, Tao; Liu, Huan; Cao, Guanqun; Liu, Dan; Li, Bin; Peng, Wei; Zou, Jintao; Pang, Xueli; Zheng, Jiang; Zhou, Hong

2016-01-01

Synthetic oligodeoxynucleotides containing unmethylated CpG dinucleotides (CpG ODN) function as potential radiosensitizers for glioma treatment, although the underlying mechanism is unclear. It was observed that CpG ODN107, when combined with irradiation, did not induce apoptosis. Herein, the effect of CpG ODN107 + irradiation on autophagy and the related signaling pathways was investigated. In vitro, CpG ODN107 + irradiation induced autophagosome formation, increased the ratio of LC3 II/LC3 I, beclin 1 and decreased p62 expression in U87 cells. Meanwhile, CpG ODN107 also increased LC3 II/LC3 I expression in U251 and CHG-5 cells. In vivo, CpG ODN107 combined with local radiotherapy induced autophagosome formation in orthotopic transplantation tumor. Investigation of the molecular mechanisms demonstrated that CpG ODN107 + irradiation increased the levels of TLR9 and p-ERK, and decreased the level of p-mTOR in glioma cells. Further, TLR9-specific siRNA could affect the expressions of p-ERK and autophagy-related proteins in glioma cells. Taken together, CpG ODN107 combined with irradiation could induce autophagic cell death, and this effect was closely related to the TLR9-ERK-mTOR signaling pathway in glioma cells, providing new insights into the investigation mechanism of CpG ODN. PMID:27251306

Synthesis of G-N2-(CH2)3-N2-G Trimethylene DNA interstrand cross-links

PubMed Central

Gruppi, Francesca; Salyard, Tracy L. Johnson; Rizzo, Carmelo J.

2014-01-01

The synthesis of G-N2-(CH2)3-N2-G trimethylene DNA interstrand cross-links (ICLs) in a 5′-CG-3′ and 5′-GC-3′ sequence from oligodeoxynucleotides containing N2-(3-aminopropyl)-2′-deoxyguanosine and 2-fluoro-O6-(trimethylsilylethyl)inosine is presented. Automated solid-phase DNA synthesis was used for unmodified bases and modified nucleotides were incorporated via their corresponding phosphoramidite reagent by a manual coupling protocol. The preparation of the phosphoramidite reagents for incorporation of N2-(3-aminopropyl)-2′-deoxyguanosine is reported. The high-purity trimethylene DNA interstrand cross-link product is obtained through a nucleophilic aromatic substitution reaction between the N2-(3-aminopropyl)-2′-deoxyguanosine and 2-fluoro-O6-(trimethylsilylethyl)inosine containing oligodeoxynucleotides. PMID:25431636

78 FR 26794 - Prospective Grant of Exclusive License: Use of Oligodeoxynucleotide as Neuroprotectants in...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-08

... following ischemic damage to the central nervous system. Structural differences between various ODNs may... ODNs mimic signals of invading pathogens. ODN motifs trigger immune system responses via Toll-like...

Alternate-strand triple-helix formation by the 3'-3'-linked oligodeoxynucleotides with the intercalators at the junction point.

PubMed

Ueno, Y; Mikawa, M; Hoshika, S; Takeba, M; Kitade, Y; Matsuda, A

2001-01-01

3'-3'-Linked oligodeoxynucleotides (ODNs) with the anthraquinonyl group at the junction point were synthesized on a DNA synthesizer using a controlled pore glass (CPG), which has pentaerythritol carrying the intercalator at one of the four hydroxymethyl groups. Stability of the triplexes with the target duplexes was studied by thermal denaturation. The 3'-3'-linked ODNs with the anthraquinonyl group enhanced the thermal stability of the triplexes when compared with those without the intercalator and the unmodified nonamer. The inhibitory activity of the 3'-3'-linked ODNs against the cleavage of the target DNA by the restriction enzyme Hind III was tested. It was found that the 3'-3'-linked ODN with the anthraquinonyl group at the junction point inhibited the cleavage by the enzyme more effectively than the nonamer and the 3'-3'-linked ODN without the intercalator.

CpG oligodeoxynucleotides are a potent adjuvant for an inactivated polio vaccine produced from Sabin strains of poliovirus.

PubMed

Yang, Chunting; Shi, Huiying; Zhou, Jun; Liang, Yanwen; Xu, Honglin

2009-11-05

Poliovirus transmission is controlled globally through world-wide use of a live attenuated oral polio vaccine (OPV). However, the imminence of global poliovirus eradication calls for a switch to the inactivated polio vaccine (IPV). Given the limited manufacturing capacity and high cost of IPV, this switch is unlikely in most developing and undeveloped countries. Adjuvantation is an effective strategy for antigen sparing. In this study, we evaluated the adjuvanticity of CpG oligodeoxynucleotides (CpG-ODN) for an experimental IPV produced from Sabin strains of poliovirus. Our results showed that CpG-ODN, alone or in combination with alum, can significantly enhance both the humoral and cellular immune responses to IPV in mice, and, consequently, the antigen dose could be reduced substantially. Therefore, our study suggests that the global use of IPV could be facilitated by using CpG-ODN or other feasible adjuvants.

Electrochemical detection of microRNAs via gap hybridization assay.

PubMed

Pöhlmann, Christopher; Sprinzl, Mathias

2010-06-01

MicroRNAs have recently been associated with cancer development by acting as tumor suppressors or oncogenes and could therefore be applied as molecular markers for early diagnosis of cancer. In this work, we established a rapid, selective, and sensitive gap hybridization assay for detection of mature microRNAs based on four components DNA/RNA hybridization and electrochemical detection using esterase 2-oligodeoxynucleotide conjugates. Complementary binding of microRNA to a gap built of capture and detector oligodeoxynucleotide, the reporter enzyme is brought to the vicinity of the electrode and produces enzymatically an electrochemical signal. In the absence of microRNA, the gap between capture and detector oligodeoxynucleotide is not filled, and missing base stacking energy destabilizes the hybridization complex. The gap hybridization assay demonstrates selective detection of miR-16 within a mixture of other miRNAs, including the feasibility of single mismatch discrimination. Applying the biosensor assay, a detection limit of 2 pM or 2 amol of miR-16 was obtained. Using isolated total RNA from human breast adenocarcinoma MCF-7 cells, the assay detected specifically miR-21 and miR-16 in parallel, and higher expression of oncogene miR-21 compared to miR-16 was demonstrated. Including RNA isolation, the gap hybridization assay was developed with a total assay time of 60 min and without the need for reverse transcription PCR amplification of the sample. The characteristics of the assay developed in this work could satisfy the need for rapid and easy methods for early cancer marker detection in clinical diagnostics.

Activation of Notch3 in Glomeruli Promotes the Development of Rapidly Progressive Renal Disease

PubMed Central

El Machhour, Fala; Keuylian, Zela; Kavvadas, Panagiotis; Dussaule, Jean-Claude

2015-01-01

Notch3 expression is found in the glomerular podocytes of patients with lupus nephritis or focal segmental GN but not in normal kidneys. Here, we show that activation of the Notch3 receptor in the glomeruli is a turning point inducing phenotypic changes in podocytes promoting renal inflammation and fibrosis and leading to disease progression. In a model of rapidly progressive GN, Notch3 expression was induced by several-fold in podocytes concurrently with disease progression. By contrast, mice lacking Notch3 expression were protected because they exhibited less proteinuria, uremia, and inflammatory infiltration. Podocyte outgrowth from glomeruli isolated from wild-type mice during the early phase of the disease was higher than outgrowth from glomeruli of mice lacking Notch3. In vitro studies confirmed that podocytes expressing active Notch3 reorganize their cytoskeleton toward a proliferative/migratory and inflammatory phenotype. We then administered antisense oligodeoxynucleotides targeting Notch3 or scramble control oligodeoxynucleotides in wild-type mice concomitant to disease induction. Both groups developed chronic renal disease, but mice injected with Notch3 antisense had lower values of plasma urea and proteinuria and inflammatory infiltration. The improvement of renal function was accompanied by fewer deposits of fibrin within the glomeruli and by decreased peritubular inflammation. Finally, abnormal Notch3 staining was observed in biopsy samples of patients with crescentic GN. These results demonstrate that abnormal activation of Notch3 may be involved in the progression of renal disease by promoting migratory and proinflammatory pathways. Inhibiting Notch3 activation could be a novel, promising approach to treat GN. PMID:25421557

Micro-array versus nano-array platforms: a comparative study for ODN detection based on SPR enhanced ellipsometry

NASA Astrophysics Data System (ADS)

Celen, Burcu; Demirel, Gökhan; Piskin, Erhan

2011-04-01

The rapid and sensitive detection of DNA has recently attracted worldwide attention for a variety of disease diagnoses and detection of harmful bacteria in food and drink. In this paper, we carried out a comparative study based on surface plasmon resonance enhanced ellipsometry (SPREE) for the detection of oligodeoxynucleotides (ODNs) using micro- and nano-array platforms. The micro-arrayed surfaces were fabricated by a photolithography approach using different types of mask having varying size and shape. Well-ordered arrays of high aspect ratio polymeric nanotubes were also obtained using high molecular weight polystyrene (PS) and anodic aluminum oxide (AAO) membranes having 200 nm pore diameters. The SPREE sensors were then prepared by direct coupling of thiolated probe-ODNs, which contain suitable spacer arms, on gold-coated micro- and nano-arrayed surfaces. We experimentally demonstrated that, for the first time, gold-coated free standing polymeric nano-arrayed platforms can easily be produced and lead to a significant sensor sensitivity gain compared to that of the conventional SPREE surfaces of about four times. We believe that such an enhancement in sensor response could be useful for next generation sensor systems.

Inhibition of Human Immunodeficiency Virus Replication by Antisense Oligodeoxynucleotides

NASA Astrophysics Data System (ADS)

Goodchild, John; Agrawal, Sudhir; Civeira, Maria P.; Sarin, Prem S.; Sun, Daisy; Zamecnik, Paul C.

1988-08-01

Twenty different target sites within human immunodeficiency virus (HIV) RNA were selected for studies of inhibition of HIV replication by antisense oligonucleotides. Target sites were selected based on their potential capacity to block recognition functions during viral replication. Antisense oligomers complementary to sites within or near the sequence repeated at the ends of retrovirus RNA (R region) and to certain splice sites were most effective. The effect of antisense oligomer length on inhibiting virus replication was also investigated, and preliminary toxicity studies in mice show that these compounds are toxic only at high levels. The results indicate potential usefulness for these oligomers in the treatment of patients with acquired immunodeficiency syndrome (AIDS) and AIDS-related complex either alone or in combination with other drugs.

Trigeminal nerve injury-induced thrombospondin-4 up-regulation contributes to orofacial neuropathic pain states in a rat model.

PubMed

Li, K-W; Kim, D-S; Zaucke, F; Luo, Z D

2014-04-01

Injury to the trigeminal nerve often results in the development of chronic pain states including tactile allodynia, or hypersensitivity to light touch, in orofacial area, but its underlying mechanisms are poorly understood. Peripheral nerve injury has been shown to cause up-regulation of thrombospondin-4 (TSP4) in dorsal spinal cord that correlates with neuropathic pain development. In this study, we examined whether injury-induced TSP4 is critical in mediating orofacial pain development in a rat model of chronic constriction injury to the infraorbital nerve. Orofacial sensitivity to mechanical stimulation was examined in a unilateral infraorbital nerve ligation rat model. The levels of TSP4 in trigeminal ganglia and associated spinal subnucleus caudalis and C1/C2 spinal cord (Vc/C2) from injured rats were examined at time points correlating with the initiation and peak orofacial hypersensitivity. TSP4 antisense and mismatch oligodeoxynucleotides were intrathecally injected into injured rats to see if antisense oligodeoxynucleotide treatment could reverse injury-induced TSP4 up-regulation and orofacial behavioural hypersensitivity. Our data indicated that trigeminal nerve injury induced TSP4 up-regulation in Vc/C2 at a time point correlated with orofacial tactile allodynia. In addition, intrathecal treatment with TSP4 antisense, but not mismatch, oligodeoxynucleotides blocked both injury-induced TSP4 up-regulation in Vc/C2 and behavioural hypersensitivity. Our data support that infraorbital nerve injury leads to TSP4 up-regulation in trigeminal spinal complex that contributes to orofacial neuropathic pain states. Blocking this pathway may provide an alternative approach in management of orofacial neuropathic pain states. © 2013 European Pain Federation - EFIC®

Oligo/Polynucleotide-Based Gene Modification: Strategies and Therapeutic Potential

PubMed Central

Sargent, R. Geoffrey; Kim, Soya

2011-01-01

Oligonucleotide- and polynucleotide-based gene modification strategies were developed as an alternative to transgene-based and classical gene targeting-based gene therapy approaches for treatment of genetic disorders. Unlike the transgene-based strategies, oligo/polynucleotide gene targeting approaches maintain gene integrity and the relationship between the protein coding and gene-specific regulatory sequences. Oligo/polynucleotide-based gene modification also has several advantages over classical vector-based homologous recombination approaches. These include essentially complete homology to the target sequence and the potential to rapidly engineer patient-specific oligo/polynucleotide gene modification reagents. Several oligo/polynucleotide-based approaches have been shown to successfully mediate sequence-specific modification of genomic DNA in mammalian cells. The strategies involve the use of polynucleotide small DNA fragments, triplex-forming oligonucleotides, and single-stranded oligodeoxynucleotides to mediate homologous exchange. The primary focus of this review will be on the mechanistic aspects of the small fragment homologous replacement, triplex-forming oligonucleotide-mediated, and single-stranded oligodeoxynucleotide-mediated gene modification strategies as it relates to their therapeutic potential. PMID:21417933

Crosslinking transcription factors to their recognition sequences with PtII complexes

NASA Technical Reports Server (NTRS)

Chu, B. C.; Orgel, L. E.

1992-01-01

We have prepared phosphorothioate-containing cyclic oligodeoxynucleotides that fold into 'dumbbells' containing CRE and TRE sequences, the binding sequences for the CREB and JUN proteins, respectively. Six phosphorothioate residues were introduced into each of the recognition sequences. K2PtCl4 crosslinks CRE to CREB and TRE to JUN. The extent of crosslinking is about eight times greater than that observed with standard oligodeoxynucleotides and amounts to 30-50% of the efficiency of non-covalent association as estimated by gel-shift assays. Crosslinking is reversed by incubation with NaCN. The crosslinking reaction is specific--a dumbbell oligonucleotide with six phosphorothioate groups introduced into the Sp1 recognition sequence could not be crosslinked efficiently to CREB or JUN proteins with K2PtCl4. The binding of TRE to CREB is not strong enough for effective detection by gel-shift assays, but the TRE-CREB complex is crosslinked efficiently by K2PtCl4 and can then readily be detected.

Polymer support oligonucleotide synthesis XVIII: use of beta-cyanoethyl-N,N-dialkylamino-/N-morpholino phosphoramidite of deoxynucleosides for the synthesis of DNA fragments simplifying deprotection and isolation of the final product.

PubMed Central

Sinha, N D; Biernat, J; McManus, J; Köster, H

1984-01-01

Various 5'O-N-protected deoxynucleoside-3'-O-beta-cyanoethyl-N,N-dialkylamino-/N- morpholinophosphoramidites were prepared from beta-cyanoethyl monochlorophosphoramidites of N,N-dimethylamine, N,N-diisopropylamine and N-morpholine. These active deoxynucleoside phosphates have successfully been used for oligodeoxynucleotide synthesis on controlled pore glass as polymer support and are very suitable for automated DNA-synthesis due to their stability in solution. The intermediate dichloro-beta- cyanoethoxyphosphine can easily be prepared free from any PC1(3) contamination. The active monomers obtained from beta-cyanoethyl monochloro N,N- diisopropylaminophosphoramidites are favoured. Cleavage of the oligonucleotide chain from the polymer support, N-deacylation and deprotection of beta-cyanoethyl group from the phosphate triester moiety can be performed in one step with concentrated aqueous ammonia. Mixed oligodeoxynucleotides are characterized by the sequencing method of Maxam and Gilbert. Images PMID:6547529

DNA containing CpG motifs induces angiogenesis

NASA Astrophysics Data System (ADS)

Zheng, Mei; Klinman, Dennis M.; Gierynska, Malgorzata; Rouse, Barry T.

2002-06-01

New blood vessel formation in the cornea is an essential step in the pathogenesis of a blinding immunoinflammatory reaction caused by ocular infection with herpes simplex virus (HSV). By using a murine corneal micropocket assay, we found that HSV DNA (which contains a significant excess of potentially bioactive "CpG" motifs when compared with mammalian DNA) induces angiogenesis. Moreover, synthetic oligodeoxynucleotides containing CpG motifs attract inflammatory cells and stimulate the release of vascular endothelial growth factor (VEGF), which in turn triggers new blood vessel formation. In vitro, CpG DNA induces the J774A.1 murine macrophage cell line to produce VEGF. In vivo CpG-induced angiogenesis was blocked by the administration of anti-mVEGF Ab or the inclusion of "neutralizing" oligodeoxynucleotides that specifically oppose the stimulatory activity of CpG DNA. These findings establish that DNA containing bioactive CpG motifs induces angiogenesis, and suggest that CpG motifs in HSV DNA may contribute to the blinding lesions of stromal keratitis.

Chemistry of the 8-Nitroguanine DNA Lesion: Reactivity, Labelling and Repair.

PubMed

Alexander, Katie J; McConville, Matthew; Williams, Kathryn R; Luzyanin, Konstantin V; O'Neil, Ian A; Cosstick, Richard

2018-02-26

The 8-nitroguanine lesion in DNA is increasingly associated with inflammation-related carcinogenesis, whereas the same modification on guanosine 3',5'-cyclic monophosphate generates a second messenger in NO-mediated signal transduction. Very little is known about the chemistry of 8-nitroguanine nucleotides, despite the fact that their biological effects are closely linked to their chemical properties. To this end, a selection of chemical reactions have been performed on 8-nitroguanine nucleosides and oligodeoxynucleotides. Reactions with alkylating reagents reveal how the 8-nitro substituent affects the reactivity of the purine ring, by significantly decreasing the reactivity of the N2 position, whilst the relative reactivity at N1 appears to be enhanced. Interestingly, the displacement of the nitro group with thiols results in an efficient and specific method of labelling this lesion and is demonstrated in oligodeoxynucleotides. Additionally, the repair of this lesion is also shown to be a chemically feasible reaction through a reductive denitration with a hydride source. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Apoptosis is rapidly triggered by antisense depletion of MCL-1 in differentiating U937 cells.

PubMed

Moulding, D A; Giles, R V; Spiller, D G; White, M R; Tidd, D M; Edwards, S W

2000-09-01

Mcl-1 is a member of the Bcl-2 protein family, which has been shown to delay apoptosis in transfection and/or overexpression experiments. As yet no gene knockout mice have been engineered, and so there is little evidence to show that loss of Mcl-1 expression is sufficient to trigger apoptosis. U937 cells constitutively express the antiapoptotic protein Bcl-2; but during differentiation, in response to the phorbol ester PMA (phorbol 12 beta-myristate 13 alpha-acetate), Mcl-1 is transiently induced. The purpose of this investigation was to determine the functional role played by Mcl-1 in this differentiation program. Mcl-1 expression was specifically disrupted by chimeric methylphosphonate/phosphodiester antisense oligodeoxynucleotides to just 5% of control levels. The depletion of Mcl-1 messenger RNA (mRNA) and protein was both rapid and specific, as indicated by the use of control oligodeoxynucleotides and analysis of the expression of other BCL2 family members and PMA-induced tumor necrosis factor-alpha (TNF-alpha). Specific depletion of Mcl-1 mRNA and protein, in the absence of changes in cellular levels of Bcl-2, results in a rapid entry into apoptosis. Levels of the proapoptotic protein Bax remained unchanged during differentiation, while Bak expression doubled within 24 hours. Apoptosis was detected within 4 hours of Mcl-1 antisense treatment by a variety of parameters including a novel live cell imaging technique allowing correlation of antisense treatment and apoptosis in individual cells. The induction of Mcl-1 is required to prevent apoptosis during differentiation of U937 cells, and the constitutive expression of Bcl-2 is unable to compensate for the loss of Mcl-1. (Blood. 2000;96:1756-1763)

Conformationally restricted analogs of BD1008 and an antisense oligodeoxynucleotide targeting sigma1 receptors produce anti-cocaine effects in mice.

PubMed

Matsumoto, R R; McCracken, K A; Friedman, M J; Pouw, B; De Costa, B R; Bowen, W D

2001-05-11

Cocaine's ability to interact with sigma receptors suggests that these proteins mediate some of its behavioral effects. Therefore, three novel sigma receptor ligands with antagonist activity were evaluated in Swiss Webster mice: BD1018 (3S-1-[2-(3,4-dichlorophenyl)ethyl]-1,4-diazabicyclo[4.3.0]nonane), BD1063 (1-[2-(3,4-dichlorophenyl)ethyl]-4-methylpiperazine), and LR132 (1R,2S-(+)-cis-N-[2-(3,4-dichlorophenyl)ethyl]-2-(1-pyrrolidinyl)cyclohexylamine). Competition binding assays demonstrated that all three compounds have high affinities for sigma1 receptors. The three compounds vary in their affinities for sigma2 receptors and exhibit negligible affinities for dopamine, opioid, GABA(A) and NMDA receptors. In behavioral studies, pre-treatment of mice with BD1018, BD1063, or LR132 significantly attenuated cocaine-induced convulsions and lethality. Moreover, post-treatment with LR132 prevented cocaine-induced lethality in a significant proportion of animals. In contrast to the protection provided by the putative antagonists, the well-characterized sigma receptor agonist di-o-tolylguanidine (DTG) and the novel sigma receptor agonist BD1031 (3R-1-[2-(3,4-dichlorophenyl)ethyl]-1,4-diazabicyclo[4.3.0]nonane) each worsened the behavioral toxicity of cocaine. At doses where alone, they produced no significant effects on locomotion, BD1018, BD1063 and LR132 significantly attenuated the locomotor stimulatory effects of cocaine. To further validate the hypothesis that the anti-cocaine effects of the novel ligands involved antagonism of sigma receptors, an antisense oligodeoxynucleotide against sigma1 receptors was also shown to significantly attenuate the convulsive and locomotor stimulatory effects of cocaine. Together, the data suggests that functional antagonism of sigma receptors is capable of attenuating a number of cocaine-induced behaviors.

Egr-1 antisense oligodeoxynucleotide administration into the olfactory bulb impairs olfactory learning in the greater short-nosed fruit bat Cynopterus sphinx.

PubMed

Ganesh, Ambigapathy; Bogdanowicz, Wieslaw; Balamurugan, Krishnaswamy; Ragu Varman, Durairaj; Rajan, Koilmani Emmanuvel

2012-08-30

Postsynaptic densities (PSDs) contain proteins that regulate synaptic transmission. We examined two important examples of these, calcium/calmodulin-dependent protein kinase II (CaMKII) and PSD-95, in regard to the functional role of early growth response gene-1 (egr-1) in regulation of olfactory learning in the greater short-nosed fruit bat Cynopterus sphinx (family Pteropodidae). To test whether activation of egr-1 in the olfactory bulb (OB) is required for olfactory memory of these bats, bilaterally canulated individuals were infused with antisense (AS) or non-sense (NS)-oligodeoxynucleotides (ODN) of egr-1, or with phosphate buffer saline (PBS), 2h before the olfactory training. Our results showed that behavioral training significantly up-regulates immediate early gene (IEG) EGR-1 and key synaptic proteins Synaptotagmin-1(SYT-1), CaMKII and PSD-95, and phosphorylation of CaMKII in the OB at the protein level per se. Subsequently, we observed that egr-1 antisense-ODN infusion in the OB impaired olfactory memory and down regulates the expression of CaMKII and PSD-95, and the phosphorylation of CaMKII but not SYT-1. In contrast, NS-ODN or PBS had no effect on the expression of the PSDs CaMKII or PSD-95, or on the phosphorylation of CaMKII. When the egr-1 NS-ODN was infused in the OB after training for the novel odor there was no effect on olfactory memory. These findings suggest that egr-1 control the activation of CaMKII and PSD-95 during the process of olfactory memory formation. Copyright © 2012 Elsevier B.V. All rights reserved.

Activation of Notch3 in Glomeruli Promotes the Development of Rapidly Progressive Renal Disease.

PubMed

El Machhour, Fala; Keuylian, Zela; Kavvadas, Panagiotis; Dussaule, Jean-Claude; Chatziantoniou, Christos

2015-07-01

Notch3 expression is found in the glomerular podocytes of patients with lupus nephritis or focal segmental GN but not in normal kidneys. Here, we show that activation of the Notch3 receptor in the glomeruli is a turning point inducing phenotypic changes in podocytes promoting renal inflammation and fibrosis and leading to disease progression. In a model of rapidly progressive GN, Notch3 expression was induced by several-fold in podocytes concurrently with disease progression. By contrast, mice lacking Notch3 expression were protected because they exhibited less proteinuria, uremia, and inflammatory infiltration. Podocyte outgrowth from glomeruli isolated from wild-type mice during the early phase of the disease was higher than outgrowth from glomeruli of mice lacking Notch3. In vitro studies confirmed that podocytes expressing active Notch3 reorganize their cytoskeleton toward a proliferative/migratory and inflammatory phenotype. We then administered antisense oligodeoxynucleotides targeting Notch3 or scramble control oligodeoxynucleotides in wild-type mice concomitant to disease induction. Both groups developed chronic renal disease, but mice injected with Notch3 antisense had lower values of plasma urea and proteinuria and inflammatory infiltration. The improvement of renal function was accompanied by fewer deposits of fibrin within the glomeruli and by decreased peritubular inflammation. Finally, abnormal Notch3 staining was observed in biopsy samples of patients with crescentic GN. These results demonstrate that abnormal activation of Notch3 may be involved in the progression of renal disease by promoting migratory and proinflammatory pathways. Inhibiting Notch3 activation could be a novel, promising approach to treat GN. Copyright © 2015 by the American Society of Nephrology.

Antisense Oligodeoxynucleotide Inhibition of HIV Gene Expression

DTIC Science & Technology

1989-03-20

synthesis using trimethoxybenzyl side chain protection for Gln, the highly efficient benzotriazolyloxy tris(dimethylamino) phosphonium hexafluorophosphate ...0 - P - 0 -0 - O - - OH + Li OLi OLi OLi R 0 Fig. 11. Fai.t atom bombardment ma.ss spectroscopy of the lithium salt of 5’-trityl-CUAA, sputtered from

Distribution of cultivated and uncultivated cyanobacteria and Chloroflexus-like bacteria in hot spring microbial mats

NASA Technical Reports Server (NTRS)

Ruff-Roberts, A. L.; Kuenen, J. G.; Ward, D. M.

1994-01-01

Oligodeoxynucleotide hybridization probes were developed to complement specific regions of the small subunit (SSU) rRNA sequences of cultivated and uncultivated cyanobacteria and Chloroflexus-like bacteria, which inhabit hot spring microbial mats. The probes were used to investigate the natural distribution of SSU rRNAs from these species in mats of Yellowstone hot springs of different temperatures and pHs as well as changes in SSU rRNA distribution resulting from 1-week in situ shifts in temperature, pH, and light intensity. Synechococcus lividus Y-7c-s SSU rRNA was detected only in the mat of a slightly acid spring, from which it may have been initially isolated, or when samples from a more alkaline spring were incubated in the more acid spring. Chloroflexus aurantiacus Y-400-fl SSU rRNA was detected only in a high-temperature mat sample from the alkaline Octopus Spring or when lower-temperature samples from this mat were incubated at the high-temperature site. SSU rRNAs of uncultivated species were more widely distributed. Temperature distributions and responses to in situ temperature shifts suggested that some of the uncultivated cyanobacteria might be adapted to high-, moderate-, and low-temperature ranges whereas an uncultivated Chloroflexus-like bacterium appears to have broad temperature tolerance. SSU rRNAs of all uncultivated species inhabiting a 48 to 51 degrees C Octopus Spring mat site were most abundant in the upper 1 mm and were not detected below a 2.5-to 3.5-mm depth, a finding consistent with their possible phototrophic nature. However, the effects of light intensity reduction on these SSU rRNAs were variable, indicating the difficulty of demonstrating a phototrophic phenotype in light reduction experiments.

Incorporation of terminal phosphorothioates into oligonucleotides.

PubMed Central

Alefelder, S; Patel, B K; Eckstein, F

1998-01-01

Considerable effort has been directed towards studying the structure and function of oligonucleotides and several approaches rely on the attachment of reporter groups to oligonucleotides. We report here the introduction of 3'- and 5'-terminal phosphorothioates into heptameric oligonucleotides and their post-synthetic modification with several reporter groups. The synthesis of terminal phosphorothioates is based on the coupling of a ribonucleoside phosphoramidite at the first or last nucleotide, respectively, which, after sulphurization, is removed by sequential oxidation of the vicinal hydroxyl groups and then beta-elimination. Product formation is of the order of 95%. The ratio of phosphorothioate- versus phosphate-terminated oligodeoxynucleotides as analysed by electrophoresis on a Hg2+gel is in general 85/15. Examples for the reactivity of the terminal phosphorothioates for conjugation with cholesterol, bimane and for sulphydryl exchange are described. PMID:9776763

A Toll-Like Receptor 9 Antagonist Improves Bladder Function and White Matter Sparing in Spinal Cord Injury

PubMed Central

David, Brian T.; Sampath, Sujitha; Dong, Wei; Heiman, Adee; Rella, Courtney E.; Elkabes, Stella

2014-01-01

Abstract Spinal cord injury (SCI) affects motor, sensory, and autonomic functions. As current therapies do not adequately alleviate functional deficits, the development of new and more effective approaches is of critical importance. Our earlier investigations indicated that intrathecal administration of a toll-like receptor 9 (TLR9) antagonist, cytidine-phosphate-guanosine oligodeoxynucleotide 2088 (CpG ODN 2088), to mice sustaining a severe, mid-thoracic contusion injury diminished neuropathic pain but did not alter locomotor deficits. These changes were paralleled by a decrease in the pro-inflammatory response at the injury epicenter. Using the same SCI paradigm and treatment regimen, the current studies investigated the effects of the TLR9 antagonist on bladder function. We report that the TLR9 antagonist decreases SCI-elicited urinary retention and ameliorates bladder morphopathology without affecting kidney function. A significant improvement in white matter sparing was also observed, most likely due to alterations in the inflammatory milieu. These findings indicate that the TLR9 antagonist has beneficial effects not only in reducing sensory deficits, but also on bladder dysfunction and tissue preservation. Thus, modulation of innate immune receptor signaling in the spinal cord can impact the effects of SCI. PMID:24936867

A toll-like receptor 9 antagonist improves bladder function and white matter sparing in spinal cord injury.

PubMed

David, Brian T; Sampath, Sujitha; Dong, Wei; Heiman, Adee; Rella, Courtney E; Elkabes, Stella; Heary, Robert F

2014-11-01

Spinal cord injury (SCI) affects motor, sensory, and autonomic functions. As current therapies do not adequately alleviate functional deficits, the development of new and more effective approaches is of critical importance. Our earlier investigations indicated that intrathecal administration of a toll-like receptor 9 (TLR9) antagonist, cytidine-phosphate-guanosine oligodeoxynucleotide 2088 (CpG ODN 2088), to mice sustaining a severe, mid-thoracic contusion injury diminished neuropathic pain but did not alter locomotor deficits. These changes were paralleled by a decrease in the pro-inflammatory response at the injury epicenter. Using the same SCI paradigm and treatment regimen, the current studies investigated the effects of the TLR9 antagonist on bladder function. We report that the TLR9 antagonist decreases SCI-elicited urinary retention and ameliorates bladder morphopathology without affecting kidney function. A significant improvement in white matter sparing was also observed, most likely due to alterations in the inflammatory milieu. These findings indicate that the TLR9 antagonist has beneficial effects not only in reducing sensory deficits, but also on bladder dysfunction and tissue preservation. Thus, modulation of innate immune receptor signaling in the spinal cord can impact the effects of SCI.

NASA Tech Briefs, September 2004

NASA Technical Reports Server (NTRS)

2004-01-01

Topics covered include: Brazing SiC/SiC Composites to Metals; Composite-Material Tanks with Chemically Resistant Liners; Thermally Conductive Metal-Tube/Carbon-Composite Joints; Improved BN Coatings on SiC Fibers in SiC Matrices; Iterative Demodulation and Decoding of Non-Square QAM; Measuring Radiation Patterns of Reconfigurable Patch Antennas on Wafers; Low-Cutoff, High-Pass Digital Filtering of Neural Signals; Further Improvement in 3DGRAPE; Ground Support Software for Spaceborne Instrumentation; MER SPICE Interface; Simulating Operation of a Planetary Rover; Analyzing Contents of a Computer Cache; Discrepancy Reporting Management System; Silicone-Rubber Microvalves Actuated by Paraffin; Hydraulic Apparatus for Mechanical Testing of Nuts; Heat Control via Torque Control in Friction Stir Welding; Manufacturing High-Quality Carbon Nanotubes at Lower Cost; Setup for Visual Observation of Carbon-Nanotube Arc Process; Solution Preserves Nucleic Acids in Body-Fluid Specimens; Oligodeoxynucleotide Probes for Detecting Intact Cells; Microwave-Spectral Signatures Would Reveal Concealed Objects; Digital Averaging Phasemeter for Heterodyne Interferometry; Optoelectronic Instrument Monitors pH in a Culture Medium; Imaging of gamma-Irradiated Regions of a Crystal; Photodiode-Based, Passive Ultraviolet Dosimeters; Discrete Wavelength-Locked External Cavity Laser; Flexible Shields for Protecting Spacecraft Against Debris; Part 2 of a Computational Study of a Drop-Laden Mixing Layer; Controllable Curved Mirrors Made from Single-Layer EAP Films; and Demonstration of a Pyrotechnic Bolt-Retractor System.

Evaluation of novel adjuvant Eimeria profilin complex on intestinal host immune responses against live E. acervulina challenge infection

USDA-ARS?s Scientific Manuscript database

The effects of two novel adjuvants, QCDC (Quil A/cholesterol/DDA/Carbopol) and QCDCRT (QCDC/Bay R1005/cytosine-phosphate-guanosine oligodeoxynucleotides, CpG) emulsified with profilin, a conserved Eimeria recombinant protein, against avian coccidiosis were determined in broiler chickens. Chickens we...

Efficacy of QCDCR formulated CpG ODN 2007 in Nile tilapia against Streptococcus iniae and identification of upregulated genes

USDA-ARS?s Scientific Manuscript database

The potential of using a QCDCR (quilA:cholesterol:dimethyl dioctadecyl ammonium bromide:carbopol:R1005 glycolipid) formulated CpG oligodeoxynucleotide (ODN), ODN 2007, to confer protection in Nile tilapia against Streptococcus iniae infection was evaluated in this study. At two days post treatment, ...

Improved strategies for postoligomerization synthesis of oligodeoxynucleotides bearing structurally defined adducts at the N2 position of deoxyguanosine.

PubMed

DeCorte, B L; Tsarouhtsis, D; Kuchimanchi, S; Cooper, M D; Horton, P; Harris, C M; Harris, T M

1996-01-01

Improved methodology has been developed for preparation of oligodeoxynucleotides bearing adducts on the N2 position of guanine in which the adduction reaction is carried out in homogeneous solution rather than while the oligonucleotide is immobilized on a solid matrix. The methodology utilizes a new synthon, 2-fluoro-O6-(trimethylsilylethyl)-2'-deoxyinosine (3). Nucleoside 3 is stable to the conditions of oligonucleotide synthesis, but the O6 protection is eliminated under very mild conditions following displacement of the 2-fluoro group by amine nucleophiles. Oligonucleotides containing 3 could be removed from the solid support by treatment with 0.1 M NaOH (8 h, rt) without disruption of 3. Reaction of the crude, partially deprotected oligonucleotide with (R)-2-amino-2-phenylethanol in homogeneous solution, followed by removal of the remaining protective groups with NH4OH (60 degrees C, 8 h) and then 0.1% acetic acid, gave the adducted oligonucleotide in good purity and yield. Alternatively, fully deprotected oligonucleotide containing 3 could be prepared by use of labile phenoxyacetyl-type protecting groups on the exocyclic amino groups.

Knockdown of mortalin within the medial prefrontal cortex impairs normal sensorimotor gating.

PubMed

Gabriele, Nicole; Pontoriero, Giuseppe F; Thomas, Nancy; Shethwala, Shazli K; Pristupa, Zdenek B; Gabriele, Joseph P

2010-11-01

The 70-kDa mitochondrial heat shock protein, mortalin, is a ubiquitously expressed, multifunctional protein that is capable of binding the neurotransmitter, dopamine, within the brain. Dopamine dysregulation has been implicated in many of the abnormal neurological behaviors. Although studies have indicated that mortalin is differentially regulated in response to dopaminergic modulation, research has yet to elucidate the role of mortalin in the regulation of dopaminergic activity. This study seeks to investigate the role of mortalin in the regulation of dopamine-dependent behavior, specifically as it pertains to schizophrenia (SCZ). Mortalin expression was knocked down through the infusion of antisense oligodeoxynucleotide molecules into the medial prefrontal cortex (mPFC). Rats infused with mortalin antisense oligodeoxynucleotide molecules exhibited significant prepulse inhibition deficits, suggestive of defects in normal sensorimotor gating. Furthermore, mortalin misexpression within the mPFC was coupled to a significant increase in mortalin protein expression within the nucleus accumbens at the molecular level. These findings demonstrate that mortalin plays an essential role in the regulation of dopamine-dependent behavior and plays an even greater role in the pathogenesis of SCZ.

Poly-L-arginine synergizes with oligodeoxynucleotides containing CpG-motifs (CpG-ODN) for enhanced and prolonged immune responses and prevents the CpG-ODN-induced systemic release of pro-inflammatory cytokines.

PubMed

Lingnau, Karen; Egyed, Alena; Schellack, Carola; Mattner, Frank; Buschle, Michael; Schmidt, Walter

2002-10-04

This study describes an entirely synthetic vaccine composed of antigenic peptides (T cell epitopes), oligodeoxynucleotides containing CpG-motifs (CpG-ODN) and poly-L-arginine (pR). CpG-ODN are known to be potent inducers of predominantly type 1-like immune responses, while polycationic amino acids, like pR, facilitate the uptake of antigens into antigen presenting cells (APCs). We demonstrate that the application of peptides and pR/CpG-ODN results in strongly enhanced peptide-specific immune responses as compared to the application of peptides with either of the immunomodulators alone. High numbers of antigen-specific T cells can be observed even after only one injection of the vaccine for a remarkably long period of time (at least 372 days). Furthermore, the potentially harmful systemic release of pro-inflammatory cytokines induced upon injection of CpG-ODN is inhibited. Thus, the combined application of CpG-ODN and pR may represent a novel vaccine strategy in humans.

Oligodeoxynucleotides Can Transiently Up- and Downregulate CHS Gene Expression in Flax by Changing DNA Methylation in a Sequence-Specific Manner

PubMed Central

Dzialo, Magdalena; Szopa, Jan; Czuj, Tadeusz; Zuk, Magdalena

2017-01-01

Chalcone synthase (CHS) has been recognized as an essential enzyme in the phenylpropanoid biosynthesis pathway. Apart from the leading role in the production of phenolic compounds with many valuable biological activities beneficial to biomedicine, CHS is well appreciated in science. Genetic engineering greatly facilitates expanding knowledge on the function and genetics of CHS in plants. The CHS gene is one of the most intensively studied genes in flax. In our study, we investigated engineering of the CHS gene through genetic and epigenetic approaches. Considering the numerous restrictions concerning the application of genetically modified (GM) crops, the main purpose of this research was optimization of the plant's modulation via epigenetics. In our study, plants modified through two methods were compared: a widely popular agrotransformation and a relatively recent oligodeoxynucleotide (ODN) strategy. It was recently highlighted that the ODN technique can be a rapid and time-serving antecedent in quick analysis of gene function before taking vector-mediated transformation. In order to understand the molecular background of epigenetic variation in more detail and evaluate the use of ODNs as a tool for predictable and stable gene engineering, we concentrated on the integration of gene expression and gene-body methylation. The treatment of flax with a series of short oligonucleotides homologous to a different part of CHS gene isoforms revealed that those directed to regulatory gene regions (5′- and 3′-UTR) activated gene expression, directed to non-coding region (introns) caused gen activity reduction, while those homologous to a coding region may have a variable influence on its activity. Gene expression changes were accompanied by changes in its methylation status. However, only certain (CCGG) motifs along the gene sequence were affected. The analyzed DNA motifs of the CHS flax gene are more accessible for methylation when located within a CpG island. The methylation motifs also led to rearrangement of the nucleosome location. The obtained results suggest high specificity of ODN action and establish a potential valuable alternative for improvement of crops. PMID:28555142

Oligodeoxynucleotides Can Transiently Up- and Downregulate CHS Gene Expression in Flax by Changing DNA Methylation in a Sequence-Specific Manner.

PubMed

Dzialo, Magdalena; Szopa, Jan; Czuj, Tadeusz; Zuk, Magdalena

2017-01-01

Chalcone synthase (CHS) has been recognized as an essential enzyme in the phenylpropanoid biosynthesis pathway. Apart from the leading role in the production of phenolic compounds with many valuable biological activities beneficial to biomedicine, CHS is well appreciated in science. Genetic engineering greatly facilitates expanding knowledge on the function and genetics of CHS in plants. The CHS gene is one of the most intensively studied genes in flax. In our study, we investigated engineering of the CHS gene through genetic and epigenetic approaches. Considering the numerous restrictions concerning the application of genetically modified (GM) crops, the main purpose of this research was optimization of the plant's modulation via epigenetics. In our study, plants modified through two methods were compared: a widely popular agrotransformation and a relatively recent oligodeoxynucleotide (ODN) strategy. It was recently highlighted that the ODN technique can be a rapid and time-serving antecedent in quick analysis of gene function before taking vector-mediated transformation. In order to understand the molecular background of epigenetic variation in more detail and evaluate the use of ODNs as a tool for predictable and stable gene engineering, we concentrated on the integration of gene expression and gene-body methylation. The treatment of flax with a series of short oligonucleotides homologous to a different part of CHS gene isoforms revealed that those directed to regulatory gene regions (5'- and 3'-UTR) activated gene expression, directed to non-coding region (introns) caused gen activity reduction, while those homologous to a coding region may have a variable influence on its activity. Gene expression changes were accompanied by changes in its methylation status. However, only certain (CCGG) motifs along the gene sequence were affected. The analyzed DNA motifs of the CHS flax gene are more accessible for methylation when located within a CpG island. The methylation motifs also led to rearrangement of the nucleosome location. The obtained results suggest high specificity of ODN action and establish a potential valuable alternative for improvement of crops.

Comparison and evaluation of gene therapy and epigenetic approaches for wound healing.

PubMed

Cutroneo, K R; Chiu, J F

2000-01-01

During the past decade considerable evidence has mounted concerning the importance of growth factors in the wound healing process both for cell replication and for stimulating reparative cells to synthesize and secrete extracellular matrix components. During normal wound healing the growth factor concentration has to be maintained at a certain level. If the growth factor concentration is too low, normal healing fails to occur. Whereas if the growth factor concentration is too high due to either over-expression of the growth factor or too much growth factor being applied to the wound, aberrant wound healing will occur. One approach for controlling the amount of growth factor at the wound site during normal healing is through gene therapy and the titration of gene dosage. However if a narrow window exists between the beneficial therapeutic effect and toxic effects with increasing gene dosage, an agent may be necessary to give in combination with gene therapy to regulate the over-expression of growth factor. In addition to genetic approaches to regulate wound healing, epigenetic approaches also exist. Antisense oligodeoxynucleotides have been shown to regulate wound repair in certain model systems and to determine the protein(s) necessary for normal wound healing. A novel approach to regulate the activity of collagen genes, thereby affecting fibrosis, is to use a sense oligodeoxynucleotide having the same sequence of the cis element which regulates the promoter activity of a particular collagen gene. This exogenous oligodeoxynucleotide will compete with the cis element in the collagen gene for the trans-acting factor which regulates promoter activity. These epigenetic approaches afford the opportunity to regulate over-expression of growth factor and therefore preclude the potential toxic effects of gene therapy. Both genetic and epigenetic approaches for regulating the wound healing process, either normal or aberrant wound healing, have certain advantages and disadvantages which are discussed in the present article.

An "egr-1" ("zif268") Antisense Oligodeoxynucleotide Infused into the Amygdala Disrupts Fear Conditioning

ERIC Educational Resources Information Center

Donley, Melanie P.; Rosen, Jeffrey B.; Malkani, Seema; Wallace, Karin J.

2004-01-01

Studies of gene expression following fear conditioning have demonstrated that the inducible transcription factor, "egr-1," is increased in the lateral nucleus of the amygdala shortly following fear conditioning. These studies suggest that "egr-1" and its protein product Egr-1 in the amygdala are important for learning and memory of fear. To…

Selective degradation of thymidine and thymine deoxynucleotides

PubMed Central

Burton, K.; Riley, W. T.

1966-01-01

1. Osmium tetroxide in dilute ammonia oxidizes various pyrimidine nucleosides at different rates. Thymidine is oxidized about 45 times as fast as deoxycytidine. The phosphate groups may be eliminated from oxidized thymine nucleotides by successive treatments with alkali and then with diphenylamine in aqueous formic acid. The reactions can be applied to the selective degradation of thymidine in oligodeoxynucleotides. PMID:5938667

The protein DIIIC-2, aggregated with a specific oligodeoxynucleotide and adjuvanted in alum, protects mice and monkeys against DENV-2.

PubMed

Gil, Lázaro; Marcos, Ernesto; Izquierdo, Alienys; Lazo, Laura; Valdés, Iris; Ambala, Peris; Ochola, Lucy; Hitler, Rikoi; Suzarte, Edith; Álvarez, Mayling; Kimiti, Prisilla; Ndung'u, James; Kariuki, Thomas; Guzmán, María Guadalupe; Guillén, Gerardo; Hermida, Lisset

2015-01-01

Previously, we reported the ability of the chimeric protein DIIIC-2 (domain III of the dengue envelope protein fused to the capsid protein of dengue-2 virus), to induce immunity and protection in mice, when it is highly aggregated with a non-defined oligodeoxynucleotide (ODN) and adjuvanted in alum. In this work, three different defined ODNs were studied as aggregating agents. Our results suggest that the nature of the ODN influences the capacity of protein DIIIC-2 to activate cell-mediated immunity in mice. Consequently, the ODN 39M was selected to perform further experiments in mice and nonhuman primates. Mice receiving the preparation 39M-DIIIC-2 were solidly protected against dengue virus (DENV) challenge. Moreover, monkeys immunized with the same preparation developed neutralizing antibodies, as measured by four different neutralization tests varying the virus strains and the cell lines used. Two of the immunized monkeys were completely protected against challenge, whereas the third animal had a single day of low-titer viremia. This is the first work describing the induction of short-term protection in monkeys by a formulation that is suitable for human use combining a recombinant protein from DENV with alum.

Capillary electrophoretic separation-based approach to determine the labeling kinetics of oligodeoxynucleotides

PubMed Central

Kanavarioti, Anastassia; Greenman, Kevin L.; Hamalainen, Mark; Jain, Aakriti; Johns, Adam M.; Melville, Chris R.; Kemmish, Kent; Andregg, William

2014-01-01

With the recent advances in electron microscopy (EM), computation, and nanofabrication, the original idea of reading DNA sequence directly from an image can now be tested. One approach is to develop heavy atom labels that can provide the contrast required for EM imaging. While evaluating tentative labels for the respective nucleobases in synthetic oligodeoxynucleotides (oligos), we developed a streamlined capillary electrophoresis (CE) protocol to assess the label stability, reactivity, and selectivity. We report our protocol using osmium tetroxide 2,2′-bipyridine (Osbipy) as a thymidine (T) specific label. The observed rates show that the labeling process is kinetically independent of both the oligo length, and the base composition. The conditions, i.e. temperature, optimal Osbipy concentration, and molar ratio of reagents, to promote 100% conversion of the starting oligo to labeled product were established. Hence the optimized conditions developed with the oligos could be leveraged to allow osmylation of effectively all Ts in single-stranded (ss) DNA, while achieving minimal mislabeling. In addition, the approach and methods employed here may be adapted to the evaluation of other prospective contrasting agents/labels to facilitate next-generation DNA sequencing by EM. PMID:23147698

Cellular uptake and ex vivo urothelial penetration by oligodeoxynucleotides for optimizing treatment of transitional cell carcinoma.

PubMed

Bolenz, Christian; Trojan, Lutz; Gabriel, Ute; Honeck, Patrick; Wendt-Nordahl, Gunnar; Schaaf, Axel; Alken, Peter; Michel, Maurice Stephan

2008-10-01

To evaluate cellular uptake and urothelial penetration of oligodeoxynucleotides (ODNs) in transitional cell carcinoma (TCC) cell lines and in a porcine ex vivo model, respectively. A panel of human TCC cell lines (RT 112, HT 1197 and UM-UC3) were exposed tofluorescein-labeled ODNs. Transfection rates were assessed byfluorescence microscopy and fluorescence-activated cell sorting (FACS). Intravesical treatment with ODNs was performed in a porcine ex vivo model. Urothelial penetration was evaluated using fluorescence microscopy of cryosections. Treatment with ODNs provided transfection rates of at least 96.8% of TCC cells, irrespective of use of a transfection agent. Effective urothelial penetration by ODNs was detected when compared with controls (p = 0.0325). The addition of a liposomal transfection agent significantly increased the penetration depth, allowing affection of deep urothelial cell layers (p = 0.0082). High transfection rates of ODNs can be achieved in TCC cells. Urothelial penetration of ODNs was observed down to the deepest cell layers when a transfection agent is added, suggesting a high potential for complementing the chemoresection effects on residual tumor areas during intravesical therapy of non-muscle-invasive TCC.

CpG oligodeoxynucleotide nanomedicines for the prophylaxis or treatment of cancers, infectious diseases, and allergies.

PubMed

Hanagata, Nobutaka

2017-01-01

Unmethylated cytosine-guanine dinucleotide-containing oligodeoxynucleotides (CpG ODNs), which are synthetic agonists of Toll-like receptor 9 (TLR9), activate humoral and cellular immunity and are being developed as vaccine adjuvants to prevent or treat cancers, infectious diseases, and allergies. Free CpG ODNs have been used in many clinical trials implemented to verify their effects. However, recent research has reported that self-assembled CpG ODNs, protein/peptide-CpG ODN conjugates, and nanomaterial-CpG ODN complexes demonstrate higher adjuvant effects than free CpG ODNs, owing to their improved uptake efficiency into cells expressing TLR9. Moreover, protein/peptide-CpG ODN conjugates and nanomaterial-CpG ODN complexes are able to deliver CpG ODNs and antigens (or allergens) to the same types of cells, which enables a higher degree of prophylaxis or therapeutic effect. In this review, the author describes recent trends in the research and development of CpG ODN nanomedicines containing self-assembled CpG ODNs, protein/peptide-CpG ODN conjugates, and nanomaterial-CpG ODN complexes, focusing mainly on the results of preclinical and clinical studies.

A guanidine-rich regulatory oligodeoxynucleotide improves type-2 diabetes in obese mice by blocking T-cell differentiation

PubMed Central

Cheng, Xiang; Wang, Jing; Xia, Ni; Yan, Xin-Xin; Tang, Ting-Ting; Chen, Han; Zhang, Hong-Jian; Liu, Juan; Kong, Wen; Sjöberg, Sara; Folco, Eduardo; Libby, Peter; Liao, Yu-Hua; Shi, Guo-Ping

2012-01-01

T lymphocytes exhibit pro-inflammatory or anti-inflammatory activities in obesity and diabetes, depending on their subtypes. Guanidine-rich immunosuppressive oligodeoxynucleotides (ODNs) effectively control Th1/Th2-cell counterbalance. This study reveals a non-toxic regulatory ODN (ODNR01) that inhibits Th1- and Th17-cell polarization by binding to STAT1/3/4 and blocking their phosphorylation without affecting Th2 and regulatory T cells. ODNR01 improves glucose tolerance and insulin sensitivity in both diet-induced obese (DIO) and genetically generated obese (ob/ob) mice. Mechanistic studies show that ODNR01 suppresses Th1- and Th17-cell differentiation in white adipose tissue, thereby reducing macrophage accumulation and M1 macrophage inflammatory molecule expression without affecting M2 macrophages. While ODNR01 shows no effect on diabetes in lymphocyte-free Rag1-deficient DIO mice, it enhances glucose tolerance and insulin sensitivity in CD4+ T-cell-reconstituted Rag1-deficient DIO mice, suggesting its beneficial effect on insulin resistance is T-cell-dependent. Therefore, regulatory ODNR01 reduces obesity-associated insulin resistance through modulation of T-cell differentiation. PMID:23027613

Immunotherapeutic potential of CpG oligodeoxynucleotides in veterinary species.

PubMed

Manuja, Anju; Manuja, Balvinder K; Kaushik, Jyoti; Singha, Harisankar; Singh, Raj Kumar

2013-10-01

Innate immunity plays a critical role in host defense against infectious diseases by discriminating between self and infectious non-self. The recognition of infectious non-self involves germ-line encoded pattern recognition receptors (PRRs) that recognize pathogen-associated molecular patterns (PAMPs). The PAMPs are the components of pathogenic microbes which include not only the cell wall constituents but also the unmethylated 2'-deoxy-ribo-cytosine-phosphate-guanosine (CpG) motifs. These CpG motifs present within bacterial and viral DNA are recognized by toll-like receptor 9 (TLR9), and signaling by this receptor triggers a proinflammatory cytokine response which, in turn, influences both innate and adaptive immune responses. The activation of TLR9 with synthetic CpG oligodeoxynucleotides (ODNs) induces powerful Th1-like immune responses. It has been shown to provide protection against infectious diseases, allergy and cancer in laboratory animal models and some domestic animal species. With better understanding of the basic biology and immune mechanisms, it would be possible to exploit the potential of CpG motifs for animal welfare. The research developments in the area of CpG and TLR9 and the potential applications in animal health have been reviewed in this article.

Photoregulating RNA digestion using azobenzene linked dumbbell antisense oligodeoxynucleotides.

PubMed

Wu, Li; He, Yujian; Tang, Xinjing

2015-06-17

Introduction of 4,4'-bis(hydroxymethyl)-azobenzene (azo) to dumbbell hairpin oligonucleotides at the loop position was able to reversibly control the stability of the whole hairpin structure via UV or visible light irradiation. Here, we designed and synthesized a series of azobenzene linked dumbbell antisense oligodeoxynucleotides (asODNs) containing two terminal hairpins that are composed of an asODN and a short inhibitory sense strand. Thermal melting studies of these azobenzene linked dumbbell asODNs indicated that efficient trans to cis photoisomerization of azobenzene moieties induced large difference in thermal stability (ΔTm = 12.1-21.3 °C). In addition, photomodulation of their RNA binding abilities and RNA digestion by RNase H was investigated. The trans-azobenzene linked asODNs with the optimized base pairs between asODN strands and inhibitory sense strands could only bind few percentage of the target RNA, while it was able to recover their binding to the target RNA and degrade it by RNase H after light irradiation. Upon optimization, it is promising to use these azobenzene linked asODNs for reversible spatial and temporal regulation of antisense activities based on both steric binding and RNA digestion by RNase H.

Targeted Blockage of Signal Transducer and Activator of Transcription 5 Signaling Pathway with Decoy Oligodeoxynucleotides Suppresses Leukemic K562 Cell Growth

PubMed Central

Wang, Xiaozhong; Zeng, Jianming; Shi, Mei; Zhao, Shiqiao; Bai, Weijun; Cao, Weixi; Tu, Zhiguang; Huang, Zonggan

2011-01-01

The protein signal transducer and activator of transcription 5 (STAT5) of the JAK/STAT pathway is constitutively activated because of its phosphorylation by tyrosine kinase activity of fusion protein BCR-ABL in chronic myelogenous leukemia (CML) cells. This study investigated the potential therapeutic effect of STAT5 decoy oligodeoxynucleotides (ODN) using leukemia K562 cells as a model. Our results showed that transfection of 21-mer-long STAT5 decoy ODN into K562 cells effectively inhibited cell proliferation and induced cell apoptosis. Further, STAT5 decoy ODN downregulated STAT5 targets bcl-xL, cyclinD1, and c-myc at both mRNA and protein levels in a sequence-specific manner. Collectively, these data demonstrate the therapeutic effect of blocking the STAT5 signal pathway by cis-element decoy for cancer characterized by constitutive STAT5 activation. Thus, our study provides support for STAT5 as a potential target downstream of BCR-ABL for CML treatment and helps establish the concept of targeting STAT5 by decoy ODN as a novel therapy approach for imatinib-resistant CML. PMID:21091189

Mechanisms of strand break formation in DNA due to the direct effect of ionizing radiation: the dependency of free base release on the length of alternating CG oligodeoxynucleotides.

PubMed

Sharma, Kiran K; Razskazovskiy, Yuriy; Purkayastha, Shubhadeep; Bernhard, William A

2009-06-11

The question of how NA base sequence influences the yield of DNA strand breaks produced by the direct effect of ionizing radiation was investigated in a series of oligodeoxynucleotides of the form (d(CG)(n))(2) and (d(GC)(n))(2). The yields of free base release from X-irradiated DNA films containing 2.5 waters/nucleotide were measured by HPLC as a function of oligomer length. For (d(CG)(n))(2), the ratio of the Gua yield to Cyt yield, R, was relatively constant at 2.4-2.5 for n = 2-4 and it decreased to 1.2 as n increased from 5 to 10. When Gua was moved to the 5' end, for example going from d(CG)(5) to d(GC)(5), R dropped from 1.9 +/- 0.1 to 1.1 +/- 0.1. These effects are poorly described if the chemistry at the oligomer ends is assumed to be independent of the remainder of the oligomer. A mathematical model incorporating charge transfer through the base stack was derived to explain these effects. In addition, EPR was used to measure the yield of trapped-deoxyribose radicals at 4 K following X-irradiation at 4 K. The yield of free base release was substantially greater, by 50-100 nmol/J, than the yield of trapped-deoxyribose radicals. Therefore, a large fraction of free base release stems from a nonradical intermediate. For this intermediate, a deoxyribose carbocation formed by two one-electron oxidations is proposed. This reaction pathway requires that the hole (electron loss site) transfers through the base stack and, upon encountering a deoxyribose hole, oxidizes that site to form a deoxyribose carbocation. This reaction mechanism provides a consistent way of explaining both the absence of trapped radical intermediates and the unusual dependence of free base release on oligomer length.

Cystic Fibrosis Gene Encodes a cAMP-Dependent Chloride Channel in Heart

NASA Astrophysics Data System (ADS)

Hart, Padraig; Warth, John D.; Levesque, Paul C.; Collier, Mei Lin; Geary, Yvonne; Horowitz, Burton; Hume, Joseph R.

1996-06-01

cAMP-dependent chloride channels in heart contribute to autonomic regulation of action potential duration and membrane potential and have been inferred to be due to cardiac expression of the epithelial cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel. In this report, a cDNA from rabbit ventricle was isolated and sequenced, which encodes an exon 5 splice variant (exon 5-) of CFTR, with >90% identity to human CFTR cDNA present in epithelial cells. Expression of this cDNA in Xenopus oocytes gave rise to robust cAMP-activated chloride currents that were absent in control water-injected oocytes. Antisense oligodeoxynucleotides directed against CFTR significnatly reduced the density of cAMP-dependent chloride currents in acutely cultured myocytes, thereby establishing a direct functional link between cardiac expression of CFTR protein and an endogenous chloride channel in native cardiac myocytes.

Inhibition of human papillomavirus expression using DNAzymes.

PubMed

Benítez-Hess, María Luisa; Reyes-Gutiérrez, Pablo; Alvarez-Salas, Luis Marat

2011-01-01

Deoxyribozymes (DXZs) are catalytic oligodeoxynucleotides capable of performing diverse functions including the specific cleavage of a target RNA. These molecules represent a new type of therapeutic oligonucleotides combining the efficiency of ribozymes and the intracellular endurance and simplicity of modified antisense oligonucleotides. Commonly used DXZs include the 8-17 and 10-23 motifs, which have been engineered to destroy disease-associated genes with remarkable efficiency. Targeting DXZs to disease-associated transcripts requires extensive biochemical testing to establish target RNA accessibility, catalytic efficiency, and nuclease sensibility. The usage of modified nucleotides to render nuclease-resistance DXZs must be counterweighted against deleterious consequences on catalytic activity. Further intracellular testing is required to establish the effect of microenvironmental conditions on DXZ activity and off-target issues. Application of modified DXZs to cervical cancer results in specific growth inhibition, cell death, and apoptosis. Thus, DXZs represent a highly effective antisense moiety with minimal secondary effects.

Plasma Exosome Profiling of Cancer Patients by a Next Generation Systems Biology Approach.

PubMed

Domenyuk, Valeriy; Zhong, Zhenyu; Stark, Adam; Xiao, Nianqing; O'Neill, Heather A; Wei, Xixi; Wang, Jie; Tinder, Teresa T; Tonapi, Sonal; Duncan, Janet; Hornung, Tassilo; Hunter, Andrew; Miglarese, Mark R; Schorr, Joachim; Halbert, David D; Quackenbush, John; Poste, George; Berry, Donald A; Mayer, Günter; Famulok, Michael; Spetzler, David

2017-02-20

Technologies capable of characterizing the full breadth of cellular systems need to be able to measure millions of proteins, isoforms, and complexes simultaneously. We describe an approach that fulfils this criterion: Adaptive Dynamic Artificial Poly-ligand Targeting (ADAPT). ADAPT employs an enriched library of single-stranded oligodeoxynucleotides (ssODNs) to profile complex biological samples, thus achieving an unprecedented coverage of system-wide, native biomolecules. We used ADAPT as a highly specific profiling tool that distinguishes women with or without breast cancer based on circulating exosomes in their blood. To develop ADAPT, we enriched a library of ~10 11 ssODNs for those associating with exosomes from breast cancer patients or controls. The resulting 10 6 enriched ssODNs were then profiled against plasma from independent groups of healthy and breast cancer-positive women. ssODN-mediated affinity purification and mass spectrometry identified low-abundance exosome-associated proteins and protein complexes, some with known significance in both normal homeostasis and disease. Sequencing of the recovered ssODNs provided quantitative measures that were used to build highly accurate multi-analyte signatures for patient classification. Probing plasma from 500 subjects with a smaller subset of 2000 resynthesized ssODNs stratified healthy, breast biopsy-negative, and -positive women. An AUC of 0.73 was obtained when comparing healthy donors with biopsy-positive patients.

Plasma Exosome Profiling of Cancer Patients by a Next Generation Systems Biology Approach

PubMed Central

Domenyuk, Valeriy; Zhong, Zhenyu; Stark, Adam; Xiao, Nianqing; O’Neill, Heather A.; Wei, Xixi; Wang, Jie; Tinder, Teresa T.; Tonapi, Sonal; Duncan, Janet; Hornung, Tassilo; Hunter, Andrew; Miglarese, Mark R.; Schorr, Joachim; Halbert, David D.; Quackenbush, John; Poste, George; Berry, Donald A.; Mayer, Günter; Famulok, Michael; Spetzler, David

2017-01-01

Technologies capable of characterizing the full breadth of cellular systems need to be able to measure millions of proteins, isoforms, and complexes simultaneously. We describe an approach that fulfils this criterion: Adaptive Dynamic Artificial Poly-ligand Targeting (ADAPT). ADAPT employs an enriched library of single-stranded oligodeoxynucleotides (ssODNs) to profile complex biological samples, thus achieving an unprecedented coverage of system-wide, native biomolecules. We used ADAPT as a highly specific profiling tool that distinguishes women with or without breast cancer based on circulating exosomes in their blood. To develop ADAPT, we enriched a library of ~1011 ssODNs for those associating with exosomes from breast cancer patients or controls. The resulting 106 enriched ssODNs were then profiled against plasma from independent groups of healthy and breast cancer-positive women. ssODN-mediated affinity purification and mass spectrometry identified low-abundance exosome-associated proteins and protein complexes, some with known significance in both normal homeostasis and disease. Sequencing of the recovered ssODNs provided quantitative measures that were used to build highly accurate multi-analyte signatures for patient classification. Probing plasma from 500 subjects with a smaller subset of 2000 resynthesized ssODNs stratified healthy, breast biopsy-negative, and -positive women. An AUC of 0.73 was obtained when comparing healthy donors with biopsy-positive patients. PMID:28218293

Quantification of DNA using the luminescent oxygen channeling assay.

PubMed

Patel, R; Pollner, R; de Keczer, S; Pease, J; Pirio, M; DeChene, N; Dafforn, A; Rose, S

2000-09-01

Simplified and cost-effective methods for the detection and quantification of nucleic acid targets are still a challenge in molecular diagnostics. Luminescent oxygen channeling assay (LOCI(TM)) latex particles can be conjugated to synthetic oligodeoxynucleotides and hybridized, via linking probes, to different DNA targets. These oligomer-conjugated LOCI particles survive thermocycling in a PCR reaction and allow quantified detection of DNA targets in both real-time and endpoint formats. The endpoint DNA quantification format utilized two sensitizer bead types that are sensitive to separate illumination wavelengths. These two bead types were uniquely annealed to target or control amplicons, and separate illuminations generated time-resolved chemiluminescence, which distinguished the two amplicon types. In the endpoint method, ratios of the two signals allowed determination of the target DNA concentration over a three-log range. The real-time format allowed quantification of the DNA target over a six-log range with a linear relationship between threshold cycle and log of the number of DNA targets. This is the first report of the use of an oligomer-labeled latex particle assay capable of producing DNA quantification and sequence-specific chemiluminescent signals in a homogeneous format. It is also the first report of the generation of two signals from a LOCI assay. The methods described here have been shown to be easily adaptable to new DNA targets because of the generic nature of the oligomer-labeled LOCI particles.

CpG Oligodeoxynucleotides Facilitate Delivery of Whole Inactivated H9N2 Influenza Virus via Transepithelial Dendrites of Dendritic Cells in Nasal Mucosa

PubMed Central

Qin, Tao; Yin, Yinyan; Yu, Qinghua; Huang, Lulu; Wang, Xiaoqing; Lin, Jian

2015-01-01

ABSTRACT The spread of the low-pathogenicity avian H9N2 influenza virus has seriously increased the risk of a new influenza pandemic. Although whole inactivated virus (WIV) vaccine via intranasal pathway is the effective method of blocking virus transmission, the mucosal barrier seems to be a major factor hampering its development. CpG oligodeoxynucleotides, a known adjuvant, can target downstream dendritic cells (DCs) and effectively enhance the mucosal and systemic immune responses. However, the ability of CpGs to assist H9N2 WIV in transepithelial transport remains unknown. Here, in vitro and in vivo, we showed that CpGs provided assistance for H9N2 WIV in recruiting DCs to the nasal epithelial cells (ECs) and forming transepithelial dendrites (TEDs) to capture luminal viruses. CD103+ DCs participated in this process. Chemokine CCL20 from nasal ECs played a key role in driving DC recruitment and TED formation. Virus-loaded DCs quickly migrated into the draining cervical lymph nodes (CLNs) for antigen presentation. In addition, the competence of CpGs was independent of direct epithelial transport via the transcellular or paracellular pathway. Taken together, our data demonstrated that CpGs enhanced the transport of H9N2 WIV via TEDs of nasal DCs, which might be a novel mechanism for optimal adaptive immune responses. IMPORTANCE This paper demonstrates by both an in vivo and an in vitro coculture model that CpG oligodeoxynucleotides, known as an adjuvant generally targeting downstream immune responses, also are crucial for the transport of H9N2 WIV across nasal epithelial cells (ECs) via the uptake of transepithelial dendrites (TEDs). Our results prove for the first time to our knowledge that the immune-potentiating mechanism of CpGs is based on strengthening the transepithelial uptake of H9N2 WIV in nasal mucosa. These findings provide a fresh perspective for further improvement of intranasal influenza vaccines, which are urgently needed in the face of the potential threat of H9N2 influenza. PMID:25810544

Reversal of human allergen-specific CRTH2+ T(H)2 cells by IL-12 or the PS-DSP30 oligodeoxynucleotide.

PubMed

Annunziato, F; Cosmi, L; Manetti, R; Brugnolo, F; Parronchi, P; Maggi, E; Nagata, K; Romagnani, S

2001-11-01

The chemoattractant receptor homologous molecule expressed on T(H)2 cells (CRTH2) is a receptor for prostaglandin D(2), which among human T cells is selectively expressed by T(H)2 and type 2 cytotoxic effectors. Our purpose was to assess whether the cytokine production profile of T(H)2 effectors could be reversed by exploiting their selective expression of CRTH2. CRTH2(+) T cells were purified from the blood of allergic subjects, stimulated with the specific allergen in the absence or presence of IL-12, and assessed by flow cytometry at the single-cell level for their ability to produce IL-4 and/or IFN-gamma after antigen or polyclonal stimulation. Both IL-12 and the PS-DSP30 oligodeoxynucleotide enabled CRTH2(+) allergen-stimulated T(H)2 cells to produce IFN-gamma. This change in the profile of cytokine production by T(H)2 cells from allergic subjects was related to the upregulation of IL-12 receptor beta2 chain and was associated with the loss of CRTH2. These data demonstrate that the cytokine production pattern of fully differentiated T(H)2 effectors can be changed to a less polarized profile, thus providing the physiologic basis for new immunotherapeutic strategies in allergic disorders.

Oligodeoxynucleotide nanostructure formation in the presence of polypropyleneimine dendrimers and their uptake in breast cancer cells

NASA Astrophysics Data System (ADS)

Chen, Alex M.; Santhakumaran, Latha M.; Nair, Sandhya K.; Amenta, Peter S.; Thomas, Thresia; He, Huixin; Thomas, T. J.

2006-11-01

We studied the efficacy of five generations of polypropyleneimine (PPI) dendrimer to provoke nanostructure formation from a 21-nucleotide antisense oligodeoxynucleotide (ODN). Nanostructure formation was observed with all generations of dendrimer by light scattering and microscopic techniques. The efficacy of the dendrimers increased with generation number. Atomic force microscopy (AFM) was used to study the morphology of the structures at different condensation stages. Based on the observed nanostructures, we propose a zipping condensation mechanism, which is very different from the condensation pathways of high molecular weight DNA polymers. Electron microscopy showed the presence of toroidal nanoparticles. Confocal microscopic analysis showed that the nanostructures formed with G-4 and G-5 dendrimers could undergo facile cellular uptake in a breast cancer cell line, MDA-MB-231, whereas nanostructures formed with G-1 to G-3 dendrimers lacked this ability. Nanoparticles formed with G-1 to G-3 dendrimers showed significantly lower zeta potential (5.2-6.5 mV) than those (12-18 mV) of particles formed with G-4 and G-5 dendrimers. These results show that the structure and charge density of the dendrimers are important in ODN nanoparticle formation and cellular transport and that G-4 and G-5 dendrimers are useful in cellular delivery of antisense ODN.

Combining Single Strand Oligodeoxynucleotides and CRISPR/Cas9 to Correct Gene Mutations in β-Thalassemia-induced Pluripotent Stem Cells.

PubMed

Niu, Xiaohua; He, Wenyin; Song, Bing; Ou, Zhanhui; Fan, Di; Chen, Yuchang; Fan, Yong; Sun, Xiaofang

2016-08-05

β-Thalassemia (β-Thal) is one of the most common genetic diseases in the world. The generation of patient-specific β-Thal-induced pluripotent stem cells (iPSCs), correction of the disease-causing mutations in those cells, and then differentiation into hematopoietic stem cells offers a new therapeutic strategy for this disease. Here, we designed a CRISPR/Cas9 to specifically target the Homo sapiens hemoglobin β (HBB) gene CD41/42(-CTTT) mutation. We demonstrated that the combination of single strand oligodeoxynucleotides with CRISPR/Cas9 was capable of correcting the HBB gene CD41/42 mutation in β-Thal iPSCs. After applying a correction-specific PCR assay to purify the corrected clones followed by sequencing to confirm mutation correction, we verified that the purified clones retained full pluripotency and exhibited normal karyotyping. Additionally, whole-exome sequencing showed that the mutation load to the exomes was minimal after CRISPR/Cas9 targeting. Furthermore, the corrected iPSCs were selected for erythroblast differentiation and restored the expression of HBB protein compared with the parental iPSCs. This method provides an efficient and safe strategy to correct the HBB gene mutation in β-Thal iPSCs. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Influence of homeobox B2 antisense oligodeoxynucleotides on the biological characteristics of in vitro cultured primary human umbilical vein endothelial cells.

PubMed

Liu, X S; Zhang, X Q; Tian, T; Liu, L; Ming, J

2008-01-01

This study aims to explore the influence of homeobox B2 (HOXB2) antisense oligodeoxynucleotides (asodn) on the biological characteristics of in vitro cultured primary human umbilical vein endothelial cells (HUVECs). The distribution of HOXB2 asodn in the HUVECs was observed by fluorescent labelling, and the influence of different concentrations of HOXB2 asodn on the DNA synthesis of HUVECs was assessed. Flow cytometry and a reverse transcriptase-polymerase chain reaction (RT- PCR) method were employed to observe the influence of HOXB2 asodn on HOXB2 expression and the HUVEC cell cycle. After the induction of liposome, the nuclear fluorescent staining of HOXB2 asodn was weaker 15 min after transfection and the staining reached the strongest level at 4-8 h but then weakened and disappeared by 16 h after transfection. This indicated that endothelial DNA synthesis could be inhibited by HOXB2 asodn in a dose-dependent manner. Furthermore, the HUVECs could be delayed in their passage from G1 to S. Simultaneously, expression of HOXB2 mRNA had decreased significantly by 24-48 h after transfection. Clearly, HOXB2 plays important roles in the proliferation of endothelial cells and also affects the cell cycle.

Photo-oxidation of 6-thioguanine by UVA: the formation of addition products with low molecular weight thiol compounds.

PubMed

Ren, Xiaolin; Xu, Yao-Zhong; Karran, Peter

2010-01-01

The thiopurine, 6-thioguanine (6-TG) is present in the DNA of patients treated with the immunosuppressant and anticancer drugs azathioprine or mercaptopurine. The skin of these patients is selectively sensitive to UVA radiation-which comprises >90% of the UV light in incident sunlight-and they suffer high rates of skin cancer. UVA irradiation of DNA 6-TG produces DNA lesions that may contribute to the development of cancer. Antioxidants can protect 6-TG against UVA but 6-TG oxidation products may undergo further reactions. We characterize some of these reactions and show that addition products are formed between UVA-irradiated 6-TG and N-acetylcysteine and other low molecular weight thiol compounds including β-mercaptoethanol, cysteine and the cysteine-containing tripeptide glutathione (GSH). GSH is also adducted to 6-TG-containing oligodeoxynucleotides in an oxygen- and UVA-dependent nucleophilic displacement reaction that involves an intermediate oxidized 6-TG, guanine sulfonate (G(SO3) ). These photochemical reactions of 6-TG, particularly the formation of a covalent oligodeoxynucleotide-GSH complex, suggest that crosslinking of proteins or low molecular weight thiol compounds to DNA may be a previously unrecognized hazard in sunlight-exposed cells of thiopurine-treated patients. © 2010 The Authors. Journal Compilation. The American Society of Photobiology.

CpG oligodeoxynucleotides augment the murine immune response to the Yersinia pestis F1-V vaccine in bubonic and pneumonic models of plague.

PubMed

Amemiya, Kei; Meyers, Jennifer L; Rogers, Taralyn E; Fast, Randy L; Bassett, Anthony D; Worsham, Patricia L; Powell, Bradford S; Norris, Sarah L; Krieg, Arthur M; Adamovicz, Jeffrey J

2009-04-06

The current U.S. Department of Defense candidate plague vaccine is a fusion between two Yersinia pestis proteins: the F1 capsular protein, and the low calcium response (Lcr) V-protein. We hypothesized that an immunomodulator, such as CpG oligodeoxynucleotide (ODN)s, could augment the immune response to the plague F1-V vaccine in a mouse model for plague. CpG ODNs significantly augmented the antibody response and efficacy of a single dose of the plague vaccine in murine bubonic and pneumonic models of plague. In the latter study, we also found an overall significant augmentation the immune response to the individual subunits of the plague vaccine by CpG ODN 2006. In a long-term, prime-boost study, CpG ODN induced a significant early augmentation of the IgG response to the vaccine. The presence of CpG ODN induced a significant increase in the IgG2a subclass response to the vaccine up to 5 months after the boost. Our studies showed that CpG ODNs significantly augmented the IgG antibody response to the plague vaccine, which increased the probability of survival in murine models of plague (P<0.0001).

Histone deacetylation during brain development is essential for permanent masculinization of sexual behavior.

PubMed

Matsuda, Ken Ichi; Mori, Hiroko; Nugent, Bridget M; Pfaff, Donald W; McCarthy, Margaret M; Kawata, Mitsuhiro

2011-07-01

Epigenetic histone modifications are emerging as important mechanisms for conveyance of and maintenance of effects of the hormonal milieu to the developing brain. We hypothesized that alteration of histone acetylation status early in development by sex steroid hormones is important for sexual differentiation of the brain. It was found that during the critical period for sexual differentiation, histones associated with promoters of essential genes in masculinization of the brain (estrogen receptor α and aromatase) in the medial preoptic area, an area necessary for male sexual behavior, were differentially acetylated between the sexes. Consistent with these findings, binding of histone deacetylase (HDAC) 2 and 4 to the promoters was higher in males than in females. To examine the involvement of histone deacetylation on masculinization of the brain at the behavioral level, we inhibited HDAC in vivo by intracerebroventricular infusion of the HDAC inhibitor trichostatin A or antisense oligodeoxynucleotide directed against the mRNA for HDAC2 and -4 in newborn male rats. Aspects of male sexual behavior in adulthood were significantly reduced by administration of either trichostatin A or antisense oligodeoxynucleotide. These results demonstrate that HDAC activity during the early postnatal period plays a crucial role in the masculinization of the brain via modifications of histone acetylation status.

Antisense oligodeoxynucleotide inhibits vascular endothelial growth factor expression in U937 foam cells.

PubMed

Yang, Peng-Yuan; Rui, Yao-Cheng; Jin, You-Xin; Li, Tie-Jun; Qiu, Yan; Zhang, Li; Wang, Jie-Song

2003-06-01

To study the expression of vascular endothelial growth factor (VEGF) induced by oxidized low density liporotein (ox-LDL) and the inhibitory effects of antisense oligodeoxynucleotide (asODN) on the levels of VEGF protein and mRNA in the U937 foam cells. U937 cells were incubated with ox-LDL 80 mg/L for 48 h, then, the foam cells were treated with asODN (0, 5, 10, and 20 micromol/L). The VEGF concentration in the media was determined by ELISA. The VEGF protein expression level in cells was measured by immuohistochemistry; the positive ratio detected by a morphometrical analysis system was used as the amount of the VEGF expression level. The VEGF mRNA level was examined by Northern blotting. After U937 cells were incubated with ox-LDL, VEGF expression level increased greatly both in the cells and in the media. asODN markedly inhibited the increase of VEGF. After treatment with asODN 20 micromol/L, the VEGF protein concentration in the media decreased by 45.0%, the VEGF positive ratio detected by immuohistochemistry in cells decreased by 64.9%, and the VEGF mRNA level decreased by 47.1%. The expression of VEGF in U937 foam cells was strong. asODN inhibited VEGF expression significantly in U937 foam cells in vitro.

Functionalized nanoparticle probes for protein detection

NASA Astrophysics Data System (ADS)

Park, Do Hyun; Lee, Jae-Seung

2015-05-01

In this Review, we discuss representative studies of recent advances in the development of nanoparticle-based protein detection methods, with a focus on the properties and functionalization of nanoparticle probes, as well as their use in detection schemes. We have focused on functionalized nanoparticle probes because they offer a number of advantages over conventional assays and because their use for detecting protein targets for diagnostic purposed has been demonstrated. In this report, we discuss nanoparticle probes classified by material type (gold, silver, silica, semiconductor, carbon, and virus) and surface functionality (antibody, aptamer, and DNA), which play a critical role in enhancing the sensitivity, selectivity, and efficiency of the detection systems. In particular, the synergistic function of each component of the nanoparticle probe is emphasized in terms of specific chemical and physical properties. This research area is in its early stages with many milestones to reach before nanoparticle probes are successfully applied in the field; however, the substantial ongoing efforts of researchers underline the great promise offered by nanoparticlebased probes for future applications. [Figure not available: see fulltext.

Behavior of Triple Langmuir Probes in Non-Equilibrium Plasmas

NASA Technical Reports Server (NTRS)

Polzin, Kurt A.; Ratcliffe, Alicia C.

2018-01-01

The triple Langmuir probe is an electrostatic probe in which three probe tips collect current when inserted into a plasma. The triple probe differs from a simple single Langmuir probe in the nature of the voltage applied to the probe tips. In the single probe, a swept voltage is applied to the probe tip to acquire a waveform showing the collected current as a function of applied voltage (I-V curve). In a triple probe three probe tips are electrically coupled to each other with constant voltages applied between each of the tips. The voltages are selected such that they would represent three points on the single Langmuir probe I-V curve. Elimination of the voltage sweep makes it possible to measure time-varying plasma properties in transient plasmas. Under the assumption of a Maxwellian plasma, one can determine the time-varying plasma temperature T(sub e)(t) and number density n(sub e)(t) from the applied voltage levels and the time-histories of the collected currents. In the present paper we examine the theory of triple probe operation, specifically focusing on the assumption of a Maxwellian plasma. Triple probe measurements have been widely employed for a number of pulsed and timevarying plasmas, including pulsed plasma thrusters (PPTs), dense plasma focus devices, plasma flows, and fusion experiments. While the equilibrium assumption may be justified for some applications, it is unlikely that it is fully justifiable for all pulsed and time-varying plasmas or for all times during the pulse of a plasma device. To examine a simple non-equilibrium plasma case, we return to basic governing equations of probe current collection and compute the current to the probes for a distribution function consisting of two Maxwellian distributions with different temperatures (the two-temperature Maxwellian). A variation of this method is also employed, where one of the Maxwellians is offset from zero (in velocity space) to add a suprathermal beam of electrons to the tail of the main Maxwellian distribution (the bump-on-the-tail distribution function). For a range of parameters in these non-Maxwellian distributions, we compute the current collection to the probes. We compare the distribution function that was assumed a priori with the distribution function one would infer when applying standard triple probe theory to analyze the collected currents. For the assumed class of non-Maxwellian distribution functions this serves to illustrate the effect a non-Maxwellian plasma would have on results interpreted using the equilibrium triple probe current collection theory, allowing us to state the magnitudes of these deviations as a function of the assumed distribution function properties.

[Chromosome study on chronic lymphocytic leukemia using CpG-oligodeoxynucleotide as immunostimulant agent].

PubMed

Wu, Yafang; Xue, Yongquan; Chen, Suning; Yao, Li; Jiang, Hui; Zhang, Jun; Shen, Juan; Pan, Jinlan; Wang, Yong; Bai, Shuxiao

2010-02-01

To investigate whether CpG-oligodeoxynucleotide (CpG-ODN) can improve the detection rate of the karyotypic abnormalities in chronic lymphocytic leukemia (CLL). The bone marrow (BM) or peripheral blood (PB) cells from 57 cases of CLL were collected and cultured with CpG-ODN DSP30+interleukin-2 (IL-2), phytohemagglutinin (PHA), pokeweed (PWM) or IL-2, respectively. Five days later cells were harvested for chromosome preparation. Karyotypic analysis was done using R banding technique. Panel fluorescence in situ hybridization (FISH) was carried out on 19 cases of CLL with normal karyotypes using the following probes: Cen12, D13S25, Rb1, ATM, p53, MYB and IgH. Genomic DNA from 21 cases of them was extracted from BM or PB leukocytes. The immunoglobulin variable heavy chain (IgVH) was amplified by polymerase chain reaction (PCR) and sequenced. CD38 and ZAP70 expressions in the leukemic cells were determined by flow cytometry (FCM). The detection rate of karyotypic abnormalities in the CpG-ODN+IL-2 group (43.85%) was obviously higher than that in the PHA (15.09%), PWM (17.31%) and IL-2 (3.13%) groups (P<0.01). Fifty-two types of karyotypic abnormalities were found. Among them, trisomy12 (+12) or +12 with other abnormalities were the most common, while translocations were the most frequent structural abnormalities including 3 unbalanced and 11 balanced translocations, among them 7 had rearrangements involving 14q32. Thirteen cases showed one or more abnormalities on FISH including trisomy 12 and p53 deletion each in one case, IgH rearrangement and partial deletion each in one case, 13q14.3 deletion in 11 cases of which 5 cases also had Rb1 deletion, 1 case had Rb1 partial deletion. No case with ATM or MYB deletions was found. PCR detected IgVH mutations in 10/21 cases. FCM showed 10/45 cases were CD38 positive, but 35 /45 were CD38 negative, 11/27 cases expressed ZAP70, but 16/27 did not. Among the 26 cases examined for CD38 and ZAP70 expressions simultaneously, 5 cases were CD38+ZAP70+, 13 were CD38-ZAP70-, 6 were CD38-ZAP70+, and 2 were CD38+ZAP70-, respectively. Statistic analysis showed a correlation between complex karyotype and IgVH without mutation, but no association between karyotype and CD38 or ZAP70 expression was observed. CpG-ODN immunostimulation can obviously raise the detection rate of abnormal karyotypes, especially translocations in CLL. FISH is an important complement to conventional karyotypic analysis. The combination of both methods can provide more comprehensive genetic information for CLL.

Cell-adhesion molecules in memory formation.

PubMed

Schmidt, R

1995-01-23

After learning events the CNS of higher organisms selects, which acquired informations are permanently stored as a memory trace. This period of memory consolidation is susceptible to interference by biochemical inhibitors of transcription and translation. Ependymin is a specific CNS glycoprotein functionally involved in memory consolidation in goldfish: after active shock-avoidance conditioning ependymin mRNA is rapidly induced in meningeal fibroblasts followed by enhanced synthesis and secretion of several closely related forms of the protein. Intracranial injections of anti-ependymin antisera or antisense oligodeoxynucleotides interfere specifically with memory consolidation, indicating that only de novo synthesized ependymin molecules are involved. Ependymin is capable of directing the growth of central axons in vitro and participates in neuronal regeneration in situ, presumably by its HNK-1 cell-adhesion epitope. Experiments reviewed in this article suggest a model that involves two regulation mechanisms for the function of ependymin in behavioural plasticity: while hormones appear to determine, how much of this cell adhesion molecule is synthesized after learning, local changes of metal cation concentrations in the micro-environment of activated neurons may polymerize ependymin at those synapses, that have to be consolidated to improve their efficacy for future use.

Long-Term Implanted cOFM Probe Causes Minimal Tissue Reaction in the Brain

PubMed Central

Hochmeister, Sonja; Asslaber, Martin; Kroath, Thomas; Pieber, Thomas R.; Sinner, Frank

2014-01-01

This study investigated the histological tissue reaction to long-term implanted cerebral open flow microperfusion (cOFM) probes in the frontal lobe of the rat brain. Most probe-based cerebral fluid sampling techniques are limited in application time due to the formation of a glial scar that hinders substance exchange between brain tissue and the probe. A glial scar not only functions as a diffusion barrier but also alters metabolism and signaling in extracellular brain fluid. cOFM is a recently developed probe-based technique to continuously sample extracellular brain fluid with an intact blood-brain barrier. After probe implantation, a 2 week healing period is needed for blood-brain barrier reestablishment. Therefore, cOFM probes need to stay in place and functional for at least 15 days after implantation to ensure functionality. Probe design and probe materials are optimized to evoke minimal tissue reaction even after a long implantation period. Qualitative and quantitative histological tissue analysis revealed no continuous glial scar formation around the cOFM probe 30 days after implantation and only a minor tissue reaction regardless of perfusion of the probe. PMID:24621608

Interlocked DNA nanostructures controlled by a reversible logic circuit.

PubMed

Li, Tao; Lohmann, Finn; Famulok, Michael

2014-09-17

DNA nanostructures constitute attractive devices for logic computing and nanomechanics. An emerging interest is to integrate these two fields and devise intelligent DNA nanorobots. Here we report a reversible logic circuit built on the programmable assembly of a double-stranded (ds) DNA [3]pseudocatenane that serves as a rigid scaffold to position two separate branched-out head-motifs, a bimolecular i-motif and a G-quadruplex. The G-quadruplex only forms when preceded by the assembly of the i-motif. The formation of the latter, in turn, requires acidic pH and unhindered mobility of the head-motif containing dsDNA nanorings with respect to the central ring to which they are interlocked, triggered by release oligodeoxynucleotides. We employ these features to convert the structural changes into Boolean operations with fluorescence labelling. The nanostructure behaves as a reversible logic circuit consisting of tandem YES and AND gates. Such reversible logic circuits integrated into functional nanodevices may guide future intelligent DNA nanorobots to manipulate cascade reactions in biological systems.

Interlocked DNA nanostructures controlled by a reversible logic circuit

PubMed Central

Li, Tao; Lohmann, Finn; Famulok, Michael

2014-01-01

DNA nanostructures constitute attractive devices for logic computing and nanomechanics. An emerging interest is to integrate these two fields and devise intelligent DNA nanorobots. Here we report a reversible logic circuit built on the programmable assembly of a double-stranded (ds) DNA [3]pseudocatenane that serves as a rigid scaffold to position two separate branched-out head-motifs, a bimolecular i-motif and a G-quadruplex. The G-quadruplex only forms when preceded by the assembly of the i-motif. The formation of the latter, in turn, requires acidic pH and unhindered mobility of the head-motif containing dsDNA nanorings with respect to the central ring to which they are interlocked, triggered by release oligodeoxynucleotides. We employ these features to convert the structural changes into Boolean operations with fluorescence labelling. The nanostructure behaves as a reversible logic circuit consisting of tandem YES and AND gates. Such reversible logic circuits integrated into functional nanodevices may guide future intelligent DNA nanorobots to manipulate cascade reactions in biological systems. PMID:25229207

Antisense oligonucleotides suppress cell-volume-induced activation of chloride channels.

PubMed

Gschwentner, M; Nagl, U O; Wöll, E; Schmarda, A; Ritter, M; Paulmichl, M

1995-08-01

Cell volume regulation is an essential feature of most cells. After swelling in hypotonic media, the simultaneous activation of potassium and chloride channels is believed to be the initial, time-determining step in cell volume regulation. The activation of both pathways is functionally linked and enables the cells to lose ions and water, subsequently leading to cell shrinkage and readjustment of the initial volume. NIH 3T3 fibroblasts efficiently regulate their volume after swelling and bear chloride channels that are activated by decreasing extracellular osmolarity. The chloride current elicited in these cells after swelling is reminiscent of the current found in oocytes expressing an outwardly rectifying chloride current termed ICln. Introduction of antisense oligodeoxynucleotides complementary to the first 30 nucleotides of the coding region of the ICln channel into NIH 3T3 fibroblasts suppresses the activation of the swelling-induced chloride current. The experiments directly demonstrate an unambiguous link between a volume-activated chloride current and a cloned protein involved in chloride transport.

Development of fluorescent probes based on protection-deprotection of the key functional groups for biological imaging.

PubMed

Tang, Yonghe; Lee, Dayoung; Wang, Jiaoliang; Li, Guanhan; Yu, Jinghua; Lin, Weiying; Yoon, Juyoung

2015-08-07

Recently, the strategy of protection-deprotection of functional groups has been widely employed to design fluorescent probes, as the protection-deprotection of functional groups often induces a marked change in electronic properties. Significant advances have been made in the development of analyte-responsive fluorescent probes based on the protection-deprotection strategy. In this tutorial review, we highlight the representative examples of small-molecule based fluorescent probes for bioimaging, which are operated via the protection-deprotection of key functional groups such as aldehyde, hydroxyl, and amino functional groups reported from 2010 to 2014. The discussion includes the general protection-deprotection methods for aldehyde, hydroxyl, or amino groups, as well as the design strategies, sensing mechanisms, and deprotection modes of the representative fluorescent imaging probes applied to bio-imaging.

A CpG Oligonucleotide Can Protect Mice from a Low Aerosol Challenge Dose of Burkholderia mallei

PubMed Central

Waag, David M.; McCluskie, Michael J.; Zhang, Ningli; Krieg, Arthur M.

2006-01-01

Treatment with an oligodeoxynucleotide (ODN) containing CPG motifs (CpG ODN 7909) was found to protect BALB/c mice from lung infection or death after aerosol challenge with Burkholderia mallei. Protection was associated with enhanced levels of gamma interferon (IFN-γ)-inducible protein 10, interleukin-12 (IL-12), IFN-γ, and IL-6. Preexposure therapy with CpG ODNs may protect victims of a biological attack from glanders. PMID:16495571

A CpG oligonucleotide can protect mice from a low aerosol challenge dose of Burkholderia mallei.

PubMed

Waag, David M; McCluskie, Michael J; Zhang, Ningli; Krieg, Arthur M

2006-03-01

Treatment with an oligodeoxynucleotide (ODN) containing CPG motifs (CpG ODN 7909) was found to protect BALB/c mice from lung infection or death after aerosol challenge with Burkholderia mallei. Protection was associated with enhanced levels of gamma interferon (IFN-gamma)-inducible protein 10, interleukin-12 (IL-12), IFN-gamma, and IL-6. Preexposure therapy with CpG ODNs may protect victims of a biological attack from glanders.

Employment of Oligodeoxynucleotide plus Interleukin-2 Improves Cytogenetic Analysis in Splenic Marginal Zone Lymphoma

PubMed Central

Bardi, Antonella; Cavazzini, Francesco; Rigolin, Gian Matteo; Tammiso, Elisa; Volta, Eleonora; Pezzolo, Elisa; Formigaro, Luca; Sofritti, Olga; Daghia, Giulia; Ambrosio, Cristina; Rizzotto, Lara; Abass, Awad E.; D'Auria, Fiorella; Musto, Pellegrino; Cuneo, Antonio

2011-01-01

To compare the efficiency of novel mitogenic agents and traditional mitosis inductors, 18 patients with splenic marginal zone lymphoma (SMZL) were studied. Three cultures using oligodeoxynucleotide (ODN) plus interleukin-2 (IL-2), or TPA, or LPS were setup in each patient. Seventeen/18 cases with ODN + IL2 had moderate/good proliferation (94, 4%) as compared with 10/18 cases with TPA and LPS (55%) (P = .015); 14/18 (77, 7%) cases with ODN + IL2 had sufficient good quality of banding as compared with 8/18 cases (44, 4%) with TPA and LPS. The karyotype could be defined from ODN + IL2-stimulated cultures in all 18 patients, 14 of whom (77, 7%) had a cytogenetic aberration, whereas clonal aberrations could be documented in 9 and in 3 cases by stimulation with LPS and TPA, respectively. Recurrent chromosome aberrations in our series were represented by aberrations of chromosome 14q in 5 patients, by trisomy 12 and 7q deletion in 4 cases each, and by abnormalities involving 11q and 13q in two cases each. These findings show that stimulation with ODN + IL2 offers more mitotic figures of better quality and results in an increased rate of clonal aberrations in SMZL, making this method ideal for prospective studies aiming at the definition of the prognostic impact of cytogenetic aberrations in this disorder. PMID:21629757

Zinc-finger Nuclease-induced Gene Repair With Oligodeoxynucleotides: Wanted and Unwanted Target Locus Modifications

PubMed Central

Radecke, Sarah; Radecke, Frank; Cathomen, Toni; Schwarz, Klaus

2010-01-01

Correcting a mutated gene directly at its endogenous locus represents an alternative to gene therapy protocols based on viral vectors with their risk of insertional mutagenesis. When solely a single-stranded oligodeoxynucleotide (ssODN) is used as a repair matrix, the efficiency of the targeted gene correction is low. However, as shown with the homing endonuclease I-SceI, ssODN-mediated gene correction can be enhanced by concomitantly inducing a DNA double-strand break (DSB) close to the mutation. Because I-SceI is hardly adjustable to cut at any desired position in the human genome, here, customizable zinc-finger nucleases (ZFNs) were used to stimulate ssODN-mediated repair of a mutated single-copy reporter locus stably integrated into human embryonic kidney-293 cells. The ZFNs induced faithful gene repair at a frequency of 0.16%. Six times more often, ZFN-induced DSBs were found to be modified by unfaithful addition of ssODN between the termini and about 60 times more often by nonhomologous end joining-related deletions and insertions. Additionally, ZFN off-target activity based on binding mismatch sites at the locus of interest was detected in in vitro cleavage assays and also in chromosomal DNA isolated from treated cells. Therefore, the specificity of ZFN-induced ssODN-mediated gene repair needs to be improved, especially regarding clinical applications. PMID:20068556

Response of immune response genes to adjuvants poly [di(sodium carboxylatoethylphenoxy)phosphazene] (PCEP), CpG oligodeoxynucleotide and emulsigen at intradermal injection site in pigs.

PubMed

Magiri, R B; Lai, K; Chaffey, A M; Wilson, H L; Berry, W E; Szafron, M L; Mutwiri, G K

2016-07-01

Understanding the mechanisms by which adjuvants mediate their effects provide critical information on how innate immunity influences the development of adaptive immunity. Despite being a critical vaccine component, the mechanisms by which adjuvants mediate their effects are not fully understood and this is especially true when they are used in large animals. This lack of understanding limits our ability to design effective vaccines. In the present study, we administered polyphosphazene (PCEP), CpG oligodeoxynucleotides (CpG), emulsigen or saline via an intradermal injection into pigs and assessed the impact on the expression of reported 'adjuvant response genes' over time. CpG induced a strong upregulation of the chemokine CXL10 several 'Interferon Response Genes', as well as TNFα, and IL-10, and a down-regulation of IL-17 genes. Emulsigen upregulated expression of chemokines CCL2 and CCL5, proinflammatory cytokines IL-6 and TNFα, as well as TLR9, and several IFN response genes. PCEP induced the expression of chemokine CCL2 and proinflammatory cytokine IL-6. These results suggest that emulsigen and CpG may promote recruitment of innate immune cells and Th1 type cytokine production but that PCEP may promote a Th-2 type immune response through the induction of IL-6, an inducer of B cell activity and differentiation. Copyright © 2016 Elsevier B.V. All rights reserved.

A bacterial reporter system for the evaluation of antisense oligodeoxynucleotides directed against human papillomavirus type 16 (HPV-16).

PubMed

Guapillo, Mario R; Márquez, Miguel A; Benítez-Hess, María L; Alvarez-Salas, Luis M

2006-07-01

Antisense oligodeoxynucleotides (AS-ODNs) are a promising alternative for the cure of many diseases because of their in vivo specificity and stability. However, AS-ODNs have a strong dependence on the target mRNA structure making necessary extensive in vivo testing. There is, therefore, a need to develop assays to rapidly evaluate in vivo ODN performance. We report a simple and inexpensive bacterial reporter system for the rapid in vivo evaluation of AS-ODNs directed against human papillomavirus type 16 (HPV-16) based on the destruction of a chimeric CFP mRNA using the reported HPV-16 nt 410-445 target. In vitro RNaseH assays confirmed target RNA accessibility after AS-ODN treatment. Expression of CFP in Escherichia coli BL21(DE3) with pGST-TSd2-CFP plasmid containing HPV-16 nt 410-445 target linked to CFP was blocked by transformed antisense PS-ODNs but not by two different scrambled ODN controls. A correlation was observed between bacterial CFP downregulation with the HPV-16 E6/E7 mRNA downregulation and the inhibition of anchorage-independent growth of HPV-16 containing cells suggesting that inhibition of HPV-16 E6/E7 expression by AS-ODNs directed against 410-445 target in cervical tumor cells can be tested in bacterial models.

Bioconjugation of Oligodeoxynucleotides Carrying 1,4-Dicarbonyl Groups via Reductive Amination with Lysine Residues.

PubMed

Yang, Bo; Jinnouchi, Akiko; Usui, Kazuteru; Katayama, Tsutomu; Fujii, Masayuki; Suemune, Hiroshi; Aso, Mariko

2015-08-19

We evaluated the efficacy of bioconjugation of oligodeoxynucleotides (ODNs) containing 1,4-dicarbonyl groups, a C4'-oxidized abasic site (OAS), and a newly designed 2'-methoxy analogue, via reductive amination with lysine residues. Dicarbonyls, aldehyde and ketone at C1- and C4-positions of deoxyribose in the ring-opened form of OAS allowed efficient reaction with amines. Kinetic studies indicated that reductive amination of OAS-containing ODNs with a proximal amine on the complementary strand proceeded 10 times faster than the corresponding reaction of an ODN containing an abasic site with C1-aldehyde. Efficient reductive amination between the DNA-binding domain of Escherichia coli DnaA protein and ODNs carrying OAS in the DnaA-binding sequence proceeded at the lysine residue in proximity to the phosphate group at the 5'-position of the OAS, in contrast to unsuccessful conjugation with abasic site ODNs, even though they have similar aldehydes. Theoretical calculation indicated that the C1-aldehyde of OAS was more accessible to the target lysine than that of the abasic site. These results demonstrate the potential utility of cross-linking strategies that use dicarbonyl-containing ODNs for the study of protein-nucleic acid interactions. Conjugation with a lysine-containing peptide that lacked specific affinity for ODN was also successful, further highlighting the advantages of 1,4-dicarbonyls.

Suppression of wear particle induced pro-inflammatory cytokine and chemokine production in macrophages via NF-κB decoy oligodeoxynucleotide: A preliminary report

PubMed Central

Lin, Tzu-hua; Yao, Zhenyu; Sato, Taishi; Keeney, Michael; Li, Chenguang; Pajarinen, Jukka; Yang, Fan; Egashira, Kensuke; Goodman, Stuart B.

2014-01-01

Total joint replacement (TJR) is a very cost-effective surgery for end-stage arthritis. One important goal is to decrease the revision rate especially because TJR has been extended to younger patients. Continuous production of ultra-high molecular weight polyethylene (UHMWPE) wear particles induces macrophage infiltration and chronic inflammation, which can lead to peri-prosthetic osteolysis. Targeting individual pro-inflammatory cytokines directly has not reversed the osteolytic process in clinical trials, due to compensatory upregulation of other pro-inflammatory factors. We hypothesized that targeting the important transcription factor NF-κB could mitigate the inflammatory response to wear particles, potentially diminishing osteolysis. In the current study, we suppressed NF-κB activity in mouse RAW264.7 and human THP1 macrophage cell lines, as well as primary mouse and human macrophages, via competitive binding with double strand decoy oligodeoxynucleotide (ODN) containing an NF-κB binding element. We found that macrophage exposure to UHMWPE particles induced multiple pro-inflammatory cytokine and chemokine expression including TNF-α, MCP1, MIP1α and others. Importantly, the decoy ODN significantly suppressed the induced cytokine and chemokine expression in both murine and human macrophages, and resulted in suppression of macrophage recruitment. The strategic use of decoy NF-κB ODN, delivered locally, could potentially diminish particle-induced peri-prosthetic osteolysis. PMID:24814879

Ultrasound microbubble-mediated transfection of NF-κB decoy oligodeoxynucleotide into gingival tissues inhibits periodontitis in rats in vivo

PubMed Central

Yamaguchi, Hiroyuki; Hosomichi, Jun; Suzuki, Jun-ichi; Hatano, Kasumi; Usumi-Fujita, Risa; Shimizu, Yasuhiro; Kaneko, Sawa; Ono, Takashi

2017-01-01

Periodontitis is a chronic infectious disease for which the fundamental treatment is to reduce the load of subgingival pathogenic bacteria by debridement. However, previous investigators attempted to implement a nuclear factor kappa B (NF-κB) decoy oligodeoxynucleotide (ODN) as a suppressor of periodontitis progression. Although we recently reported the effectiveness of the ultrasound-microbubble method as a tool for transfecting the NF-κB decoy ODN into healthy rodent gingival tissue, this technique has not yet been applied to the pathological gingiva of periodontitis animal models. Therefore, the aim of this study was to investigate the effectiveness of the technique in transfecting the NF-κB decoy ODN into rats with ligature-induced periodontitis. Micro computed tomography (micro-CT) analysis demonstrated a significant reduction in alveolar bone loss following treatment with the NF-κB decoy ODN in the experimental group. RT-PCR showed that NF-κB decoy ODN treatment resulted in significantly reduced expression of inflammatory cytokine transcripts within rat gingival tissues. Thus, we established a transcutaneous transfection model of NF-κB decoy ODN treatment of periodontal tissues using the ultrasound-microbubble technique. Our findings suggest that the NF-κB decoy ODN could be used as a significant suppressor of gingival inflammation and periodontal disease progression. PMID:29091721

Oral and intraperitoneal administration of phosphorothioate oligodeoxynucleotides leads to control of Cryptosporidium parvum infection in neonatal mice.

PubMed

Barrier, Mathieu; Lacroix-Lamandé, Sonia; Mancassola, Roselyne; Auray, Gaël; Bernardet, Nelly; Chaussé, Anne-Marie; Uematsu, Satoshi; Akira, Shizuo; Laurent, Fabrice

2006-05-15

Neonates are particularly vulnerable to infections, in part because of the incomplete development of their immune system. Recent advances in immunostimulatory treatments based on conserved microbial components led us to assess the potential of oligodeoxynucleotides (ODNs) for decreasing the sensitivity of neonates to Cryptosporidium parvum infection. Neonate mice were treated orally or intraperitoneally (ip) with CpG ODNs or non-CpG ODNs 24 h before C. parvum infection, and parasite load and cytokine up-regulation were evaluated. CpG ODN 1668 and non-CpG ODN 1668 administered orally, as well as CpG ODN 1668 administered ip, induced an 80%-95% decrease in intestinal parasite load 6 days after infection. Intraperitoneal and oral pretreatment with CpG ODN 1668 led to a strong initial up-regulation of cytokines and CD69 messenger RNA in the intestine and a decrease in parasite load by a Toll-like receptor 9 (TLR9)-dependent mechanism. By contrast, oral administration of non-CpG ODN 1668 decreased parasite load by a TLR9-independent mechanism. The control of neonatal C. parvum infection by ip or oral administration of ODNs is feasible by 2 different mechanisms: (1) the well-known interaction involving CpG/TLR9, leading to the production of cytokines and lymphocyte activation, and (2) a new unknown mechanism that is independent of TLR9 and effective orally.

Attachment of micro- and nano-particles on tipless cantilevers for colloidal probe microscopy.

PubMed

D'Sa, Dexter J; Chan, Hak-Kim; Chrzanowski, Wojciech

2014-07-15

Current colloidal probe preparation techniques face several challenges in the production of functional probes using particles ⩽5 μm. Challenges include: glue encapsulated particles, glue altered particle properties, improper particle or agglomerate attachment, and lengthy procedures. We present a method to rapidly and reproducibly produce functional micro and nano-colloidal probes. Using a six-step procedure, cantilevers mounted on a custom designed 45° holder were used to approach and obtain a minimal amount of epoxy resin (viscosity of ∼14,000 cP) followed by a single micron/nano particle on the apex of a tipless cantilever. The epoxy and particles were prepared on individual glass slides and subsequently affixed to a 10× or 40× optical microscope lens using another custom designed holder. Scanning electron microscopy and comparative glue-colloidal probe measurements were used to confirm colloidal probe functionality. The method presented allowed rapid and reproducible production of functional colloidal probes (80% success). Single nano-particles were prominently affixed to the apex of the cantilever, unaffected by the epoxy. Nano-colloidal probes were used to conduct topographical, instantaneous force, and adhesive force mapping measurements in dry and liquid media conveying their versatility and functionality in studying nano-colloidal systems. Copyright © 2014 Elsevier Inc. All rights reserved.

Homogeneous versus heterogeneous probes for microbial ecological microarrays.

PubMed

Bae, Jin-Woo; Park, Yong-Ha

2006-07-01

Microbial ecological microarrays have been developed for investigating the composition and functions of microorganism communities in environmental niches. These arrays include microbial identification microarrays, which use oligonucleotides, gene fragments or microbial genomes as probes. In this article, the advantages and disadvantages of each type of probe are reviewed. Oligonucleotide probes are currently useful for probing uncultivated bacteria that are not amenable to gene fragment probing, whereas the functional gene fragments amplified randomly from microbial genomes require phylogenetic and hierarchical categorization before use as microbial identification probes, despite their high resolution for both specificity and sensitivity. Until more bacteria are sequenced and gene fragment probes are thoroughly validated, heterogeneous bacterial genome probes will provide a simple, sensitive and quantitative tool for exploring the ecosystem structure.

Multiple-scanning-probe tunneling microscope with nanoscale positional recognition function.

PubMed

Higuchi, Seiji; Kuramochi, Hiromi; Laurent, Olivier; Komatsubara, Takashi; Machida, Shinichi; Aono, Masakazu; Obori, Kenichi; Nakayama, Tomonobu

2010-07-01

Over the past decade, multiple-scanning-probe microscope systems with independently controlled probes have been developed for nanoscale electrical measurements. We developed a quadruple-scanning-probe tunneling microscope (QSPTM) that can determine and control the probe position through scanning-probe imaging. The difficulty of operating multiple probes with submicrometer precision drastically increases with the number of probes. To solve problems such as determining the relative positions of the probes and avoiding of contact between the probes, we adopted sample-scanning methods to obtain four images simultaneously and developed an original control system for QSPTM operation with a function of automatic positional recognition. These improvements make the QSPTM a more practical and useful instrument since four images can now be reliably produced, and consequently the positioning of the four probes becomes easier owing to the reduced chance of accidental contact between the probes.

Effects of intratracheal administration of nuclear factor-kappaB decoy oligodeoxynucleotides on long-term cigarette smoke-induced lung inflammation and pathology in mice

PubMed Central

2009-01-01

To determine if nuclear factor-κB (NF-κB) activation may be a key factor in lung inflammation and respiratory dysfunction, we investigated whether NF-κB can be blocked by intratracheal administration of NF-κB decoy oligodeoxynucleotides (ODNs), and whether decoy ODN-mediated NF-κB inhibition can prevent smoke-induced lung inflammation, respiratory dysfunction, and improve pathological alteration in the small airways and lung parenchyma in the long-term smoke-induced mouse model system. We also detected changes in transcriptional factors. In vivo, the transfection efficiency of NF-κB decoy ODNs to alveolar macrophages in BALF was measured by fluorescein isothiocyanate (FITC)-labeled NF-κB decoy ODNs and flow cytometry post intratracheal ODN administration. Pulmonary function was measured by pressure sensors, and pathological changes were assessed using histology and the pathological Mias software. NF-κB and activator protein 1(AP-1) activity was detected by the electrophoretic motility shift assay (EMSA). Mouse cytokine and chemokine pulmonary expression profiles were investigated by enzyme-linked immunosorbent assay (ELISA) in bronchoalveolar lavage fluid (BALF) and lung tissue homogenates, respectively, after repeated exposure to cigarette smoke. After 24 h, the percentage of transfected alveolar macrophages was 30.00 ± 3.30%. Analysis of respiratory function indicated that transfection of NF-κB decoy ODNs significantly impacted peak expiratory flow (PEF), and bronchoalveolar lavage cytology displayed evidence of decreased macrophage infiltration in airways compared to normal saline-treated or scramble NF-κB decoy ODNs smoke exposed mice. NF-κB decoy ODNs inhibited significantly level of macrophage inflammatory protein (MIP) 1α and monocyte chemoattractant protein 1(MCP-1) in lung homogenates compared to normal saline-treated smoke exposed mice. In contrast, these NF-κB decoy ODNs-treated mice showed significant increase in the level of tumor necrosis factor-α(TNF-α) and pro-MMP-9(pro-matrix metalloproteinase-9) in mice BALF. Further measurement revealed administration of NF-κB decoy ODNs did not prevent pathological changes. These findings indicate that NF-κB activation play an important role on the recruitment of macrophages and pulmonary dysfunction in smoke-induced chronic lung inflammation, and with the exception of NF-κB pathway, there might be complex mechanism governing molecular dynamics of pro-inflammatory cytokines expression and structural changes in small airways and pulmonary parenchyma in vivo. PMID:19706153

Transdominant Rev and Protease Mutant Proteins of HIV-SIV as Potential Antiviral Agents in Vitro and in Vivo (AIDS)

DTIC Science & Technology

1993-10-30

hammerhead ribozymes (7-9) and a hairpin ribozyme (10) directed against HIV-l RNA has been shown to confer significant resistance to HIV-I infection...antisense oligodeoxynucleotides (ODN) directed to the Rev Response Element (RRE) and ribozymes that target viral mRNAs. The ribozyme approach, in...particular, has yielded extremely encouraging positive data. We showed that a hairpin ribozyme designed to cleave HIV-1 RNA in the 5’ leader sequence

Cancer Vaccine Composed of Oligonucleotides Conjugated to Apoptotic Tumor Cells | NCI Technology Transfer Center | TTC

Cancer.gov

Synthetic oligodeoxynucleotides (ODN) containing unmethylated Cytosine-Guanine (CpG) motifs mimic the immunostimulatory activity of bacterial DNA. CpG ODN directly stimulate B cells and plasmacytoid dendritic cells (pDC), promote the production of T Helper 1 cells (Th1) and pro-inflammatory cytokines, and  trigger the maturation/activation of professional antigen presenting cells. The National Cancer Institute, Laboratory of Experimental Immunology, seeks interested parties to co- develop methods for inducing an immune response to tumors.

Transient decrease in nociceptor GRK2 expression produces long–term enhancement in inflammatory pain

PubMed Central

Ferrari, Luiz F.; Bogen, Oliver; Alessandri–Haber, Nicole; Levine, Emma; Gear, Robert W.; Levine, Jon D.

2012-01-01

In heterozygous mice, attenuation of G-protein-coupled receptor kinase 2 (GRK2) level in nociceptors is associated with enhanced and prolonged inflammatory hyperalgesia. To further elucidate the role of GRK2 in nociceptor function we reversibly decreased GRK2 expression using intrathecal antisense oligodeoxynucleotide (AS-ODN). GRK2 AS-ODN administration led to an enhanced and prolonged hyperalgesia induced by prostaglandin E 2, epinephrine and carrageenan. Morover, this effect persisted unattenuated 2 weeks after the last dose of antisense, well after GRK2 protein recovered, suggesting that transient attenuation of GRK2 produced neuroplastic changes in nociceptor function. Unlike hyperalgesic priming induced by transient attenuation of GRK2 produced neuroplastic changes in nociceptor function. Unlike hyperalgesic priming induced by transient activation of protein kinase C epsilon (PKCε), (Aley et al., 2000, Parada et al., 2003b), the enhanced and prolonged hyperalgesia following attenuation of GRK2 is PKCε- and cytoplasmic polyadenylation element binding protein (CPEB)-independent and is protein kinase A (PKA)- and Src tyrosine kinase (Src)-dependent. Finally, rats treated with GRK2 AS-ODN exhibited enhanced and prolonged hyperalgesia induced by direct activation of second messengers, adenyl cyclase, Epac or PKA, suggesting changes downstream of G-protein-coupled receptors. Because inflammation can produce a decrease in GRK2, such a mechanism could help explain a predilection to develop chronic pain, after resolution of acute inflammation. PMID:22796071

Stimulation of Chronic Lymphocytic Leukemia (CLL) Cells with CpG Oligodeoxynucleotide (ODN) Gives Consistent Karyotypic Results among Laboratories: a CLL Research Consortium (CRC)h Study

PubMed Central

Heerema, Nyla A.; Byrd, John C.; Cin, Paola Dal; Dell’ Aquila, Marie L.; Koduru, Prasad; Aviram, Ayala; Smoley, Stephanie; Rassenti, Laura Z.; Greaves, Andrew W.; Brown, Jennifer R.; Rai, Kanti R.; Kipps, Thomas J.; Kay, Neil E.; van Dyke, Daniel

2010-01-01

Cytogenetic abnormalities in CLL are important prognostic indicators. Historically, only interphase cytogenetics was clinically useful in CLL because traditional mitogens are not effective mitotic stimulants. Recently, CpG-oligodeoxynucleotide (ODN) stimulation has shown effectiveness in CLL. The CLL Research Consortium (CRC) tested the effectiveness and reproducibility of CpG-ODN stimulation to detect chromosomally abnormal clones by five laboratories. More clonal abnormalities were observed after culture of CLL cells with CpG-ODN than with pokeweed mitogen (PWM)+12-O-tetradecanoyl-phorobol-13-acetate (TPA). All clonal abnormalities in PWM+TPA cultures were observed in CpG-ODN cultures, whereas CpG-ODN identified some clones not found by PWM+TPA. CpG-ODN stimulation of one normal control and 12 CLL samples showed that excepting clones of del(13q) in low frequencies and one translocation, results in all five laboratories were consistent, and all abnormalities were concordant with FISH. Thus, abnormal clones in CLL are more readily detected with CpG-ODN stimulation than with traditional B-cell mitogens. After CpG-ODN stimulation, abnormalities were reproducible among cytogenetic laboratories. CpG-ODN did not appear to induce aberrations in cell culture and enhanced detection of abnormalities and complexity in CLL. Since karyotypic complexity is prognostic and is not detectable by standard FISH analyses, stimulation with CpG-ODN is useful to identify this additional prognostic factor in CLL. PMID:21156225

Differential production of immunoglobulin classes and subclasses by mucosal-type human B-lymphocytes exposed in vitro to CpG oligodeoxynucleotides.

PubMed

Cognasse, Fabrice; Acquart, Sophie; Beniguel, Lydie; Sabido, Odile; Chavarin, Patricia; Genin, Christian; Garraud, Olivier

2005-01-01

As B-lymphocytes play an important role in innate and adaptive immunity, we aimed to examine the effects of CpG oligodeoxynucleotides (ODNs) on purified tonsil-originating CD19+ B-cells, representing mucosal B-cells. We screened various K-type ODNs, reactive with human B-cells, and tested for the production of immunoglobulins in vitro. Using one CpG-ODN, DSP30, we observed that it could upregulate not only Toll-like receptor 9 (TLR9) mRNA expression in activated B-cells, but also the early expression of CD69 followed by the sequential expression of CD80, CD86 and the nuclear factor (NF)-kappaB pathway. Furthermore, mRNA expression of certain B-cell-derived cytokines was influenced by exposure to DSP30, with a strong upregulation of interleukin 6 (IL-6) and downregulation of IL1-beta. Stimulation of B-cells, co-stimulated with IL-2, IL-10 and soluble CD40 ligand (sCD40L) with different CpG-ODNs, had differing effects on the terminal differentiation in vitro of B-cells into immunoglobulin-secreting cells. TLR9 is involved in innate immunity and the recognition of bound CpG DNA from invading bacterial pathogens. As tonsillar B-cells are mucosal-type B-lymphocytes, this study suggests that CpG-ODNs show promise as mucosal adjuvants in modulating the local production of immunoglobulins of certain classes and subclasses, a crucial issue in vaccine perspectives.

The effect of TLR9 agonist CpG oligodeoxynucleotides on the intestinal immune response of cobia (Rachycentron canadum).

PubMed

Byadgi, Omkar; Puteri, Dinda; Lee, Jai-Wei; Chang, Tsung-Chou; Lee, Yan-Horn; Chu, Chun-Yen; Cheng, Ta-Chih

2014-01-01

Cytosine-guanine oligodeoxynucleotide (CpG ODN) motifs of bacterial DNA are recognized through toll-like receptor 9 (TLR9) and are potent activators of innate immunity. However, the interaction between TLR9 and CpG ODN in aquatic species has not been well characterized. Hence, cobia TLR9 isoform B (RCTLR9B) was cloned and its expression and induction in intestine were investigated. RCTLR9B cDNA consists of 3113bp encoding 1009 amino acids containing three regions, leucine rich repeats, transmembrane domain, and toll/interleukin-1 receptor (TIR) domain. Intraperitoneal injection of CpG ODN 2395 upregulated RCTLR9 A and B and MyD88 and also induced the expressions of Mx, chemokine CC, and interleukin IL-1 β . Cobia intraperitoneally injected with CpG ODN 1668 and 2395 had increased survival rates after challenge with Photobacterium damselae subsp. piscicida. In addition, formulation of CpG ODN with formalin-killed bacteria (FKB) and aluminum hydroxide gel significantly increased expressions of RCTLR9 A (50 folds) and B (30 folds) isoforms at 10 dpi (CpG ODN 1668) and MyD88 (21 folds) at 6 dpv (CpG ODN 2395). Subsequently, IL-1 β increased at 6 dpv in 1668 group. No histopathological damage and inflammatory responses were observed in the injected cobia. Altogether, these results facilitate CpG ODNs as an adjuvant to increase bacterial disease resistance and efficacy of vaccines in cobia.

The Effect of TLR9 Agonist CpG Oligodeoxynucleotides on the Intestinal Immune Response of Cobia (Rachycentron canadum)

PubMed Central

Byadgi, Omkar; Puteri, Dinda; Lee, Jai-Wei; Chang, Tsung-Chou; Lee, Yan-Horn; Chu, Chun-Yen; Cheng, Ta-Chih

2014-01-01

Cytosine-guanine oligodeoxynucleotide (CpG ODN) motifs of bacterial DNA are recognized through toll-like receptor 9 (TLR9) and are potent activators of innate immunity. However, the interaction between TLR9 and CpG ODN in aquatic species has not been well characterized. Hence, cobia TLR9 isoform B (RCTLR9B) was cloned and its expression and induction in intestine were investigated. RCTLR9B cDNA consists of 3113bp encoding 1009 amino acids containing three regions, leucine rich repeats, transmembrane domain, and toll/interleukin-1 receptor (TIR) domain. Intraperitoneal injection of CpG ODN 2395 upregulated RCTLR9 A and B and MyD88 and also induced the expressions of Mx, chemokine CC, and interleukin IL-1β. Cobia intraperitoneally injected with CpG ODN 1668 and 2395 had increased survival rates after challenge with Photobacterium damselae subsp. piscicida. In addition, formulation of CpG ODN with formalin-killed bacteria (FKB) and aluminum hydroxide gel significantly increased expressions of RCTLR9 A (50 folds) and B (30 folds) isoforms at 10 dpi (CpG ODN 1668) and MyD88 (21 folds) at 6 dpv (CpG ODN 2395). Subsequently, IL-1β increased at 6 dpv in 1668 group. No histopathological damage and inflammatory responses were observed in the injected cobia. Altogether, these results facilitate CpG ODNs as an adjuvant to increase bacterial disease resistance and efficacy of vaccines in cobia. PMID:24991578

Comparative inhibition of rabbit globin mRNA translation by modified antisense oligodeoxynucleotides.

PubMed Central

Cazenave, C; Stein, C A; Loreau, N; Thuong, N T; Neckers, L M; Subasinghe, C; Hélène, C; Cohen, J S; Toulmé, J J

1989-01-01

We have studied the translation of rabbit globin mRNA in cell free systems (reticulocyte lysate and wheat germ extract) and in microinjected Xenopus oocytes in the presence of anti-sense oligodeoxynucleotides. Results obtained with the unmodified all-oxygen compounds were compared with those obtained when phosphorothioate or alpha-DNA was used. In the wheat germ system a 17-mer sequence targeted to the coding region of beta-globin mRNA was specifically inhibitory when either the unmodified phosphodiester oligonucleotide or its phosphorothioate analogue were used. In contrast no effect was observed with the alpha-oligomer. These results were ascribed to the fact that phosphorothioate oligomers elicit an RNase-H activity comparable to the all-oxygen congeners, while alpha-DNA/mRNA hybrids were a poor substrate. Microinjected Xenopus oocytes followed a similar pattern. The phosphorothioate oligomer was more efficient to prevent translation than the unmodified 17-mer. Inhibition of beta-globin synthesis was observed in the nanomolar concentration range. This result can be ascribed to the nuclease resistance of phosphorothioates as compared to natural phosphodiester linkages, alpha-oligomers were devoid of any inhibitory effect up to 30 microM. Phosphorothioate oligodeoxyribonucleotides were shown to be non-specific inhibitors of protein translation, at concentrations in the micromolar range, in both cell-free systems and oocytes. Non-specific inhibition of translation was dependent on the length of the phosphorothioate oligomer. These non-specific effects were not observed with the unmodified or the alpha-oligonucleotides. Images PMID:2472605

A novel nonsteroidal antifibrotic oligo decoy containing the TGF-beta element found in the COL1A1 gene which regulates murine schistosomiasis liver fibrosis.

PubMed

Boros, D L; Singh, K P; Gerard, H C; Hudson, A P; White, S L; Cutroneo, K R

2005-08-01

Schistosomiasis mansoni disseminated worm eggs in mice and humans induce granulomatous inflammations and cumulative fibrosis causing morbidity and possibly mortality. In this study, intrahepatic and I.V. injections of a double-stranded oligodeoxynucleotide decoy containing the TGF-beta regulatory element found in the distal promoter of the COL1A1 gene into worm-infected mice suppressed TGF-beta1, COL1A1, tissue inhibitor of metalloproteinase-1, and decreased COL3A1 mRNAs to a lesser extent. Sequence comparisons within the mouse genome found homologous sequences within the COL3A1, TGF-beta1, and TIMP-1 5' flanking regions. Cold competition gel mobility shift assays using these homologous sequences with 5' and 3' flanking regions found in the natural COL1A1 gene showed competition. Competitive gel mobility assays in a separate experiment showed no competition using a 5-base mutated or scrambled sequence. Explanted liver granulomas from saline-injected mice incorporated 10.45 +/- 1.7% (3)H-proline into newly synthesized collagen, whereas decoy-treated mice showed no collagen synthesis. Compared with the saline control schistosomiasis mice phosphorothioate double-stranded oligodeoxynucleotide treatment decreased total liver collagen content (i.e. hydroxy-4-proline) by 34%. This novel molecular approach has the potential to be employed as a novel antifibrotic treatment modality. (c) 2005 Wiley-Liss, Inc.

Spirodi(iminohydantoin) Products from Oxidation of 2′-Deoxyguanosine in the Presence of NH4Cl in Nucleoside and Oligodeoxynucleotide Contexts

PubMed Central

2015-01-01

Upon oxidation of the heterocyclic ring in 2′-deoxyguanosine (dG), the initial electrophilic intermediate displays a wide range of reactivities with nucleophiles leading to many downstream products. In the present study, the product profiles were mapped when aqueous solutions of dG were allowed to react with NH4Cl in the presence of the photooxidants riboflavin and Rose Bengal as well as the diffusible one-electron oxidant Na2IrCl6. Product characterization identified the 2′-deoxyribonucleosides of spiroiminodihydantoin, 5-guanidinohydantoin, and oxazolone resulting from H2O as the nucleophile. When NH3 was the nucleophile, a set of constitutional isomers that are diastereotopic were also observed, giving characteristic masses of dG + 31. ESI+-MS/MS of these NH3 adducts identified them to be spirocycles with substitution of either the C5 or C8 carbonyl with an amine. The NH3 adducts exhibit acid-catalyzed hydrolysis to spiroiminodihydantoin. Quantification of the NH3 and H2O adducts resulting from oxidation of dG in the nucleoside, single-stranded, and duplex oligodeoxynucleotide contexts were monitored allowing mechanisms for product formation to be proposed. These data also provide a cautionary note to those who purify their oligonucleotide samples with ammonium salts before oxidation because this will lead to unwanted side reactions in which ammonia participates in product formation. PMID:25539403

AP-1 Oligodeoxynucleotides Reduce Aortic Elastolysis in a Murine Model of Marfan Syndrome.

PubMed

Arif, Rawa; Zaradzki, Marcin; Remes, Anca; Seppelt, Philipp; Kunze, Reiner; Schröder, Hannes; Schwill, Simon; Ensminger, Stephan M; Robinson, Peter N; Karck, Matthias; Müller, Oliver J; Hecker, Markus; Wagner, Andreas H; Kallenbach, Klaus

2017-12-15

Marfan syndrome is characterized by high expression of matrix metalloproteinases (MMPs) in aortic smooth muscle cells (AoSMCs) associated with medial elastolysis and aortic root aneurysm. We aimed to reduce aortic elastolysis through decrease of MMP expression with decoy oligodeoxynucleotides (dODNs) neutralizing the transcription factor activating factor-1 (AP-1). AP-1 abundance in nuclear extracts as well as MMP-2 and MMP-9 expression were significantly increased in isolated mAoSMC of mgR/mgR Marfan mice compared to wild-type cells. Exposure to AP-1 neutralizing dODNs resulted in a significant reduction of basal and interleukin-1β-stimulated MMP expression and activity in mAoSMCs. Moreover, increased migration and formation of superoxide radical anions was substantially decreased in mAoSMCs by AP-1 dODN treatment. Aortic grafts from donor Marfan mice were treated with AP-1- dODN ex vivo and implanted as infrarenal aortic interposition grafts in mgR/mgR mice. Pretreatment of aortic grafts with AP-1 dODN led to reduced elastolysis, macrophage infiltration, and MMP activity. Permeability of the endothelial monolayer was increased for dODN in mgR/mgR aortae with observed loss of tight junction proteins ZO-1 and occludin, enabling dODN to reach the tunica media. Targeting AP-1 activity offers a new potential strategy to treat the vascular phenotype associated with Marfan syndrome. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Seamless Genetic Conversion of SMN2 to SMN1 via CRISPR/Cpf1 and Single-Stranded Oligodeoxynucleotides in Spinal Muscular Atrophy Patient-Specific Induced Pluripotent Stem Cells.

PubMed

Zhou, Miaojin; Hu, Zhiqing; Qiu, Liyan; Zhou, Tao; Feng, Mai; Hu, Qian; Zeng, Baitao; Li, Zhuo; Sun, Qianru; Wu, Yong; Liu, Xionghao; Wu, Lingqian; Liang, Desheng

2018-05-09

Spinal muscular atrophy (SMA) is a kind of neuromuscular disease characterized by progressive motor neuron loss in the spinal cord. It is caused by mutations in the survival motor neuron 1 (SMN1) gene. SMN1 has a paralogous gene, survival motor neuron 2 (SMN2), in humans that is present in almost all SMA patients. The generation and genetic correction of SMA patient-specific induced pluripotent stem cells (iPSCs) is a viable, autologous therapeutic strategy for the disease. Here, c-Myc-free and non-integrating iPSCs were generated from the urine cells of an SMA patient using an episomal iPSC reprogramming vector, and a unique crRNA was designed that does not have similar sequences (≤3 mismatches) anywhere in the human reference genome. In situ gene conversion of the SMN2 gene to an SMN1-like gene in SMA-iPSCs was achieved using CRISPR/Cpf1 and single-stranded oligodeoxynucleotide with a high efficiency of 4/36. Seamlessly gene-converted iPSC lines contained no exogenous sequences and retained a normal karyotype. Significantly, the SMN expression and gems localization were rescued in the gene-converted iPSCs and their derived motor neurons. This is the first report of an efficient gene conversion mediated by Cpf1 homology-directed repair in human cells and may provide a universal gene therapeutic approach for most SMA patients.

NF-κB Decoy Oligodeoxynucleotide Enhanced Osteogenesis in Mesenchymal Stem Cells Exposed to Polyethylene Particle

PubMed Central

Lin, Tzu-Hua; Sato, Taishi; Barcay, Katherine R.; Waters, Heather; Loi, Florence; Zhang, Ruth; Pajarinen, Jukka; Egashira, Kensuke; Yao, Zhenyu

2015-01-01

Excessive generation of wear particles after total joint replacement may lead to local inflammation and periprosthetic osteolysis. Modulation of the key transcription factor NF-κB in immune cells could potentially mitigate the osteolytic process. We previously showed that local delivery of ultrahigh-molecular-weight polyethylene (UHMWPE) particles recruited osteoprogenitor cells and reduced osteolysis. However, the biological effects of modulating the NF-κB signaling pathway on osteoprogenitor/mesenchymal stem cells (MSCs) remain unclear. Here we showed that decoy oligodeoxynucleotide (ODN) increased cell viability when primary murine MSCs were exposed to UHMWPE particles, but had no effects on cellular apoptosis. Decoy ODN increased transforming growth factor-beta 1 (TGF-β1) and osteoprotegerin (OPG) in MSCs exposed to UHMWPE particles. Mechanistic studies showed that decoy ODN upregulated OPG expression through a TGF-β1-dependent pathway. By measuring the alkaline phosphatase activity, osteocalcin levels, Runx2 and osteopontin expression, and performing a bone mineralization assay, we found that decoy ODN increased MSC osteogenic ability when the cells were exposed to UHMWPE particles. Furthermore, the cellular response to decoy ODN and UHMWPE particles with regard to cell phenotype, cell viability, and osteogenic ability was confirmed using primary human MSCs. Our results suggest that modulation of wear particle-induced inflammation by NF-κB decoy ODN had no adverse effects on MSCs and may potentially further mitigate periprosthetic osteolysis by protecting MSC viability and osteogenic ability. PMID:25518013

Orthopaedic wear particle-induced bone loss and exogenous macrophage infiltration is mitigated by local infusion of NF-κB decoy oligodeoxynucleotide.

PubMed

Lin, Tzuhua; Pajarinen, Jukka; Nabeshima, Akira; Córdova, Luis A; Loi, Florence; Gibon, Emmanuel; Lu, Laura; Nathan, Karthik; Jämsen, Eemeli; Yao, Zhenyu; Goodman, Stuart B

2017-11-01

Excessive production of wear particles from total joint replacements induces chronic inflammation, macrophage infiltration, and consequent bone loss (periprosthetic osteolysis). This inflammation and bone remodeling are critically regulated by the transcription factor NF-κB. We previously demonstrated that inhibition of NF-κB signaling by using the decoy oligodeoxynucleotide (ODN) mitigates polyethylene wear particle-induced bone loss using in vitro and in vivo models. However, the mechanisms of NF-κB decoy ODN action, and in particular its impact on systemic macrophage recruitment, remain unknown. In the current study, this systemic macrophage infiltration was examined in our established murine femoral continuous particle infusion model. RAW264.7 murine macrophages expressing a luciferase reporter gene were injected into the systemic circulation. Quantification of bioluminescence showed that NF-κB decoy ODN reduced the homing of these reporter macrophages into the distal femurs exposed to continuous particle delivery. Particle-induced reduction in bone mineral density at the distal diaphysis of the femur was also mitigated by infusion of decoy ODN. Histological staining showed that the decoy ODN infusion decreased osteoclast and macrophage numbers, but had no significant effects on osteoblasts. Local infusion of NF-κB decoy ODN reduced systemic macrophage infiltration and mitigated particle-induced bone loss, thus providing a potential strategy to treat periprosthetic osteolysis. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 3169-3175, 2017. © 2017 Wiley Periodicals, Inc.

Effect of Antisense Oligodeoxynucleotides Glucose Transporter-1 on Enhancement of Radiosensitivity of Laryngeal Carcinoma

PubMed Central

Yan, Sen-Xiang; Luo, Xing-Mei; Zhou, Shui-Hong; Bao, Yang-Yang; Fan, Jun; Lu, Zhong-Jie; Liao, Xin-Biao; Huang, Ya-Ping; Wu, Ting-Ting; Wang, Qin-Ying

2013-01-01

Purpose: Laryngeal carcinomas always resist to radiotherapy. Hypoxia is an important factor in radioresistance of laryngeal carcinoma. Glucose transporter-1 (GLUT-1) is considered to be a possible intrinsic marker of hypoxia in malignant tumors. We speculated that the inhibition of GLUT-1 expression might improve the radiosensitivity of laryngeal carcinoma. Methods: We assessed the effect of GLUT-1 expression on radioresistance of laryngeal carcinoma and the effect of GLUT-1 expressions by antisense oligodeoxynucleotides (AS-ODNs) on the radiosensitivity of laryngeal carcinoma in vitro and in vivo. Results: After transfection of GLUT-1 AS-ODNs: MTS assay showed the survival rates of radiation groups were reduced with the prolongation of culture time (p<0.05); Cell survival rates were significantly reduced along with the increasing of radiation dose (p<0.05). There was significant difference in the expression of GLUT-1mRNA and protein in the same X-ray dose between before and after X-ray radiation (p<0.05). In vivo, the expressions of GLUT-1 mRNA and protein after 8Gy radiation plus transfection of GLUT-1 AS-ODNs were significant decreased compared to 8Gy radiation alone (p<0.001). Conclusion: Radioresistance of laryngeal carcinoma may be associated with increased expression of GLUT-1 mRNA and protein. GLUT-1 AS-ODNs may enhance the radiosensitivity of laryngeal carcinoma mainly by inhibiting the expression of GLUT-1. PMID:23983599

Modification of antisense phosphodiester oligodeoxynucleotides by a 5' cholesteryl moiety increases cellular association and improves efficacy.

PubMed

Krieg, A M; Tonkinson, J; Matson, S; Zhao, Q; Saxon, M; Zhang, L M; Bhanja, U; Yakubov, L; Stein, C A

1993-02-01

Phosphodiester oligodeoxynucleotides bearing a 5' cholesteryl (chol) modification bind to low density lipoprotein (LDL), apparently by partitioning the chol-modified oligonucleotides into the lipid layer. Both HL60 cells and primary mouse spleen T and B cells incubated with fluorescently labeled chol-modified oligonucleotide showed substantially increased cellular association by flow cytometry and increased internalization by confocal microscopy compared to an identical molecule not bearing the chol group. Cellular internalization of chol-modified oligonucleotide occurred at least partially through the LDL receptor; it was increased in mouse spleen cells by cell culture in lipoprotein-deficient medium and/or lovastatin, and it was decreased by culture in high serum medium. To determine whether chol-modified oligonucleotides are more potent antisense agents, we titered antisense unmodified phosphodiester and chol-modified oligonucleotides targeted against a mouse immunosuppressive protein. Murine spleen cells cultured with 20 microM phosphodiester antisense oligonucleotides had a 2-fold increase in RNA synthesis, indicating the expected lymphocyte activation. Antisense chol-modified oligonucleotides showed an 8-fold increase in relative potency: they caused a 2-fold increase in RNA synthesis at just 2.5 microM. The increased efficacy was blocked by heparin and was further increased by cell culture in 1% (vs. 10%) fetal bovine serum, suggesting that the effect may, at least in part, be mediated via the LDL receptor. Antisense chol-modified oligonucleotides are sequence specific and have increased potency as compared to unmodified oligonucleotides.

Cloning of a cDNA encoding bovine mitochondrial NADP(+)-specific isocitrate dehydrogenase and structural comparison with its isoenzymes from different species.

PubMed Central

Huh, T L; Ryu, J H; Huh, J W; Sung, H C; Oh, I U; Song, B J; Veech, R L

1993-01-01

Mitochondrial NADP(+)-specific isocitrate dehydrogenase (IDP) was co-purified with the pyruvate dehydrogenase complex from bovine kidney mitochondria. The determination of its N-terminal 16-amino-acid sequence revealed that it is highly similar to the IDP from yeast. A cDNA clone (1.8 kb long) encoding this protein was isolated from a bovine kidney lambda gt11 cDNA library using a synthetic oligodeoxynucleotide. The deduced protein sequence of this cDNA clone rendered a precursor protein of 452 amino-acid residues (50,830 Da) and a mature protein of 413 amino-acid residues (46,519 Da). It is 100% identical to the internal tryptic peptide sequences of the autologous form from pig heart and 62% similar to that from yeast. However, it shares little similarity with the mitochondrial NAD(+)-specific isoenzyme from yeast. Structural analyses of the deduced proteins of IDP isoenzymes from different species indicated that similarity exists in certain regions, which may represent the common domains for the active sites or coenzyme-binding sites. In Northern-blot analysis, one species of mRNA (about 2.2 kb for both bovine and human) was hybridized with a 32P-labelled cDNA probe. Southern-blot analysis of genomic DNAs verified simple patterns of hybridization with this cDNA. These results strongly indicate that the mitochondrial IDP may be derived from a single gene family which does not appear to be closely related to that of the NAD(+)-specific isoenzyme. Images Figure 1 Figure 3 Figure 4 Figure 5 PMID:8318002

Radionuclide evaluation of left ventricular function with nonimaging probes.

PubMed

Wexler, J P; Blaufox, M D

1979-10-01

Portable nonimaging probes have been developed that can evaluate left ventricular function using radionuclide techniques. Two modes of data acquisition are possible with these probe systems, first-pass and gated. Precordial radiocardiograms obtained after a bolus injection can be used to determine cardiac output, pulmonary transit time, pulmonary blood volume, left ventricle ejection fraction, and left-to-right shunts. Gated techniques can be used to determine left ventricular ejection fraction and sytolic time intervals. Probe-determined indices of left ventricular function agree excellently with comparable measurements determined by conventional camera-computer methods as well as by invasive techniques. These have begun to be used in a preliminary manner in a variety of clinical problems associated with left ventricular dysfunction. This review discusses the types of probe systems available, the methods used in positioning them, and details the specifics of their data acquisition and processing capacity. The major criticisms of probe methods are that they are nonimaging and that they measure global rather than regional left ventricular function. In spite of these criticisms, probe systems, because of their portability, high sensitivity, and relatively low cost are useful supplements to conventional camera-computer systems for the measurement of parameters of left ventricular performance using radionuclide techniques.

Colorimetric DNA detection of transgenic plants using gold nanoparticles functionalized with L-shaped DNA probes

NASA Astrophysics Data System (ADS)

Nourisaeid, Elham; Mousavi, Amir; Arpanaei, Ayyoob

2016-01-01

In this study, a DNA colorimetric detection system based on gold nanoparticles functionalized with L-shaped DNA probes was prepared and evaluated. We investigated the hybridization efficiency of the L-shaped probes and studied the effect of nanoparticle size and the L-shaped DNA probe length on the performance of the as-prepared system. Probes were attached to the surface of gold nanoparticles using an adenine sequence. An optimal sequence of 35S rRNA gene promoter from the cauliflower mosaic virus, which is frequently used in the development of transgenic plants, and the two complementary ends of this gene were employed as model target strands and probe molecules, respectively. The spectrophotometric properties of the as-prepared systems indicated that the large NPs show better changes in the absorption spectrum and consequently present a better performance. The results of this study revealed that the probe/Au-NPs prepared using a vertical spacer containing 5 thymine oligonucleotides exhibited a stronger spectrophotometric response in comparison to that of larger probes. These results in general indicate the suitable performance of the L-shaped DNA probe-functionalized Au-NPs, and in particular emphasize the important role of the gold nanoparticle size and length of the DNA probes in enhancing the performance of such a system.

Implications of contamination and surface area ratios for Langmuir probe diagnostics on CubeSats

NASA Astrophysics Data System (ADS)

Suresh, P.; Swenson, C.

2009-12-01

Theories describing the current collected by a biased probe under various conditions are necessary for such observation to be used to accurately determine plasma properties. Langmuir probes are routinely used on spacecraft to measure plasma parameters such as density, temperature, and vehicle charging. The collected current is a function of the potential between the surrounding plasma and probe surface. There have been both observations of and concepts for unaccounted variations of this potential which limit the application of Langmuir probe theory for determining plasma properties. These variations occur due to spatial variations of the work function across the probe surface due to non-uniformity of the crystalline surface properties and surface contamination of the probe. Currently we do not have theoretical expressions which consider these factors as first principles in their derivation. In the event of these surface potential variations, the analysis of the plasma using the currently available theories of the Langmuir probe yield erroneous results. We present a theory which models the current as a function of the surface potential variations. Another consideration for Langmuir probes on CubeSats is the ratio of the probe area to the return current collection area. If the area ratio is unfavorable this can also lead to erroneous results in the interpretation of observations. A mathematical formulation of the current collected by the probe for contaminated surfaces is presented and compared with data from a Langmuir probe flown on a sounding rocket mission. The implications of using Langmuir probes on CubeSats given the engineering limitations of probe cleanliness and area ratios are reviewed.

Bioactivity of 2′-deoxyinosine-incorporated aptamer AS1411

PubMed Central

Fan, Xinmeng; Sun, Lidan; Wu, Yun; Zhang, Lihe; Yang, Zhenjun

2016-01-01

Aptamers can be chemically modified to enhance nuclease resistance and increase target affinity. In this study, we performed chemical modification of 2′-deoxyinosine in AS1411, an anti-proliferative G-rich oligodeoxynucleotide aptamer, which binds selectively to the nucleolin protein. Its function was augmented when 2′-deoxyinosine was incorporated at positions 12, 13, 15, and 24 of AS1411, respectively. In addition, double incorporation of 2′-deoxyinosine at positions 12 and 24 (FAN-1224dI), 13 and 24 (FAN-1324dI), and 15 and 24 (FAN-1524dI) promoted G-quartet formation, as well as inhibition of DNA replication and tumor cell growth, and induced S-phase cell cycle arrest. In further animal experiments, FAN-1224dI, FAN-1324dI and FAN-1524dI resulted in enhanced treatment effects than AS1411 alone. These results suggested that the position and number of modification substituents in AS1411 are critical parameters to improve the diagnostic and therapeutic function of the aptamer. Structural investigations of the FAN-1524dI/nucleolin complex structure, using molecular dynamics simulation, revealed the critical interactions involving nucleolin and 2′-dI incorporated AS1411 compared with AS1411 alone. These findings augment understanding of the role of 2′-deoxyinosine moieties in interactive binding processes. PMID:27194215

Bioactivity of 2'-deoxyinosine-incorporated aptamer AS1411.

PubMed

Fan, Xinmeng; Sun, Lidan; Wu, Yun; Zhang, Lihe; Yang, Zhenjun

2016-05-19

Aptamers can be chemically modified to enhance nuclease resistance and increase target affinity. In this study, we performed chemical modification of 2'-deoxyinosine in AS1411, an anti-proliferative G-rich oligodeoxynucleotide aptamer, which binds selectively to the nucleolin protein. Its function was augmented when 2'-deoxyinosine was incorporated at positions 12, 13, 15, and 24 of AS1411, respectively. In addition, double incorporation of 2'-deoxyinosine at positions 12 and 24 (FAN-1224dI), 13 and 24 (FAN-1324dI), and 15 and 24 (FAN-1524dI) promoted G-quartet formation, as well as inhibition of DNA replication and tumor cell growth, and induced S-phase cell cycle arrest. In further animal experiments, FAN-1224dI, FAN-1324dI and FAN-1524dI resulted in enhanced treatment effects than AS1411 alone. These results suggested that the position and number of modification substituents in AS1411 are critical parameters to improve the diagnostic and therapeutic function of the aptamer. Structural investigations of the FAN-1524dI/nucleolin complex structure, using molecular dynamics simulation, revealed the critical interactions involving nucleolin and 2'-dI incorporated AS1411 compared with AS1411 alone. These findings augment understanding of the role of 2'-deoxyinosine moieties in interactive binding processes.

Possible Existence of Extra-Terrestrial Technology in the Solar System

NASA Astrophysics Data System (ADS)

Burke-Ward, R.

Potential features of the design and function of extra-terrestrial probes are discussed with the aim of establishing criteria for search, detection and contact. Probes are categorised according to three primary areas of function - data-gathering, direct action, and sentient entities. Conclusions are drawn about possible probe technologies and modes of behaviour.

Discrimination of heterogenous mRNAs encoding strychnine-sensitive glycine receptors in Xenopus oocytes by antisense oligonucleotides.

PubMed Central

Akagi, H; Patton, D E; Miledi, R

1989-01-01

Three synthetic oligodeoxynucleotides complementary to different parts of an RNA encoding a glycine receptor subunit were used to discriminate heterogenous mRNAs coding for glycine receptors in adult and neonatal rat spinal cord. Injection of the three antisense oligonucleotides into Xenopus oocytes specifically inhibited the expression of glycine receptors by adult spinal cord mRNA. In contrast, the antisense oligonucleotides were much less potent in inhibiting the expression of glycine receptors encoded by neonatal spinal cord mRNA. Northern blot analysis revealed that the oligonucleotides hybridized mostly to an adult cord transcript of approximately 10 kilobases in size. This band was also present in neonatal spinal cord mRNA but its density was about one-fourth of the adult cord message. There was no intense band in the low molecular weight position (approximately 2 kilobases), the existence of which was expected from electrophysiological studies with size-fractionated mRNA of neonatal spinal cord. Our results suggest that in the rat spinal cord there are at least three different types of mRNAs encoding functional strychnine-sensitive glycine receptors. Images PMID:2479016

An efficient and scalable pipeline for epitope tagging in mammalian stem cells using Cas9 ribonucleoprotein

PubMed Central

Dewari, Pooran Singh; Southgate, Benjamin; Mccarten, Katrina; Monogarov, German; O'Duibhir, Eoghan; Quinn, Niall; Tyrer, Ashley; Leitner, Marie-Christin; Plumb, Colin; Kalantzaki, Maria; Blin, Carla; Finch, Rebecca; Bressan, Raul Bardini; Morrison, Gillian; Jacobi, Ashley M; Behlke, Mark A; von Kriegsheim, Alex; Tomlinson, Simon; Krijgsveld, Jeroen

2018-01-01

CRISPR/Cas9 can be used for precise genetic knock-in of epitope tags into endogenous genes, simplifying experimental analysis of protein function. However, Cas9-assisted epitope tagging in primary mammalian cell cultures is often inefficient and reliant on plasmid-based selection strategies. Here, we demonstrate improved knock-in efficiencies of diverse tags (V5, 3XFLAG, Myc, HA) using co-delivery of Cas9 protein pre-complexed with two-part synthetic modified RNAs (annealed crRNA:tracrRNA) and single-stranded oligodeoxynucleotide (ssODN) repair templates. Knock-in efficiencies of ~5–30%, were achieved without selection in embryonic stem (ES) cells, neural stem (NS) cells, and brain-tumor-derived stem cells. Biallelic-tagged clonal lines were readily derived and used to define Olig2 chromatin-bound interacting partners. Using our novel web-based design tool, we established a 96-well format pipeline that enabled V5-tagging of 60 different transcription factors. This efficient, selection-free and scalable epitope tagging pipeline enables systematic surveys of protein expression levels, subcellular localization, and interactors across diverse mammalian stem cells. PMID:29638216

CpG Oligodeoxynucleotide and Montanide ISA 51 Adjuvant Combination Enhanced the Protective Efficacy of a Subunit Malaria Vaccine

DTIC Science & Technology

2004-02-01

Doolan, D. L., and S. L. Hoffman. 2002. Nucleic acid vaccines against ma- laria. Chem. Immunol. 80, p. 308–320. In P. Perlman and M. Troye - Bloomberg (ed...and M. T. Troye - Blomberg (ed.), Malaria immunology. Karger, Basel, Switzerland, Germany. 30. Kumar, S., F. Villinger, M. Oakley, J. C. Aguiar, T. R...and pathology, p. 204–221. In P. Perlman and M. T. Troye -Blomberg (ed.), Malaria immunology. Karger, Basel, Switzerland. 32. Ling, I. T., S. A. Ogun

Potent inhibition of HhaI DNA methylase by the aglycon of 2-(1H)-pyrimidinone riboside (zebularine) at the GCGC recognition domain.

PubMed

Marquez, Victor E; Eritja, Ramon; Kelley, James A; Vanbemmel, Dana; Christman, Judith K

2003-12-01

A short oligodeoxynucleotide (ODN) with 2-(1H)-pyrimidinone at the HhaI DNA methyltransferase target site (GCGC) is shown to induce a level of inhibition of methyl transfer and thermal stability of the complex with the enzyme identical to that achieved with a similar ODN substituted with 5-azacytosine. The drugs responsible for these effects-zebularine and 5-azacytidine/2'-deoxy-5-azacytidine-are contrasted in terms of chemical stability and possible metabolic activation by a brief structure-activity analysis.

Probabilistic determination of probe locations from distance data

PubMed Central

Xu, Xiao-Ping; Slaughter, Brian D.; Volkmann, Niels

2013-01-01

Distance constraints, in principle, can be employed to determine information about the location of probes within a three-dimensional volume. Traditional methods for locating probes from distance constraints involve optimization of scoring functions that measure how well the probe location fits the distance data, exploring only a small subset of the scoring function landscape in the process. These methods are not guaranteed to find the global optimum and provide no means to relate the identified optimum to all other optima in scoring space. Here, we introduce a method for the location of probes from distance information that is based on probability calculus. This method allows exploration of the entire scoring space by directly combining probability functions representing the distance data and information about attachment sites. The approach is guaranteed to identify the global optimum and enables the derivation of confidence intervals for the probe location as well as statistical quantification of ambiguities. We apply the method to determine the location of a fluorescence probe using distances derived by FRET and show that the resulting location matches that independently derived by electron microscopy. PMID:23770585

Dual representation of item positions in verbal short-term memory: Evidence for two access modes.

PubMed

Lange, Elke B; Verhaeghen, Paul; Cerella, John

Memory sets of N = 1~5 digits were exposed sequentially from left-to-right across the screen, followed by N recognition probes. Probes had to be compared to memory list items on identity only (Sternberg task) or conditional on list position. Positions were probed randomly or in left-to-right order. Search functions related probe response times to set size. Random probing led to ramped, "Sternbergian" functions whose intercepts were elevated by the location requirement. Sequential probing led to flat search functions-fast responses unaffected by set size. These results suggested that items in STM could be accessed either by a slow search-on-identity followed by recovery of an associated location tag, or in a single step by following item-to-item links in study order. It is argued that this dual coding of location information occurs spontaneously at study, and that either code can be utilised at retrieval depending on test demands.

Dynamic characterization of AFM probes by laser Doppler vibrometry and stroboscopic holographic methodologies

NASA Astrophysics Data System (ADS)

Kuppers, J. D.; Gouverneur, I. M.; Rodgers, M. T.; Wenger, J.; Furlong, C.

2006-08-01

In atomic probe microscopy, micro-probes of various sizes, geometries, and materials are used to define the interface between the samples under investigation and the measuring detectors and instrumentation. Therefore, measuring resolution in atomic probe microscopy is highly dependent on the transfer function characterizing the micro-probes used. In this paper, characterization of the dynamic transfer function of specific micro-cantilever probes used in an Atomic Force Microscope (AFM) operating in the tapping mode is presented. Characterization is based on the combined application of laser Doppler vibrometry (LDV) and real-time stroboscopic optoelectronic holographic microscopy (OEHM) methodologies. LDV is used for the rapid measurement of the frequency response of the probes due to an excitation function containing multiple frequency components. Data obtained from the measured frequency response is used to identify the principal harmonics. In order to identify mode shapes corresponding to the harmonics, full-field of view OEHM is applied. This is accomplished by measurements of motion at various points on the excitation curve surrounding the identified harmonics. It is shown that the combined application of LDV and OEHM enables the high-resolution characterization of mode shapes of vibration, damping characteristics, as well as transient response of the micro-cantilever probes. Such characterization is necessary in high-resolution AFM measurements.

Intramuscular Administration of a Synthetic CpG-Oligodeoxynucleotide Modulates Functional Responses of Neutrophils of Neonatal Foals

PubMed Central

Cohen, Noah D.; Bourquin, Jessica R.; Bordin, Angela I.; Kuskie, Kyle R.; Brake, Courtney N.; Weaver, Kaytee B.; Liu, Mei; Felippe, M. Julia B.; Kogut, Michael H.

2014-01-01

Neutrophils play an important role in protecting against infection. Foals have age-dependent deficiencies in neutrophil function that may contribute to their predisposition to infection. Thus, we investigated the ability of a CpG-ODN formulated with Emulsigen to modulate functional responses of neutrophils in neonatal foals. Eighteen foals were randomly assigned to receive either a CpG-ODN with Emulsigen (N = 9) or saline intramuscularly at ages 1 and 7 days. At ages 1, 3, 9, 14, and 28, blood was collected and neutrophils were isolated from each foal. Neutrophils were assessed for basal and Rhodococcus equi-stimulated mRNA expression of the cytokines interferon-γ (IFN-γ), interleukin (IL)-4, IL-6, and IL-8 using real-time PCR, degranulation by quantifying the amount of β-D glucuronidase activity, and reactive oxygen species (ROS) generation using flow cytometry. In vivo administration of the CpG-ODN formulation on days 1 and 7 resulted in significantly (P<0.05) increased IFN-γ mRNA expression by foal neutrophils on days 3, 9, and 14. Degranulation was significantly (P<0.05) lower for foals in the CpG-ODN-treated group than the control group at days 3 and 14, but not at other days. No effect of treatment on ROS generation was detected. These results indicate that CpG-ODN administration to foals might improve innate and adaptive immune responses that could protect foals against infectious diseases and possibly improve responses to vaccination. PMID:25333660

Antagonism of immunostimulatory CpG-oligodeoxynucleotides by quinacrine, chloroquine, and structurally related compounds.

PubMed

Macfarlane, D E; Manzel, L

1998-02-01

Phosphorothioate oligodeoxynucleotides containing CpG (CpG-ODN) activate immune responses. We report that quinacrine, chloroquine, and structurally related compounds completely inhibit the antiapoptotic effect of CpG-ODN on WEHI 231 murine B lymphoma cells and inhibit CpG-ODN-induced secretion of IL-6 by WEHI 231. They also inhibit IL-6 synthesis and thymidine uptake by human unfractionated PBMC induced by CpG-ODN. The compounds did not inhibit LPS-induced responses. Half-maximal inhibition required 10 nM quinacrine or 100 nM chloroquine. Inhibition was noncompetitive with respect to CpG-ODN. Quinine, quinidine, and primaquine were much less powerful. Quinacrine was effective even when added after the CpG-ODN. Near-toxic concentrations of ammonia plus bafilomycin A1 (used to inhibit vesicular acidification) did not reduce the efficacy of the quinacrine, but the effects of both quinacrine and chloroquine were enhanced by inhibition of the multidrug resistance efflux pump by verapamil. Agents that bind to DNA, including propidium iodide, Hoechst dye 33258, and coralyne chloride did not inhibit CpG-ODN effect, nor did 4-bromophenacyl bromide, an inhibitor of phospholipase A2. Examination of the structure-activity relationship of seventy 4-aminoquinoline and 9-aminoacridine analogues reveals that increased activity was conferred by bulky hydrophobic substituents on positions 2 and 6 of the quinoline nucleus. No correlation was found between published antimalarial activity and ability to block CpG-ODN-induced effects. These results are discussed in the light of the ability of quinacrine and chloroquine to induce remission of rheumatoid arthritis and lupus erythematosus.

Regulating gene expression in human leukemia cells using light-activated oligodeoxynucleotides

PubMed Central

Tang, XinJing; Swaminathan, Jyothishmathi; Gewirtz, Alan M.; Dmochowski, Ivan J.

2008-01-01

Light-activated antisense oligodeoxynucleotides (asODNs) were developed to control the degradation of target mRNA in living cells by RNase H. A 20-mer asODN previously shown to target c-myb, a hematopoietic transcription factor, was covalently attached via a photocleavable linker (PL) to partially complementary 20-mer sense strands (sODNs). In the ‘caged’ state, the sODN blocked hybridization of the asODN to c-myb mRNA. Six asODN-PL-sODN conjugates, C1-C6, were synthesized. C5, with twelve complementary bases, gave the largest decrease in melting temperature (Tm) upon UV irradiation (ΔTm = −29°C). The most thermally stable conjugate, C6 (Tm = 84°C), gave the lowest background RNase H activity, with just 8.6% degradation of an RNA 40-mer after 1 h incubation. In biochemical assays with C6, RNA digestion increased 10-fold 10 min after UV irradiation. Finally, phosphorothioated analogs S-C5 and S-C6 were synthesized to test activity in cultured K562 (human leukemia) cells. No knockdown of c-myb mRNA or protein was observed with intact S-C5 or S-C6, whereas more than half of c-myb mRNA was degraded 24 h after photoactivation. Two-fold photomodulation of c-MYB protein levels was also observed with S-C5. However, no photomodulation of c-MYB protein levels was observed with S-C6, perhaps due to the greater stability of this duplex. PMID:18056083

Reciprocal repression between microRNA-133 and calcineurin regulates cardiac hypertrophy: a novel mechanism for progressive cardiac hypertrophy.

PubMed

Dong, De-Li; Chen, Chang; Huo, Rong; Wang, Ning; Li, Zhe; Tu, Yu-Jie; Hu, Jun-Tao; Chu, Xia; Huang, Wei; Yang, Bao-Feng

2010-04-01

Cardiac hypertrophy involves a remodeling process of the heart in response to diverse pathological stimuli. Both calcineurin/nuclear factor of activated T cells pathway and microRNA-133 (miR-133) have been shown to play a critical role in cardiac hypertrophy. It has been recognized that the expression and activity of calcineurin increases and miR-133 expression decreases in the hypertrophic heart, and inhibition of calcineurin or increase of miR-133 expression protects against cardiac hypertrophy. Here we tested the interaction between miR-133 and calcineurin in cardiac hypertrophy. Cardiac hypertrophy in vivo and in vitro was induced by transverse aortic constriction and phenylephrine treatment. mRNA levels were measured by using real-time PCR methods. Luciferase assays showed that transfection of miR-133 in HEK293 cells downregulated calcineurin expression, which was reversed by cotransfection with the miR-133-specific 2'-O-methyl antisense inhibitory oligoribonucleotides. These results were confirmed in cultured primary cardiomyocytes. miR-133 expression was downregulated, and calcineurin activity was enhanced in both in vivo and in vitro cardiac hypertrophy models. Treatment of cells and animals with cyclosporin A, an inhibitor of calcineurin, prevented miR-133 downregulation. Moreover, the antisense oligodeoxynucleotides against the catalytic subunits of calcineurin Abeta and the decoy oligodeoxynucleotides targeting nuclear factor of activated T cells transcription factor, a calcineurin downstream effector, increased miR-133 expression in cultured primary cardiomyocytes. Our data show that reciprocal repression between miR-133 and calcineurin regulates cardiac hypertrophy.

An Animal Model of Abacavir-Induced HLA-Mediated Liver Injury.

PubMed

Song, Binbin; Aoki, Shigeki; Liu, Cong; Susukida, Takeshi; Ito, Kousei

2018-04-01

Genome-wide association studies indicate that several idiosyncratic adverse drug reactions are highly associated with specific human leukocyte antigen (HLA) alleles. For instance, abacavir, a human immunodeficiency virus reverse transcriptase inhibitor, induces multiorgan toxicity exclusively in patients carrying the HLA-B*57:01 allele. However, the underlying mechanism is unclear due to a lack of appropriate animal models. Previously, we developed HLA-B*57:01 transgenic mice and found that topical application of abacavir to the ears induced proliferation of CD8+ lymphocytes in local lymph nodes. Here, we attempted to reproduce abacavir-induced liver injury in these mice. However, oral administration of abacavir alone to HLA-B*57:01 transgenic mice did not increase levels of the liver injury marker alanine aminotransferase. Considering the importance of innate immune activation in mouse liver, we treated mice with CpG oligodeoxynucleotide, a toll-like receptor 9 agonist, plus abacavir. This resulted in a marked increase in alanine aminotransferase, pathological changes in liver, increased numbers of activated CD8+ T cells, and tissue infiltration by immune cells exclusively in HLA-B*57:01 transgenic mice. These results indicate that CpG oligodeoxynucleotide-induced inflammatory reactions and/or innate immune activation are necessary for abacavir-induced HLA-mediated liver injury characterized by infiltration of CD8+ T cells. Thus, we developed the first mouse model of HLA-mediated abacavir-induced idiosyncratic liver injury. Further investigation will show that the proposed HLA-mediated liver injury model can be applied to other combinations of drugs and HLA types, thereby improving drug development and contributing to the development of personalized medicine.

Preliminary evaluation of cytosine-phosphate-guanine oligodeoxynucleotides bound to gelatine nanoparticles as immunotherapy for canine atopic dermatitis.

PubMed

Wagner, I; Geh, K J; Hubert, M; Winter, G; Weber, K; Classen, J; Klinger, C; Mueller, R S

2017-07-29

Cytosine-phosphate-guanine oligodeoxynucleotides (CpG ODN) are a promising new immunotherapeutic treatment option for canine atopic dermatitis (AD). The aim of this uncontrolled pilot study was to evaluate clinical and immunological effects of gelatine nanoparticle (GNP)-bound CpG ODN (CpG GNP) on atopic dogs. Eighteen dogs with AD were treated for 8 weeks (group 1, n=8) or 18 weeks (group 2, n=10). Before inclusion and after 2 weeks, 4 weeks, 6 weeks (group 1+2), 8 weeks, 12 weeks and 16 weeks (group 2) 75 µg CpG ODN/dog (bound to 1.5 mg GNP) were injected subcutaneously. Pruritus was evaluated daily by the owner. Lesions were evaluated and serum concentrations and mRNA expressions of interferon-γ, tumour necrosis factor-α, transforming growth factor-β, interleukin (IL) 10 and IL-4 (only mRNA expression) were determined at inclusion and after 8 weeks (group 1+2) and 18 weeks (group 2). Lesions and pruritus improved significantly from baseline to week 8. Mean improvements from baseline to week 18 were 23 per cent and 44 per cent for lesions and pruritus, respectively, an improvement of ≥50 per cent was seen in six out of nine and three out of six dogs, respectively. IL-4 mRNA expression decreased significantly. The results of this study show a clinical improvement of canine AD with CpG GNP comparable to allergen immunotherapy. Controlled studies are needed to confirm these findings. British Veterinary Association.

Therapeutic Efficacy of Adenoviral-Mediated p53 Gene Transfer Is Synergistically Enhanced by Combined Use of Antisense Oligodeoxynucleotide Targeting Clusterin Gene in a Human Bladder Cancer Model1

PubMed Central

Miyake, Hideaki; Yamanaka, Kazuki; Muramaki, Mototsugu; Hara, Isao; Gleave, Martin E

2005-01-01

Abstract To establish a more effective therapeutic strategy against advanced bladder cancer, we investigated the effects of combined treatment with antisense (AS) oligodeoxynucleotide (ODN) targeting the antiapoptotic gene clusterin and adenoviral-mediated p53 gene transfer (Ad5CMV-p53) using the human bladder cancer KoTCC-1 model. Clusterin expression in KoTCC-1 cells was highly upregulated by Ad5CMV-p53 treatment; however, AS clusterin ODN treatment further suppressed clusterin expression in KoTCC-1 cells after Ad5CMV-p53 treatment. AS clusterin ODN treatment synergistically enhanced the cytotoxic effect of Ad5CMV-p53, and DNA fragmentation characteristic of apoptosis was observed only after combined treatment with AS clusterin ODN and Ad5CMV-p53, but not after treatment with either agent alone. Administration of AS clusterin ODN and Ad5CMV-p53 into nude mice resulted in a significant inhibition of KoTCC-1 tumor growth as well as lymph node metastases compared to administration of either agent alone. Furthermore, combined treatment with AS clusterin ODN, Ad5CMV-p53, and cisplatin completely eradicated KoTCC-1 tumors and lymph node metastases in 60% and 100% of mice, respectively. These findings suggest that combined treatment with AS clusterin ODN and Ad5CMV-p53 could be a novel strategy to inhibit bladder cancer progression, and that further additional use of a chemotherapeutic agent may substantially enhance the efficacy of this combined regimen. PMID:15802022

Microscale Electrode Implantation during Nerve Repair: Effects on Nerve Morphology, Electromyography, and Recovery of Muscle Contractile Function

PubMed Central

Urbanchek, Melanie G; Wei, Benjamin; Egeland, Brent M; Abidian, Mohammad R; Kipke, Daryl R; Cederna, Paul S

2011-01-01

Background Our goal is to develop a peripheral nerve electrode with long-term stability and fidelity for use in nerve-machine interfaces. Microelectromechanical systems (MEMS) use silicon probes that contain multi-channel actuators, sensors, and electronics. We tested the null hypothesis that implantation of MEMS probes do not have a detrimental effect on peripheral nerve function or regeneration. Methods A rat hindlimb, peroneal nerve model was utilized in all experimental groups: a) intact nerve (Control, n= 10); b) nerve division and repair (Repair, n= 9); and c) Nerve division, insertion of MEMS probe, and repair (Repair + Probe, n=9). Nerve morphology, nerve to muscle compound action potential (CMAP) studies, walking tracks, and extensor digitorum longus (EDL) muscle function tests were evaluated following an 80 day recovery. Results Repair and Repair + Probe showed no differences in axon count, axon size, percent non-neural area, CMAP amplitude, latency, muscle mass, muscle force, or walking track scores. Though there was some local fibrosis around each MEMS probe, this did not lead to measurable detrimental effects in any anatomic or functional outcome measurements. Conclusions The lack of a significant difference between Repair and Repair + Probe groups in histology, CMAP, walking tracks, and muscle force suggests that MEMS electrodes are compatible with regenerating axons and show promise for establishing chemical and electrical interfaces with peripheral nerves. PMID:21921739

A dual-function fluorescent probe for monitoring the degrees of hypoxia in living cells via the imaging of nitroreductase and adenosine triphosphate.

PubMed

Fang, Yu; Shi, Wen; Hu, Yiming; Li, Xiaohua; Ma, Huimin

2018-05-24

A new dual-function fluorescent probe is developed for detecting nitroreductase (NTR) and adenosine triphosphate (ATP) with different responses. Imaging application of the probe reveals that intracellular NTR and ATP display an adverse changing trend during a hypoxic process and ATP can serve as a new sign for cell hypoxia.

Method for reducing measurement errors of a Langmuir probe with a protective RF shield

NASA Astrophysics Data System (ADS)

Riaby, V.; Masherov, P.; Savinov, V.; Yakunin, V.

2018-04-01

Probe measurements were conducted in the middle cross-section of an inductive, low-pressure xenon plasma using a straight cylindrical Langmuir probe with a bare metal shield that protected the probe from radio frequency interference. As a result, reliable radial distributions of the plasma parameters were obtained. Subsequent analyses of these measurements revealed that the electron energy distribution function (EEDF) deviated substantially from the Maxwellian functions and that this deviation depended on the length of the probe shield. To evaluate the shield's influence on the measurement results, in addition to the probe (which was moved radially as its shield length varied in the range of lsh1 = lmax-0), an additional L-shaped probe was inserted at a different location. This probe was moved differently from the first probe and provided confirmational measurements in the common special position where lsh1 = 0 and lsh2 ≠ 0. In this position, the second shield decreased all the plasma parameters. A comparison of the probe datasets identified the principles of the relationships between measurement errors and EEDF distortions caused by the bare probe shields. This dependence was used to correct the measurements performed using the first probe by eliminating the influence of its shield. Physical analyses based on earlier studies showed that these peculiarities are caused by a short-circuited double-probe effect that occurs in bare metal probe protective shields.

Innovative SPM Probes for Energy-Storage Science: MWCNT-Nanopipettes to Nanobattery Probes

NASA Astrophysics Data System (ADS)

Larson, Jonathan; Talin, Alec; Pearse, Alexander; Kozen, Alexander; Reutt-Robey, Janice

As energy-storage materials and designs continue to advance, new tools are needed to direct and explore ion insertion/de-insertion at well-defined battery materials interfaces. Scanned probe tips, assembled from actual energy-storage materials, permit SPM measures of local cathode-anode (tip-sample) interactions, including ion transfer. We present examples of ``cathode'' MWCNT-terminated STM probe tips interacting with Li(s)/Si(111) anode substrates. The MWCNT tip functions as both SPM probe and Li-nanopipette,[1] for controlled transport and manipulation of Li. Local field conditions for lithium ionization and transfer are determined and compared to electrostatic models. Additional lithium metallic and oxide tips have been prepared by thin film deposition on conventional W tips, the latter of which effectively functions as a nanobattery. We demonstrate use of these novel probe materials in the local lithiation of low-index Si anode interfaces, probing local barriers for lithium insertion. Prospects and limitations of these novel SPM probes will be discussed. U.S. Department of Energy Award Number DESC0001160.

Efficacy of probing for children with congenital nasolacrimal duct obstruction: a retrospective study using fluorescein dye disappearance test and lacrimal sac echography.

PubMed

Steindler, Piero; Mantovani, Enrico; Incorvaia, Carlo; Parmeggiani, Francesco

2009-06-01

To evaluate B-scan echography for the assessment of lacrimal sac (LS) in pediatric epiphora secondary to congenital nasolacrimal duct obstruction (CNLDO), and to verify its predictive role in functional efficacy of nasolacrimal duct probing. Thirty-nine eyes of 23 consecutive children, treated with a single probing for persistent CNLDO-related epiphora, were retrospectively studied. These cases were investigated both collectively and considering two sub-groups: group A (ten patients [20 eyes] 13 months. Fluorescein dye disappearance test at 10 minutes (FDDT-10) and ultrasound examination of LS were performed before and after probing. An echographic LS scoring system (grade 0 = no LS enlargement; grade 1 = slight longitudinal LS enlargement; grade 2 = longitudinal and slight transverse LS enlargement; grade 3 = marked longitudinal and transverse LS enlargement) was introduced as a predictor of probing efficacy, estimating FDDT-10 modification between pre- and post-operative checks. Echographic LS evaluation was easily practicable without sedation. In the total cluster and in both age sub-groups, post-probing FDDT-10 decreased with respect to pre-probing value (p < 0.001). Post-probing LS score improved with respect to pre-probing check within the total cluster and group A (p < 0.05). Strong correlation between pre-probing LS alteration and functional probing failure was present in each studied cluster (all p values <0.0001). Within group B, a greater gain of post-probing FDDT-10 was more frequent in patients with a better pre-probing LS score, as well as in younger children (both p values <0.0001). In children with CNLDO-related epiphora, B-scan echography of the LS can represent a reliable and useful examination for a better understanding of the functional prognosis after probing treatment.

What do you measure when you measure the Hall effect?

NASA Astrophysics Data System (ADS)

Koon, D. W.; Knickerbocker, C. J.

1993-02-01

A formalism for calculating the sensitivity of Hall measurements to local inhomogeneities of the sample material or the magnetic field is developed. This Hall weighting function g(x,y) is calculated for various placements of current and voltage probes on square and circular laminar samples. Unlike the resistivity weighting function, it is nonnegative throughout the entire sample, provided all probes lie at the edge of the sample. Singularities arise in the Hall weighting function near the current and voltage probes except in the case where these probes are located at the corners of a square. Implications of the results for cross, clover, and bridge samples, and the implications of our results for metal-insulator transition and quantum Hall studies are discussed.

Multi-function diamond film fiberoptic probe and measuring system employing same

DOEpatents

Young, Jack P.

1998-01-01

A fused fiberoptic probe having a protective cover, a fiberoptic probe system, and embodiments thereof for conducting electromagnetic spectral measurements are disclosed. The fused fiberoptic probe comprises a probe tip having a specific geometrical configuration, an exciting optical fiber and at least one collection optical fiber fused within a housing, preferrably silica, with a protective cover disposed over at least a portion of the probe tip. The specific geometrical configurations in which the probe tip can be shaped include a slanted probe tip with an angle greater than 0.degree., an inverted cone-shaped probe tip, and a lens head.

Modulation of the Foreign Body Reaction for Implants in the Subcutaneous Space: Microdialysis Probes as Localized Drug Delivery/Sampling Devices

PubMed Central

Mou, Xiaodun; Lennartz, Michelle R; Loegering, Daniel J; Stenken, Julie A

2011-01-01

Modulation of the foreign body reaction is considered to be an important step toward creation of implanted sensors with reliable long-term performance. In this work, microdialysis probes were implanted into the subcutaneous space of Sprague-Dawley rats. The probe performance was evaluated by comparing collected endogenous glucose concentrations with internal standard calibration (2-deoxyglucose, antipyrine, and vitamin B12). Probes were tested until failure, which for this work was defined as loss of fluid flow. In order to determine the effect of fibrous capsule formation on probe function, monocyte chemoattractant protein-1/CC chemokine ligand 2 (MCP-1/CCL2) was delivered locally via the probe to increase capsule thickness and dexamethasone 21-phosphate was delivered to reduce capsule thickness. Probes delivering MCP-1 had a capsule that was twice the thickness (500–600 μm) of control probes (200–225 μm) and typically failed 2 days earlier than control probes. Probes delivering dexamethasone 21-phosphate had more fragile capsules and the probes typically failed 2 days later than controls. Unexpectedly, extraction efficiency and collected glucose concentrations exhibited minor differences between groups. This is an interesting result in that the foreign body capsule formation was related to the duration of probe function but did not consistently relate to probe calibration. PMID:21722577

Enhancement of fluorescence quenching and exciplex formation in DNA major groove by double incorporation of modified fluorescent deoxyuridines.

PubMed

Tanaka, Makiko; Oguma, Kazuhiro; Saito, Yoshio; Saito, Isao

2012-06-15

5-(1-Naphthalenylethynyl)-2'-deoxyuridine ((N)U) and 5-[(4-cyano-1-naphthalenyl)ethynyl]-2'-deoxyuridine ((CN)U) were synthesized and incorporated into oligodeoxynucleotides. Fluorescence emissions of modified duplexes containing double (N)U were efficiently quenched depending upon the sequence pattern of the naphthalenes in DNA major groove, as compared to the duplex possessing single (N)U. When one of the naphthalene moieties has a cyano substituent, the exciplex emission from the chromophores in DNA major groove was observed at longer wavelength. Copyright © 2012 Elsevier Ltd. All rights reserved.

Peptide-substituted oligonucleotide synthesis and non-toxic, passive cell delivery

PubMed Central

Shang, Shiying; Monfregola, Luca; Caruthers, Marvin H

2016-01-01

Chemically modified oligodeoxynucleotides (ODNs) are known to modulate gene expression by interacting with RNA. An efficient approach for synthesizing amino acid- or peptide-substituted triazolylphosphonate analogs (TP ODNs) has been developed to provide improved stability and cell uptake. The chemistry is quite general, as peptides can be introduced throughout the TP ODN at any preselected internucleotide linkage. These synthetic TP ODNs enter cells through endocytosis in the absence of transfection reagents and localize into perinuclear organelles. The entrapped ODNs are released into the cytoplasm by treatment with endosomal-releasing agents and several are then active as microRNA inhibitors. PMID:29263901

Dissimilar Kinetic Behavior of Electrically Manipulated Single- and Double-Stranded DNA Tethered to a Gold Surface

PubMed Central

Rant, Ulrich; Arinaga, Kenji; Tornow, Marc; Kim, Yong Woon; Netz, Roland R.; Fujita, Shozo; Yokoyama, Naoki; Abstreiter, Gerhard

2006-01-01

We report on the electrical manipulation of single- and double-stranded oligodeoxynucleotides that are end tethered to gold surfaces in electrolyte solution. The response to alternating repulsive and attractive electric surface fields is studied by time-resolved fluorescence measurements, revealing markedly distinct dynamics for the flexible single-stranded and stiff double-stranded DNA, respectively. Hydrodynamic simulations rationalize this finding and disclose two different kinetic mechanisms: stiff polymers undergo rotation around the anchoring pivot point; flexible polymers, on the other hand, are pulled onto the attracting surface segment by segment. PMID:16473909

Dissimilar kinetic behavior of electrically manipulated single- and double-stranded DNA tethered to a gold surface.

PubMed

Rant, Ulrich; Arinaga, Kenji; Tornow, Marc; Kim, Yong Woon; Netz, Roland R; Fujita, Shozo; Yokoyama, Naoki; Abstreiter, Gerhard

2006-05-15

We report on the electrical manipulation of single- and double-stranded oligodeoxynucleotides that are end tethered to gold surfaces in electrolyte solution. The response to alternating repulsive and attractive electric surface fields is studied by time-resolved fluorescence measurements, revealing markedly distinct dynamics for the flexible single-stranded and stiff double-stranded DNA, respectively. Hydrodynamic simulations rationalize this finding and disclose two different kinetic mechanisms: stiff polymers undergo rotation around the anchoring pivot point; flexible polymers, on the other hand, are pulled onto the attracting surface segment by segment.

The prebiotic synthesis of oligonucleotides

NASA Technical Reports Server (NTRS)

Oro, J.; Stephen-Sherwood, E.

1974-01-01

This paper is primarily a review of recent developments in the abiotic synthesis of nucleotides, short chain oligonucleotides, and their mode of replication in solution. It also presents preliminary results from this laboratory on the prebiotic synthesis of thymidine oligodeoxynucleotides. A discussion, based on the physicochemical properties of RNA and DNA oligomers, relevant to the molecular evolution of these compounds leads to the tentative hypothesis that oligodeoxyribonucleotides of about 12 units may have been of sufficient length to initiate a self replicating coding system. Two models are suggested to account for the synthesis of high molecular weight oligomers using short chain templates and primers.

Chloroquine and inhibition of Toll-like receptor 9 protect from sepsis-induced acute kidney injury

PubMed Central

Yasuda, Hideo; Leelahavanichkul, Asada; Tsunoda, Shinichiro; Dear, James W.; Takahashi, Yoshiyuki; Ito, Shuichi; Hu, Xuzhen; Zhou, Hua; Doi, Kent; Childs, Richard; Klinman, Dennis M.; Yuen, Peter S.T.; Star, Robert A.

2008-01-01

Mortality from sepsis has remained high despite recent advances in supportive and targeted therapies. Toll-like receptors (TLRs) sense bacterial products and stimulate pathogenic innate immune responses. Mice deficient in the common adapter protein MyD88, downstream from most TLRs, have reduced mortality and acute kidney injury (AKI) from polymicrobial sepsis. However, the identity of the TLR(s) responsible for the host response to polymicrobial sepsis is unknown. Here, we show that chloroquine, an inhibitor of endocytic TLRs (TLR3, 7, 8, 9), improves sepsis-induced mortality and acute kidney injury in a clinically relevant polymicrobial sepsis mouse model, even when administered 6h after the septic insult. Chloroquine administration attenuated the decline in renal function, splenic apoptosis, serum markers of damage to other organs, and prototypical serum pro- and anti-inflammatory cytokines TNF-alpha and IL-10. An oligodeoxynucleotide inhibitor (H154) of TLR9 and TLR9-deficient mice mirror the actions of chloroquine in all functional parameters that we tested. In addition, chloroquine decreased TLR9 protein abundance in spleen, further suggesting that TLR9 signaling may be a major target for the protective actions of chloroquine. Our findings indicate that chloroquine improves survival by inhibiting multiple pathways leading to polymicrobial sepsis, and that chloroquine and TLR9 inhibitors represent viable broad-spectrum and targeted therapeutic strategies, respectively, that are promising candidates for further clinical development. PMID:18305095

Development of Nano/Micro Probes for Femtoliter Volume and Single Cell Measurements

NASA Astrophysics Data System (ADS)

Gao, Yang

Single cell analysis has recently emerged as an important field of biomedical re- search. It is now clear that heterogeneity of cell metabolism functions in complex biological systems is correlated to changes in biological function and disease processes. A variety of nano/micro probes were developed to enable investigation of cells properties such as membrane stiffness, pH value. However, very few designs were focused on single cell metabolic function studies. There is a critical need for technologies that provide analysis of heterogeneity of cell metabolic functions, especially on metabolism. Nevertheless, the few existing approaches suffer from fundamental defects and need to be improved. This work focused on developing nano/micro probes that are suitable for single cell functionality investigation. Both types of probes are designed to measure cell-to-cell/time-to-time heterogeneity in metabolic functions over a long period of time. Lab-made carbon nanoprobes were developed especially for electro-physiological measurement. The unique structure of the carbon nanoprobes makes them suitable for important intracellular applications like trans-membrane potential measurements and various electrochemical measurement for cell function studies. While it is important of have ability to carry out intracellular measure, there are also occasions where the information of a cell as a whole is collected. One of the most important indicator of a cells metabolic functions is cell respiration rate/oxygen consumption rate. A micro-perfusion based multi-functional single cell sensing probe was the developed to carry out measurements on cell as a whole. Formed by a double-barrel theta pipette, the perfusion flow enables the direct measurement of the metabolic flux for example oxygen consumption rate. In conclusion, this work developed nano/micro-probes as novel single cell investigation tools. The data acquired from these tools could provide valuable assistance on applications including cell metabolism studies, cancer diagnoses, and therapy evaluations.

Characteristics of ion distribution functions in dipolarizing flux bundles: Event studies

NASA Astrophysics Data System (ADS)

Runov, A.; Angelopoulos, V.; Artemyev, A.; Birn, J.; Pritchett, P. L.; Zhou, X.-Z.

2017-06-01

Taking advantage of multipoint observations from a repeating configuration of the five Time History of Events and Macroscale Interactions during Substorms (THEMIS) probes separated by 1 to 2 Earth radii (RE) along X, Y, and Z in the geocentric solar magnetospheric system (GSM), we study ion distribution functions collected by the probes during three dipolarizing flux bundle (DFB) events observed at geocentric distances 9 < R < 14 RE. By comparing these probes' observations, we characterize changes in the ion distribution functions with respect to probe separation along the X and Y GSM directions and |Bx| levels, which characterize the distance from the neutral sheet. We found that the characteristics of the ion distribution functions strongly depended on the |Bx| level, whereas changes with respect to X and Y were minor. In all three events, ion distribution functions f(v) observed inside DFBs were organized by magnetic and electric fields. The probes near the magnetic equator observed perpendicular anisotropy of the phase space density in the range between thermal energy and twice the thermal energy, although the distribution in the ambient plasma sheet was isotropic. The anisotropic ion distribution in DFBs injected toward the inner magnetosphere may provide the free energy for waves and instabilities, which are important elements of particle energization.

Multi-function diamond film fiber optic probe and measuring system employing same

DOEpatents

Young, J.P.

1998-11-24

A fused fiber optic probe having a protective cover, a fiber optic probe system, and embodiments thereof for conducting electromagnetic spectral measurements are disclosed. The fused fiber optic probe comprises a probe tip having a specific geometrical configuration, an exciting optical fiber and at least one collection optical fiber fused within a housing, preferably silica, with a protective cover disposed over at least a portion of the probe tip. The specific geometrical configurations in which the probe tip can be shaped include a slanted probe tip with an angle greater than 0{degree}, an inverted cone-shaped probe tip, and a lens head. 9 figs.

Current-Voltage and Floating-Potential characteristics of cylindrical emissive probes from a full-kinetic model based on the orbital motion theory

NASA Astrophysics Data System (ADS)

Chen, Xin; Sánchez-Arriaga, Gonzalo

2018-02-01

To model the sheath structure around an emissive probe with cylindrical geometry, the Orbital-Motion theory takes advantage of three conserved quantities (distribution function, transverse energy, and angular momentum) to transform the stationary Vlasov-Poisson system into a single integro-differential equation. For a stationary collisionless unmagnetized plasma, this equation describes self-consistently the probe characteristics. By solving such an equation numerically, parametric analyses for the current-voltage (IV) and floating-potential (FP) characteristics can be performed, which show that: (a) for strong emission, the space-charge effects increase with probe radius; (b) the probe can float at a positive potential relative to the plasma; (c) a smaller probe radius is preferred for the FP method to determine the plasma potential; (d) the work function of the emitting material and the plasma-ion properties do not influence the reliability of the floating-potential method. Analytical analysis demonstrates that the inflection point of an IV curve for non-emitting probes occurs at the plasma potential. The flat potential is not a self-consistent solution for emissive probes.

Development of Simple Designs of Multitip Probe Diagnostic Systems for RF Plasma Characterization

PubMed Central

Naz, M. Y.; Shukrullah, S.; Ghaffar, A.; Rehman, N. U.

2014-01-01

Multitip probes are very useful diagnostics for analyzing and controlling the physical phenomena occurring in low temperature discharge plasmas. However, DC biased probes often fail to perform well in processing plasmas. The objective of the work was to deduce simple designs of DC biased multitip probes for parametric study of radio frequency plasmas. For this purpose, symmetric double probe, asymmetric double probe, and symmetric triple probe diagnostic systems and their driving circuits were designed and tested in an inductively coupled plasma (ICP) generated by a 13.56 MHz radio frequency (RF) source. Using I-V characteristics of these probes, electron temperature, electron number density, and ion saturation current was measured as a function of input power and filling gas pressure. An increasing trend was noticed in electron temperature and electron number density for increasing input RF power whilst a decreasing trend was evident in these parameters when measured against filling gas pressure. In addition, the electron energy probability function (EEPF) was also studied by using an asymmetric double probe. These studies confirmed the non-Maxwellian nature of the EEPF and the presence of two groups of the energetic electrons at low filling gas pressures. PMID:24683326

CW (Continuous Wave) Measurement System. Operating Manual

DTIC Science & Technology

1982-08-02

A probe calibration program for probes with analyti- cal transfer functions . Such probes include the EG&G MGL series of B-dot field sensors. Non ...response to the SIGNAL PROBE> prompt in the primary menu which appears during calibration of a non -analytic probe (see Section 5-3.2 for more...OPERATION AND CALIBRATION .......... 107 4-2.1 Operation in the Primary Configu- ration .............................. 107 4-2.2 Operation in the Secondary

NeuroMEMS: Neural Probe Microtechnologies

PubMed Central

HajjHassan, Mohamad; Chodavarapu, Vamsy; Musallam, Sam

2008-01-01

Neural probe technologies have already had a significant positive effect on our understanding of the brain by revealing the functioning of networks of biological neurons. Probes are implanted in different areas of the brain to record and/or stimulate specific sites in the brain. Neural probes are currently used in many clinical settings for diagnosis of brain diseases such as seizers, epilepsy, migraine, Alzheimer's, and dementia. We find these devices assisting paralyzed patients by allowing them to operate computers or robots using their neural activity. In recent years, probe technologies were assisted by rapid advancements in microfabrication and microelectronic technologies and thus are enabling highly functional and robust neural probes which are opening new and exciting avenues in neural sciences and brain machine interfaces. With a wide variety of probes that have been designed, fabricated, and tested to date, this review aims to provide an overview of the advances and recent progress in the microfabrication techniques of neural probes. In addition, we aim to highlight the challenges faced in developing and implementing ultra-long multi-site recording probes that are needed to monitor neural activity from deeper regions in the brain. Finally, we review techniques that can improve the biocompatibility of the neural probes to minimize the immune response and encourage neural growth around the electrodes for long term implantation studies. PMID:27873894

A Holding Function for Conflict Probe Appiications

NASA Technical Reports Server (NTRS)

McNally, Dave; Walton, Joe

2004-01-01

Conflict Alerts for aircraft in holding patterns are often missed or in error due to fact that holding trajectories are not modeled in Conflict Alert or Conflict Probe logic. In addition, a controller in one sector may not know when aircraft are holding in a neighboring sector. These factors can lead to an increased potential for loss of separation while aircraft are flying in holding patterns. A holding function for conflict probe applications has been developed and tested with air traffic data from Fort Worth Center. The holding function automatically determines when an aircraft enters a holding pattern, builds a holding region around the pattern and then probes the region for conflict with other traffic. The operational concept of use assumes that air traffic controllers are very busy during periods when aircraft are in holding and therefore don't have time to manually enter information which defines a holding pattern and activates conflict probing. For this reason, it is important the holding function automatically detect aircraft in holding and compute a holding region for conflict analysis. The controller is then alerted if other aircraft are predicted to fly through the holding region at the holding altitude.

The Probe Profile and Lateral Resolution of Scanning Transmission Electron Microscopy of Thick Specimens

PubMed Central

Demers, Hendrix; Ramachandra, Ranjan; Drouin, Dominique; de Jonge, Niels

2012-01-01

Lateral profiles of the electron probe of scanning transmission electron microscopy (STEM) were simulated at different vertical positions in a micrometers-thick carbon sample. The simulations were carried out using the Monte Carlo method in the CASINO software. A model was developed to fit the probe profiles. The model consisted of the sum of a Gaussian function describing the central peak of the profile, and two exponential decay functions describing the tail of the profile. Calculations were performed to investigate the fraction of unscattered electrons as function of the vertical position of the probe in the sample. Line scans were also simulated over gold nanoparticles at the bottom of a carbon film to calculate the achievable resolution as function of the sample thickness and the number of electrons. The resolution was shown to be noise limited for film thicknesses less than 1 μm. Probe broadening limited the resolution for thicker films. The validity of the simulation method was verified by comparing simulated data with experimental data. The simulation method can be used as quantitative method to predict STEM performance or to interpret STEM images of thick specimens. PMID:22564444

Antisense oligodeoxynucleotide inhibition of a swelling-activated cation channel in osteoblast-like osteosarcoma cells

NASA Technical Reports Server (NTRS)

Duncan, R. L.; Kizer, N.; Barry, E. L.; Friedman, P. A.; Hruska, K. A.

1996-01-01

By patch-clamp analysis, we have shown that chronic, intermittent mechanical strain (CMS) increases the activity of stretch-activated cation channels of osteoblast-like UMR-106.01 cells. CMS also produces a swelling-activated whole-cell conductance (Gm) regulated by varying strain levels. We questioned whether the swelling-activated conductance was produced by stretch-activated cation channel activity. We have identified a gene involved in the increase in conductance by using antisense oligodeoxynucleotides (ODN) derived from the alpha 1-subunit genes of calcium channels found in UMR-106.01 cells (alpha1S, alpha1C, and alpha1D). We demonstrate that alpha 1C antisense ODNs abolish the increase in Gm in response to hypotonic swelling following CMS. Antisense ODNs to alpha1S and alpha1D, sense ODNs to alpha1C, and sham permeabilization had no effect on the conductance increase. In addition, during cell-attached patch-clamp studies, antisense ODNs to alpha1c completely blocked the swelling-activated and stretch-activated nonselective cation channel response to strain. Antisense ODNs to alpha1S treatment produced no effect on either swelling-activated or stretch-activated cation channel activity. There were differences in the stretch-activated and swelling-activated cation channel activity, but whether they represent different channels could not be determined from our data. Our data indicate that the alpha1C gene product is involved in the Gm and the activation of the swelling-activated cation channels induced by CMS. The possibility that swelling-activated cation channel genes are members of the calcium channel superfamily exists, but if alpha1c is not the swelling-activated cation channel itself, then its expression is required for induction of swelling-activated cation channel activity by CMS.

Ex vivo gene editing of the dystrophin gene in muscle stem cells mediated by peptide nucleic acid single stranded oligodeoxynucleotides induces stable expression of dystrophin in a mouse model for Duchenne muscular dystrophy.

PubMed

Nik-Ahd, Farnoosh; Bertoni, Carmen

2014-07-01

Duchenne muscular dystrophy (DMD) is a fatal disease caused by mutations in the dystrophin gene, which result in the complete absence of dystrophin protein throughout the body. Gene correction strategies hold promise to treating DMD. Our laboratory has previously demonstrated the ability of peptide nucleic acid single-stranded oligodeoxynucleotides (PNA-ssODNs) to permanently correct single-point mutations at the genomic level. In this study, we show that PNA-ssODNs can target and correct muscle satellite cells (SCs), a population of stem cells capable of self-renewing and differentiating into muscle fibers. When transplanted into skeletal muscles, SCs transfected with correcting PNA-ssODNs were able to engraft and to restore dystrophin expression. The number of dystrophin-positive fibers was shown to significantly increase over time. Expression was confirmed to be the result of the activation of a subpopulation of SCs that had undergone repair as demonstrated by immunofluorescence analyses of engrafted muscles using antibodies specific to full-length dystrophin transcripts and by genomic DNA analysis of dystrophin-positive fibers. Furthermore, the increase in dystrophin expression detected over time resulted in a significant improvement in muscle morphology. The ability of transplanted cells to return into quiescence and to activate upon demand was confirmed in all engrafted muscles following injury. These results demonstrate the feasibility of using gene editing strategies to target and correct SCs and further establish the therapeutic potential of this approach to permanently restore dystrophin expression into muscle of DMD patients. © 2014 AlphaMed Press.

MiR-132 regulated olfactory bulb proteins linked to olfactory learning in greater short-nosed fruit bat Cynopterus sphinx.

PubMed

Mukilan, Murugan; Rajathei, David Mary; Jeyaraj, Edwin; Kayalvizhi, Nagarajan; Rajan, Koilmani Emmanuvel

2018-05-30

Earlier, we showed that micro RNA-132 (miR-132) regulate the immediate early genes (IEGs) in the olfactory bulb (OB) of fruit bat Cynopterus sphinx during olfactory learning. This study was designed to examine whether the miR-132 regulate other proteins in OB during olfactory learning. To test this, miR-132 anti-sense oligodeoxynucleotide (AS-ODN) was delivered to the OB and then trained to novel odor. The 2-dimensional gel electrophoresis analysis showed that inhibition of miR-132 altered olfactory training induced expression of 321 proteins. Further, liquid chromatography-mass spectrometry (LC-MS/MS) analysis reveals the identity of differently expressed proteins such as phosphoribosyl transferase domain containing protein (PRTFDC 1), Sorting nexin-8 (SNX8), Creatine kinase B-type (CKB) and Annexin A11 (ANX A11). Among them PRTFDC 1 showing 189 matching peptides with highest sequence coverage (67.0%) and protein-protein interaction analysis showed that PRTFDC 1 is a homolog of hypoxanthine phosphoribosyltransferase-1 (HPRT-1). Subsequent immunohistochemical analysis (IHC) showed that inhibition of miR-132 down-regulated HPRT expression in OB of C. sphinx. In addition, western blot analysis depicts that HPRT, serotonin transporter (SERT), N-methyl-d-asparate (NMDA) receptors (2A,B) were down-regulated, but not altered in OB of non-sense oligodeoxynucleotide (NS-ODN) infused groups. These analyses suggest that miR-132 regulates the process of olfactory learning and memory formation through SERT and NMDA receptors signalling, which is possibly associated with the PRTFDC1-HPRT interaction. Copyright © 2017. Published by Elsevier B.V.

Survival of Mice with Gastrointestinal Acute Radiation Syndrome through Control of Bacterial Translocation.

PubMed

Suzuki, Fujio; Loucas, Bradford D; Ito, Ichiaki; Asai, Akira; Suzuki, Sumihiro; Kobayashi, Makiko

2018-07-01

Macrophages (Mϕ) with the M2b phenotype (Pheno2b-Mϕ) in bacterial translocation sites have been described as cells responsible for the increased susceptibility of mice with gastrointestinal acute radiation syndrome to sepsis caused by gut bacteria. In this study, we tried to reduce the mortality of mice exposed to 7-10 Gy of gamma rays by controlling Pheno2b-Mϕ polarization in bacterial translocation sites. MicroRNA-222 was induced in association with gamma irradiation. Pheno2b-Mϕ polarization was promoted and maintained in gamma-irradiated mice through the reduction of a long noncoding RNA growth arrest-specific transcript 5 (a CCL1 gene silencer) influenced by this microRNA. Therefore, the host resistance of 7-9-Gy gamma-irradiated mice to sepsis caused by bacterial translocation was improved after treatment with CCL1 antisense oligodeoxynucleotide. However, the mortality of 10-Gy gamma-irradiated mice was not alleviated by this treatment. The crypts and villi in the ileum of 10-Gy gamma-irradiated mice were severely damaged, but these were markedly improved after transplantation of intestinal lineage cells differentiated from murine embryonic stem cells. All 10-Gy gamma-irradiated mice given both of the oligodeoxynucleotide and intestinal lineage cells survived, whereas all of the same mice given either of them died. These results indicate that high mortality rates of mice irradiated with 7-10 Gy of gamma rays are reducible by depleting CCL1 in combination with the intestinal lineage cell transplantation. These findings support the novel therapeutic possibility of victims who have gastrointestinal acute radiation syndrome for the reduction of their high mortality rates. Copyright © 2018 by The American Association of Immunologists, Inc.

Effects of immunization against alpha-inhibin using two adjuvants on daily sperm production and hormone concentrations in ram lambs.

PubMed

Voge, J L; Parker, J B; Wheaton, J E

2009-11-01

Twenty-five ram lambs were immunized against alpha-inhibin peptide emulsified in Freund's adjuvant (FRA), Emulsigen (EML) containing an oligodeoxynucleotide as an immunostimulant, or adjuvant without alpha-inhibin antigen (control). Four immunizations were administered during an 85-d period, after which testes were obtained for determination of daily sperm production (DSP) and histological evaluation. alpha-Inhibin antibody (Ab) titers were 70-fold greater in lambs treated with FRA than in EML-treated ram lambs. alpha-Inhibin immunization had no effect on testes weight or on plasma concentrations of follicle-stimulating hormone (FSH), luteinizing hormone (LH), and testosterone. Mean DSP/g tended (P=0.1) to be greater in alpha-inhibin-immunized (EML=17.6x10(6); FRA=15.8x10(6)) ram lambs than in control animals (14.4x10(6)). One of the 8 control ram lambs had an elevated DSP/g, which was a statistical outlier. Without data from this lamb, DSP/g was increased (P<0.01) in alpha-inhibin-immunized ram lambs by 28% over controls. No association was found between the titer of alpha-inhibin Ab developed and DSP/g. Histologically, the percentage of testicular area occupied by seminiferous tubules differed (P=0.01) by treatment and was greatest (82%) in EML-treated ram alpha-inhibin-immunized lambs and lowest (74%) in control animals. Percentage tubular area and DSP/g were correlated (r=0.57, P=0.003). Findings show that (1) the extent of the increase in DSP/g is not dependent on the titer of alpha-inhibin Ab; (2) the increase in DSP/g is achieved through an increase in the mass of seminiferous tubules; and (3) FRA elicits a greater alpha-inhibin Ab titer than EML containing an oligodeoxynucleotide.

Inhibition of Lactate Transport Erases Drug Memory and Prevents Drug Relapse.

PubMed

Zhang, Yan; Xue, Yanxue; Meng, Shiqiu; Luo, Yixiao; Liang, Jie; Li, Jiali; Ai, Sizhi; Sun, Chengyu; Shen, Haowei; Zhu, Weili; Wu, Ping; Lu, Lin; Shi, Jie

2016-06-01

Drug memories that associate drug-paired stimuli with the effects of abused drugs contribute to relapse. Exposure to drug-associated contexts causes consolidated drug memories to be in a labile state, during which manipulations can be given to impair drug memories. Although substantial evidence demonstrates the crucial role of neuronal signaling in addiction, little is known about the contribution of astrocyte-neuron communication. Rats were trained for cocaine-induced conditioned place preference (CPP) or self-administration and microinjected with the glycogen phosphorylation inhibitor 1,4-dideoxy-1,4-imino-D-arabinitol into the basolateral amygdala (BLA) immediately after retrieval. The concentration of lactate was measured immediately after retrieval via microdialysis, and the CPP score and number of nosepokes were recorded 24 hours later. Furthermore, we used antisense oligodeoxynucleotides to disrupt the expression of astrocytic lactate transporters (monocarboxylate transporters 1 and 2) in the BLA after retrieval, tested the expression of CPP 1 day later, and injected L-lactate into the BLA 15 minutes before retrieval to rescue the effects of the oligodeoxynucleotides. Injection of 1,4-dideoxy-1,4-imino-D-arabinitol into the BLA immediately after retrieval prevented the subsequent expression of cocaine-induced CPP, decreased the concentration of lactate in the BLA, and reduced the number of nosepokes for cocaine self-administration. Disrupting the expression of monocarboxylate transporters 1 and 2 in the BLA also caused subsequent deficits in the expression of cocaine-induced CPP, which was rescued by pretreatment with L-lactate. Our results suggest that astrocyte-neuron lactate transport in the BLA is critical for the reconsolidation of cocaine memory. Copyright © 2016 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

In vitro effects of CpG oligodeoxynucleotides delivered by gelatin nanoparticles on canine peripheral blood mononuclear cells of atopic and healthy dogs - a pilot study.

PubMed

Prélaud, Ana Rostaher; Fuchs, Sebastian; Weber, Karin; Winter, Gerhard; Coester, Conrad; Mueller, Ralf S

2013-10-01

Cytosine-phosphate-guanine (CpG) oligodeoxynucleotides offer a novel promising immunotherapeutic approach for atopic dermatitis (AD) both in humans and animals. Gelatin nanoparticles (GNP) enhance and prolong CpG-associated immunomodulatory effects and minimize adverse effects both in vitro and in vivo. Information about the effects of this combination in dogs is lacking. The aim of this study was to evaluate immunological effects of CpG coupled to GNP on canine peripheral blood mononuclear cells (PBMCs) in vitro. Eight dogs with AD, diagnosed by standard criteria and with a concurrent immediate hypersensitivity to house dust mites were included. Control samples were taken from eight healthy, age-matched control dogs without history or evidence of cutaneous or systemic illness. Peripheral blood mononuclear cells of healthy and allergic dogs were incubated with CpG-GNP and the uptake of CpG-GNP was demonstrated using confocal laser scanning microscopy. Cell culture supernatant concentrations of interferon gamma (IFN-γ), interleukin (IL)-4, IL-6 and IL-10 were measured by Canine Cytokine Milliplex. No significant changes in IFN-γ and IL-4 were found when comparing PBMCs incubated with CpG and CpG-GNP with the negative controls in atopic and healthy dogs. Interleukin-6 was not detected in any of the groups. However, a statistically significant increase in IL-10 concentration was found after 24 h stimulation with CpG-GNP compared with CpG alone both in atopic and healthy dogs. As IL-10 is considered an immunosuppressive cytokine playing a key role in peripheral tolerance; the reported CpG-GNP formulation could be a new approach in allergy treatment. © 2013 ESVD and ACVD.

Immune stimulation by a CpG-containing oligodeoxynucleotide is enhanced when encapsulated and delivered in lipid particles.

PubMed

Mui, B; Raney, S G; Semple, S C; Hope, M J

2001-09-01

The therapeutic benefit from phosphorothioate oligodeoxynucleotides (PS ODN) containing immune stimulatory sequences (ISS) has been demonstrated in animal models of cancer and infection. In particular, when CpG-containing PS ODN are administered to mice, activation of macrophages and dendritic, NK, T, and B cells occurs, resulting in the release of an array of cytokines, including interleukin-12 (IL-12), interferon-gamma (IFN-gamma), and tumor necrosis factor-alpha (TNF-alpha). We have previously described stabilized antisense-lipid particles (SALP) for the i.v. administration of antisense ODN [Biochim Biophys Acta (2001) 1510:152--166]. Given the propensity for SALP to target macrophages in vivo it was of interest to determine whether they could enhance the potency of CpG ODN to induce an immune response. In this report we show that when CpG-containing SALP are administered intravenously to ICR mice the plasma concentrations of IL-12, IFN-gamma, IL-6, monocyte chemoattractant protein-1, and TNF-alpha are greatly increased compared with the same dose of free ODN. The pattern of cytokine induction indicates that the immune response is T helper cell type 1-biased, similar to that observed for PS CpG ODN ISS in general. Furthermore, when phosphodiester (PO) ODN is substituted for PS ODN in the SALP formulation cytokine induction is even greater at the early time points, in marked contrast to free PO ODN, which is inactive. These results demonstrate that the immunogenicity of ISS is not only enhanced by encapsulation in lipid particles, which more closely mimic the way ISS DNA would normally be presented to antigen presenting cells by pathogens in vivo, but also SALP enable unmodified PO CpG ODN to be used as immune stimulants.

Intraperitoneal prophylaxis with CpG oligodeoxynucleotides protects neutropenic mice against intracerebral Escherichia coli K1 infection.

PubMed

Ribes, Sandra; Meister, Tanja; Ott, Martina; Redlich, Sandra; Janova, Hana; Hanisch, Uwe-Karsten; Nessler, Stefan; Nau, Roland

2014-01-23

Prophylaxis with unmethylated cytosine phosphate guanidine (CpG) oligodeoxynucleotides (ODN) protects against several systemic experimental infections. Escherichia coli is a major cause of Gram-negative neonatal bacterial meningitis and also causes meningitis and meningoencephalitis in older and immunocompromised patients. Wild-type (wt) and Toll-like receptor 9 (TLR9)-deficient mice were rendered neutropenic by intraperitoneal administration of the anti-Ly-6G monoclonal antibody. Immunocompetent and neutropenic mice received intraperitoneal CpG ODN or vehicle 72 h prior to induction of E. coli K1 meningoencephalitis. Pre-treatment with CpG ODN significantly increased survival of neutropenic wt mice from 33% to 75% (P = 0.0003) but did not protect neutropenic TLR9-/- mice. The protective effect of CpG ODN was associated with an enhanced production of interleukin (IL)-12/IL-23p40 with sustained increased levels in serum and spleen at least for 17 days after conditioning compared to buffer-treated animals. CpG-treated neutropenic wt mice showed reduced bacterial concentrations and increased recruitment of Ly6ChighCCR2+ monocytes in brain and spleen 42 h after infection. The levels of macrophage inflammatory protein 1α (MIP-1α) and interferon gamma (IFN-γ) in spleen were higher 42 h after infection in CpG-treated compared to buffer-treated neutropenic animals. In immunocompetent mice, prophylaxis with CpG ODN did not significantly increase survival compared to the buffer group (60% vs. 45%, P = 0.2). These findings suggest that systemic administration of CpG ODN may help to prevent bacterial CNS infections in immunocompromised individuals.

A CpG-containing oligodeoxynucleotide as an efficient adjuvant counterbalancing the Th1/Th2 immune response in diphtheria-tetanus-pertussis vaccine.

PubMed

Sugai, Toshiyuki; Mori, Masaaki; Nakazawa, Masatoshi; Ichino, Motohide; Naruto, Takuya; Kobayashi, Naoki; Kobayashi, Yoshinori; Minami, Mutsuhiko; Yokota, Shumpei

2005-11-16

Adjuvants in vaccines are immune stimulants that play an important role in the induction of effective and appropriate immune responses to vaccine component(s). Diphtheria-tetanus-pertussis (DPT) vaccine contains not only aluminum hydrate (alum) to enhance the immune response to the vaccine ingredients, but also, both for that purpose and as a principal ingredient, pertussis toxin (PT). However, both adjuvants strongly promote T helper (Th) 2 type immune responses. Th1 and Th2 type immune responses are counterbalanced in vivo, and a Th2-prone immune response is not effective against intracellular infections but promotes IgE production, which is related to allergic disease. In this study, we used the CpG motif contained in oligodeoxynucleotide (CpG-ODN), which has an adjuvant effect and also induces the Th1 response, as an adjuvant to this vaccine, and we investigated its adjuvanticity and its potential to modulate immune responses to DPT vaccine. Administration of DPT vaccine with CpG-ODN (DPT-alum/ODN) to mice significantly reduced the total IgE levels and increased the anti-PT specific IgG2a titer in serum, in comparison with ordinary DPT vaccine (DPT-alum). Moreover, we investigated the antibody response to orally administrated ovalbumin (OVA) after vaccine administration. In the DPT-alum/ODN-administered group, the OVA specific IgE production in serum greatly decreased in comparison with that in the DPT-alum-administered group. These data indicate that CpG-ODN was not useful only as an efficient vaccine adjuvant but also shifted the immune responses substantially toward Th1 and modulated the Th1/Th2 immune response in DPT vaccine. These data suggested new applications of CpG-ODN as adjuvants in DPT vaccine.

Cytosine-phosphate-guanine oligodeoxynucleotides containing GACGTT motifs enhance the immune responses elicited by keyhole limpet hemocyanin antigen in dairy cattle.

PubMed

Chu, Chun-Yen; Lee, Shang-Chun; Liu, Shyh-Shyan; Lin, Yu-Ming; Shen, Perng-Chi; Yu, Chi; Lee, Kuo-Hua; Zhao, Xin; Lee, Jai-Wei

2011-10-01

Adjuvants are important components of vaccine formulations. Effective adjuvants line innate and adaptive immunity by signaling through pathogen recognition receptors. Synthetic cytosine-phosphate-guanine (CpG) oligodeoxynucleotides (ODNs) have been shown to have potentials as adjuvants for vaccines. However, the immunostimulatory effect of CpG is species-specific and depends on the sequence of CpG motifs. A CpG ODN (2135), containing 3 identical copies of GTCGTT motif, was previously reported to have the strongest effects on bovine peripheral blood mononuclear cells (PBMC). Based on the sequence of 2135, we replaced the GTCGTT motif with 11 other sequences containing CG and investigated their effects on bovine lymphocyte proliferation. Results showed that the CpG ODNs containing 3 copies of GACGTT motif had the highest lymphocyte stimulation index (7.91±1.18), which was significantly (P<0.05) higher than that of 2135 (4.25±0.56). The CpG ODNs containing 3 copies of GACGTT motif also significantly increased the mRNA expression of interferon (IFN)-α, interleukin (IL)-12, and IL-21 in bovine PBMC. When dairy cows were immunized with the keyhole limpet hemocyanin (KLH) antigen formulated with CpG ODNs containing 3 copies of GACGTT, production of KLH-specific antibodies in serum and in milk whey was significantly (P<0.05) enhanced. IFN-γ in whole blood stimulated by KLH was also significantly (P<0.05) increased in cows immunized with KLH plus CpG ODNs. Our results indicate that CpG ODNs containing 3 copies of the GACGTT motifs is a potential adjuvant for bovine vaccines.

Effect of antisense oligodeoxynucleotides for ICAM-1 on renal ischaemia–reperfusion injury in the anaesthetised rat

PubMed Central

Kiew, Lik Voon; Munavvar, Abdul Sattar; Law, Chung Hiong; Azizan, Abdullah Nor; Nazarina, Abdul Rahman; Sidik, Khalifah; Johns, Edward J

2004-01-01

An antisense oligodeoxynucleotide (As-ODN) to the 3′ untranslated region of the mRNA sequence expressing the intracellular adhesion molecule-1 (ICAM-1) was employed to determine ICAM-1's role in renal ischaemia–reperfusion injury in the rat. Wistar-Kyoto rats receiving i.v. either lipofectin–As-ODN (As-ODN group), lipofectin–reverse ODN (Rv-ODN group) or lipofectin (ischaemia control group) 8 h prior to study were anaesthetized and subjected to 30 min of renal artery occlusion. Renal haemodynamic and excretory parameters were monitored before and after renal ischaemia. On termination of the study renal tissue was subjected to histological and Western blot analysis. Renal blood flow decreased in the 3 h post-ischaemia period in the ischaemia control and Rv-ODN groups, but was maintained in the As-ODN group. Glomerular filtration rate was depressed initially but gradually increased to 10% above basal levels in the ischaemia control and Rv-ODN groups, but was below basal levels (20%) in the As-ODN group. There was a three- to fourfold increase in sodium and water excretion following ischaemia in the ischaemia control and reverse-ODN groups but not in the As-ODN treated group. The As-ODN ameliorated the histological evidence of ischaemic damage and reduced ICAM-1 protein levels to a greater extent in the medulla than cortex. These observations suggested that in the post-ischaemic period afferent and efferent arteriolar tone was increased with a loss of reabsorptive capacity which was in part due to ICAM-1. The possibility arises that the action of ICAM-1 at vascular and tubular sites in the deeper regions of the kidney contributes to the ischaemia–reperfusion injury. PMID:15047774

Novel biological strategies for treatment of wear particle-induced periprosthetic osteolysis of orthopaedic implants for joint replacement

PubMed Central

Goodman, S. B.; Gibon, E.; Pajarinen, J.; Lin, T.-H.; Keeney, M.; Ren, P.-G.; Nich, C.; Yao, Z.; Egashira, K.; Yang, F.; Konttinen, Y. T.

2014-01-01

Wear particles and by-products from joint replacements and other orthopaedic implants may result in a local chronic inflammatory and foreign body reaction. This may lead to persistent synovitis resulting in joint pain and swelling, periprosthetic osteolysis, implant loosening and pathologic fracture. Strategies to modulate the adverse effects of wear debris may improve the function and longevity of joint replacements and other orthopaedic implants, potentially delaying or avoiding complex revision surgical procedures. Three novel biological strategies to mitigate the chronic inflammatory reaction to orthopaedic wear particles are reported. These include (i) interference with systemic macrophage trafficking to the local implant site, (ii) modulation of macrophages from an M1 (pro-inflammatory) to an M2 (anti-inflammatory, pro-tissue healing) phenotype in the periprosthetic tissues, and (iii) local inhibition of the transcription factor nuclear factor kappa B (NF-κB) by delivery of an NF-κB decoy oligodeoxynucleotide, thereby interfering with the production of pro-inflammatory mediators. These three approaches have been shown to be viable strategies for mitigating the undesirable effects of wear particles in preclinical studies. Targeted local delivery of specific biologics may potentially extend the lifetime of orthopaedic implants. PMID:24478281

Covalent protein-oligonucleotide conjugates by copper-free click reaction

PubMed Central

Khatwani, Santoshkumar L.; Mullen, Daniel G.; Hast, Michael A.; Beese, Lorena S.; Distefano, Mark D.; Taton, T. Andrew

2013-01-01

Covalent protein-oligodeoxynucleotide (protein-ODN) conjugates are useful in a number of biological applications, but synthesizing discrete conjugates—where the connection between the two components is at a defined location in both the protein and the ODN—under mild conditions with significant yield can be a challenge. In this article, we demonstrate a strategy for synthesizing discrete protein-ODN conjugates using strain-promoted azide-alkyne [3+2] cycloaddition (SPAAC, a copper-free “click” reaction). Azide-functionalized proteins, prepared by enzymatic prenylation of C-terminal CVIA tags with synthetic azidoprenyl diphosphates, were “clicked” to ODNs that had been modified with a strained dibenzocyclooctyne (DIBO-ODN). The resulting protein-ODN conjugates were purified and characterized by size-exclusion chromatography and gel electrophoresis. We find that the yields and reaction times of the SPAAC bioconjugation reactions are comparable to those previously reported for copper-catalyzed azide-alkyne [3+2] cycloaddition (CuAAC) bioconjugation, but require no catalyst. The same SPAAC chemistry was used to immobilize azide-modified proteins onto surfaces, using surface-bound DIBO-ODN as a heterobifunctional linker. Cu-free click bioconjugation of proteins to ODNs is a simple and versatile alternative to Cu-catalyzed click methods. PMID:22682299

A role for NF-κB–dependent gene transactivation in sunburn

PubMed Central

Abeyama, Kazuhiro; Eng, William; Jester, James V.; Vink, Arie A.; Edelbaum, Dale; Cockerell, Clay J.; Bergstresser, Paul R.; Takashima, Akira

2000-01-01

Exposure of skin to ultraviolet (UV) radiation is known to induce NF-κB activation, but the functional role for this pathway in UV-induced cutaneous inflammation remains uncertain. In this study, we examined whether experimentally induced sunburn reactions in mice could be prevented by blocking UV-induced, NF-κB–dependent gene transactivation with oligodeoxynucleotides (ODNs) containing the NF-κB cis element (NF-κB decoy ODNs). UV-induced secretion of IL-1, IL-6, TNF-α, and VEGF by skin-derived cell lines was inhibited by the decoy ODNs, but not by the scrambled control ODNs. Systemic or local injection of NF-κB decoy ODNs also inhibited cutaneous swelling responses to UV irradiation. Moreover, local UV-induced inflammatory changes (swelling, leukocyte infiltration, epidermal hyperplasia, and accumulation of proinflammatory cytokines) were all inhibited specifically by topically applied decoy ODNs. Importantly, these ODNs had no effect on alternative types of cutaneous inflammation caused by irritant or allergic chemicals. These results indicate that sunburn reactions culminate from inflammatory events that are triggered by UV-activated transcription of NF-κB target genes, rather than from nonspecific changes associated with tissue damage. PMID:10862790

Photonic Crystal Biosensor with In-Situ Synthesized DNA Probes for Enhanced Sensitivity

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

Hu, Shuren; Zhao, Y.; Retterer, Scott T

2013-01-01

We report on a nearly 8-fold increase in multi-hole defect photonic crystal biosensor response by incorporating in-situ synthesis of DNA probes, as compared to the conventional functionalization method employing pre-synthesized DNA probe immobilization.

Noncontact Measurement Of Sizes And Eccentricities Of Holes

NASA Technical Reports Server (NTRS)

Chern, Engmin J.

1993-01-01

Semiautomatic eddy-current-probe apparatus makes noncontact measurements of nominally round holes in electrically conductive specimens and processes measurement data into diameters and eccentricities of holes. Includes x-y translation platform, which holds specimen and moves it horizontally. Probe mounted on probe scanner, positioning probe along vertical (z) direction and rotates probe about vertical axis at preset low speed. Eddy-current sensing coil mounted in side of probe near tip. As probe rotates, impedance analyzer measures electrical impedance (Z) of coil as function of instantaneous rotation angle. Translation and rotation mechanisms and impedance analyzer controlled by computer, which also processes impedance-measurement data.

MPAI (mass probes aided ionization) method for total analysis of biomolecules by mass spectrometry.

PubMed

Honda, Aki; Hayashi, Shinichiro; Hifumi, Hiroki; Honma, Yuya; Tanji, Noriyuki; Iwasawa, Naoko; Suzuki, Yoshio; Suzuki, Koji

2007-01-01

We have designed and synthesized various mass probes, which enable us to effectively ionize various molecules to be detected with mass spectrometry. We call the ionization method using mass probes the "MPAI (mass probes aided ionization)" method. We aim at the sensitive detection of various biological molecules, and also the detection of bio-molecules by a single mass spectrometry serially without changing the mechanical settings. Here, we review mass probes for small molecules with various functional groups and mass probes for proteins. Further, we introduce newly developed mass probes for proteins for highly sensitive detection.

Temporal masking functions for listeners with real and simulated hearing loss

PubMed Central

Desloge, Joseph G.; Reed, Charlotte M.; Braida, Louis D.; Perez, Zachary D.; Delhorne, Lorraine A.

2011-01-01

A functional simulation of hearing loss was evaluated in its ability to reproduce the temporal masking functions for eight listeners with mild to severe sensorineural hearing loss. Each audiometric loss was simulated in a group of age-matched normal-hearing listeners through a combination of spectrally-shaped masking noise and multi-band expansion. Temporal-masking functions were obtained in both groups of listeners using a forward-masking paradigm in which the level of a 110-ms masker required to just mask a 10-ms fixed-level probe (5-10 dB SL) was measured as a function of the time delay between the masker offset and probe onset. At each of four probe frequencies (500, 1000, 2000, and 4000 Hz), temporal-masking functions were obtained using maskers that were 0.55, 1.0, and 1.15 times the probe frequency. The slopes and y-intercepts of the masking functions were not significantly different for listeners with real and simulated hearing loss. The y-intercepts were positively correlated with level of hearing loss while the slopes were negatively correlated. The ratio of the slopes obtained with the low-frequency maskers relative to the on-frequency maskers was similar for both groups of listeners and indicated a smaller compressive effect than that observed in normal-hearing listeners. PMID:21877806

A novel magneto-DNA duplex probe for bacterial DNA detection based on exonuclease III-aided cycling amplification.

PubMed

Zeng, Yan; Wan, Yi; Zhang, Dun; Qi, Peng

2015-01-01

A novel magneto-DNA duplex probe for bacterial DNA detection based on exonuclease III (Exo-III) aided cycling amplification has been developed. This magneto-DNA duplex probe contains a partly hybrid fluorophore-modified capture probe and a fluorophore-modified signal probe with magnetic microparticle as carrier. In the presence of a perfectly matched target bacterial DNA, blunt 3'-terminus of the capture probe is formed, activating the Exo-III aided cycling amplification. Thus, Exo-III catalyzes the stepwise removal of mononucleotides from this terminus, releasing both fluorophore-modified signal probe, fluorescent dyes of the capture probe and target DNA. The released target DNA then starts a new cycle, while released fluorescent fragments are recovered with magnetic separation for fluorescence signal collection. This system exhibited sensitive detection of bacterial DNA, with a detection limit of 14 pM because of the unique cleavage function of Exo-III, high fluorescence intensity, and separating function of magneto-DNA duplex probes. Besides this sensitivity, this strategy exhibited excellent selectivity with mismatched bacterial DNA targets and other bacterial species targets and good applicability in real seawater samples, hence, this strategy could be potentially used for qualitative and quantitative analysis of bacteria. Copyright © 2014 Elsevier B.V. All rights reserved.

Measurement of Electron Density Using the Multipole Resonance Probe, Langmuir Probe and Optical Emission Spectroscopy in Low Pressure Plasmas with Different Electron Energy Distribution Functions

NASA Astrophysics Data System (ADS)

Oberberg, Moritz; Bibinov, Nikita; Ries, Stefan; Awakowicz, Peter; Institute of Electrical Engineering; Plasma Technology Team

2016-09-01

In recently publication, the young diagnostic tool Multipole Resonance Probe (MRP) for electron density measurements was introduced. It is based on active plasma resonance spectroscopy (APRS). The probe was simulated und evaluated for different devices. The geometrical and electrical symmetry simplifies the APRS model, so that the electron density can be easily calculated from the measured resonance. In this work, low pressure nitrogen mixture plasmas with different electron energy distribution functions (EEDF) are investigated. The results of the MRP measurement are compared with measurements of a Langmuir Probe (LP) and Optical Emission Spectroscopy (OES). Probes and OES measure in different regimes of kinetic electron energy. Both probes measure electrons with low kinetic energy (<10 eV), whereas the OES is influenced by electrons with high kinetic energy which are needed for transitions of molecule bands. By the determination of the absolute intensity of N2(C-B) and N2+(B-X)electron temperature and density can be calculated. In a non-maxwellian plasma, all plasma diagnostics need to be combined.

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.

Fluorescent coumarin-based probe for cysteine and homocysteine with live cell application

NASA Astrophysics Data System (ADS)

Wei, Ling-Fang; Thirumalaivasan, Natesan; Liao, Yu-Cheng; Wu, Shu-Pao

2017-08-01

Cysteine (Cys) and homocysteine (Hcy) are two of important biological thiols and function as important roles in several biological processes. The development of Cys and Hcy probes will help to explore the functions of biothiols in biological systems. In this work, a new coumarin-based probe AC, containing an acryloyl moiety, was developed for Cys and Hcy detection in cells. Cys and Hcy undergo a nucleophilic addition and subsequent cyclization reaction to remove to the acryloyl group and yield a fluorescent product, 7-hydroxylcomuarin. The probe AC showed good selectivity for cysteine and homocysteine over glutathione and other amino acids and had low detection limits of 65 nM for Cys and 79 nM for Hcy, respectively. Additionally, confocal imaging experiments demonstrated that the probe AC can be applied to visualize Cys and Hcy in living cells.

Note: A calibration method to determine the lumped-circuit parameters of a magnetic probe.

PubMed

Li, Fuming; Chen, Zhipeng; Zhu, Lizhi; Liu, Hai; Wang, Zhijiang; Zhuang, Ge

2016-06-01

This paper describes a novel method to determine the lumped-circuit parameters of a magnetic inductive probe for calibration by using Helmholtz coils with high frequency power supply (frequency range: 10 kHz-400 kHz). The whole calibration circuit system can be separated into two parts: "generator" circuit and "receiver" circuit. By implementing the Fourier transform, two analytical lumped-circuit models, with respect to these separated circuits, are constructed to obtain the transfer function between each other. Herein, the precise lumped-circuit parameters (including the resistance, inductance, and capacitance) of the magnetic probe can be determined by fitting the experimental data to the transfer function. Regarding the fitting results, the finite impedance of magnetic probe can be used to analyze the transmission of a high-frequency signal between magnetic probes, cables, and acquisition system.

Coating flexible probes with an ultra fast degrading polymer to aid in tissue insertion

PubMed Central

Wang, Shuwu; Singh, Sagar; Damodaran, Vinod B.; Kaplan, Hilton M.; Kohn, Joachim; Shreiber, David I.; Zahn, Jeffrey D.

2016-01-01

We report a fabrication process for coating neural probes with an ultrafast degrading polymer to create consistent and reproducible devices for neural tissue insertion. The rigid polymer coating acts as a probe insertion aid, but resorbs within hours post-implantation. Despite the feasibility for short term neural recordings from currently available neural prosthetic devices, most of these devices suffer from long term gliosis, which isolates the probes from adjacent neurons, increasing the recording impedance and stimulation threshold. The size and stiffness of implanted probes have been identified as critical factors that lead to this long term gliosis. Smaller, more flexible probes that match the mechanical properties of brain tissue could allow better long term integration by limiting the mechanical disruption of the surrounding tissue during and after probe insertion, while being flexible enough to deform with the tissue during brain movement. However, these small flexible probes inherently lack the mechanical strength to penetrate the brain on their own. In this work, we have developed a micromolding method for coating a non-functional miniaturized SU-8 probe with an ultrafast degrading tyrosine-derived polycarbonate (E5005(2K)). Coated, non-functionalized probes of varying dimensions were reproducibly fabricated with high yields. The polymer erosion/degradation profiles of the probes were characterized in vitro. The probes were also mechanically characterized in ex vivo brain tissue models by measuring buckling and insertion forces during probe insertion. The results demonstrate the ability to produce polymer coated probes of consistent quality for future in vivo use, for example to study the effects of different design parameters that may affect tissue response during long term chronic intra-cortical microelectrode neural recordings. PMID:25681971

Coating flexible probes with an ultra fast degrading polymer to aid in tissue insertion.

PubMed

Lo, Meng-chen; Wang, Shuwu; Singh, Sagar; Damodaran, Vinod B; Kaplan, Hilton M; Kohn, Joachim; Shreiber, David I; Zahn, Jeffrey D

2015-04-01

We report a fabrication process for coating neural probes with an ultrafast degrading polymer to create consistent and reproducible devices for neural tissue insertion. The rigid polymer coating acts as a probe insertion aid, but resorbs within hours post-implantation. Despite the feasibility for short term neural recordings from currently available neural prosthetic devices, most of these devices suffer from long term gliosis, which isolates the probes from adjacent neurons, increasing the recording impedance and stimulation threshold. The size and stiffness of implanted probes have been identified as critical factors that lead to this long term gliosis. Smaller, more flexible probes that match the mechanical properties of brain tissue could allow better long term integration by limiting the mechanical disruption of the surrounding tissue during and after probe insertion, while being flexible enough to deform with the tissue during brain movement. However, these small flexible probes inherently lack the mechanical strength to penetrate the brain on their own. In this work, we have developed a micromolding method for coating a non-functional miniaturized SU-8 probe with an ultrafast degrading tyrosine-derived polycarbonate (E5005(2K)). Coated, non-functionalized probes of varying dimensions were reproducibly fabricated with high yields. The polymer erosion/degradation profiles of the probes were characterized in vitro. The probes were also mechanically characterized in ex vivo brain tissue models by measuring buckling and insertion forces during probe insertion. The results demonstrate the ability to produce polymer coated probes of consistent quality for future in vivo use, for example to study the effects of different design parameters that may affect tissue response during long term chronic intra-cortical microelectrode neural recordings.

Chemical Probes for the Functionalization of Polyketide Intermediates**

PubMed Central

Riva, Elena; Wilkening, Ina; Gazzola, Silvia; Li, W M Ariel; Smith, Luke; Leadlay, Peter F; Tosin, Manuela

2014-01-01

A library of functionalized chemical probes capable of reacting with ketosynthase-bound biosynthetic intermediates was prepared and utilized to explore in vivo polyketide diversification. Fermentation of ACP mutants of S. lasaliensis in the presence of the probes generated a range of unnatural polyketide derivatives, including novel putative lasalocid A derivatives characterized by variable aryl ketone moieties and linear polyketide chains (bearing alkyne/azide handles and fluorine) flanking the polyether scaffold. By providing direct information on microorganism tolerance and enzyme processing of unnatural malonyl-ACP analogues, as well as on the amenability of unnatural polyketides to further structural modifications, the chemical probes constitute invaluable tools for the development of novel mutasynthesis and synthetic biology. PMID:25212788

Preventing probe induced topography correlated artifacts in Kelvin Probe Force Microscopy.

PubMed

Polak, Leo; Wijngaarden, Rinke J

2016-12-01

Kelvin Probe Force Microscopy (KPFM) on samples with rough surface topography can be hindered by topography correlated artifacts. We show that, with the proper experimental configuration and using homogeneously metal coated probes, we are able to obtain amplitude modulation (AM) KPFM results on a gold coated sample with rough topography that are free from such artifacts. By inducing tip inhomogeneity through contact with the sample, clear potential variations appear in the KPFM image, which correlate with the surface topography and, thus, are probe induced artifacts. We find that switching to frequency modulation (FM) KPFM with such altered probes does not remove these artifacts. We also find that the induced tip inhomogeneity causes a lift height dependence of the KPFM measurement, which can therefore be used as a check for the presence of probe induced topography correlated artifacts. We attribute the observed effects to a work function difference between the tip and the rest of the probe and describe a model for such inhomogeneous probes that predicts lift height dependence and topography correlated artifacts for both AM and FM-KPFM methods. This work demonstrates that using a probe with a homogeneous work function and preventing tip changes is essential for KPFM on non-flat samples. From the three investigated probe coatings, PtIr, Au and TiN, the latter appears to be the most suitable, because of its better resistance against coating damage. Copyright © 2016 Elsevier B.V. All rights reserved.

A relay identification fluorescence probe for Fe3 + and phosphate anion and its applications

NASA Astrophysics Data System (ADS)

Tang, Xu; Wang, Yun; Han, Juan; Ni, Liang; Wang, Lei; Li, Longhua; Zhang, Huiqin; Li, Cheng; Li, Jing; Li, Haoran

2018-02-01

A simple relay identification fluorescence probe for Fe3 + and phosphate anion with ;on-off-on; switching was designed and synthesized based on the phenylthiazole and biphenylcarbonitrile. Probe 1 displayed highly selective and sensitive recognition to Fe3 + in HEPES aqueous buffer (EtOH/H2O = 2:8, v/v, pH = 7.4) solutions. The optimized structures and HOMO and LUMO of probe 1 and [1-Fe3 +] complex were obtained by the density functional theory (DFT) calculations with B3LYP as the exchange and correlation functional using a suite of Gaussian 09 programs. The [1-Fe3 +] complex solution also showed a high selectivity toward PO43 -. The lower limits of detection of probe 1 to Fe3 + and [1-Fe3 +] complex to PO43 - were estimated to 1.09 × 10- 7 M and 1.86 × 10- 7 M. Besides, the probe 1 also was used to detected the target ions in real water sample and living cells successfully.

Look-Ahead Distance of a fiber probe used to assist neurosurgery: Phantom and Monte Carlo study

NASA Astrophysics Data System (ADS)

Qian, Zhiyu; Victor, Sunder S.; Gu, Yueqing; Giller, Cole A.; Liu, Hanli

2003-08-01

A short-separation, optical reflectance probe has been developed to assist the neurosurgeon in functional neurosurgery for accurate localization of the surgical target. Because of the scattering nature of tissue, the optical probe has a "Look Ahead Distance" (LAD), at which the measured optical reflectance starts to "see" or "sense" the underlying brain structure due to the difference in light scattering of tissue. To quantify the LAD, 2-layer laboratory phantoms have been developed to mimic gray and white matter of the brain, and Monte Carlo simulations have been also used to confirm the experimental findings. Based on both the laboratory and simulation results, a quantitative empirical equation is developed to express the LAD as a function of scattering coefficient of the measured tissue for a 400-micron-diameter fiber probe. The quantified LAD of the probe is highly desirable so as to improve the spatial resolution of the probe for better surgery guidance.

Fluorescent Probes for Single-Step Detection and Proteomic Profiling of Histone Deacetylases.

PubMed

Xie, Yusheng; Ge, Jingyan; Lei, Haipeng; Peng, Bo; Zhang, Huatang; Wang, Danyang; Pan, Sijun; Chen, Ganchao; Chen, Lanfang; Wang, Yi; Hao, Quan; Yao, Shao Q; Sun, Hongyan

2016-12-07

Histone deacetylases (HDACs) play important roles in regulating various physiological and pathological processes. Developing fluorescent probes capable of detecting HDAC activity can help further elucidate the roles of HDACs in biology. In this study, we first developed a set of activity-based fluorescent probes by incorporating the Kac residue and the O-NBD group. Upon enzymatic removal of the acetyl group in the Kac residue, the released free amine reacted intramolecularly with the O-NBD moiety, resulting in turn-on fluorescence. These designed probes are capable of detecting HDAC activity in a continuous fashion, thereby eliminating the extra step of fluorescence development. Remarkably, the amount of turn-on fluorescence can be as high as 50-fold, which is superior to the existing one-step HDAC fluorescent probes. Inhibition experiments further proved that the probes can serve as useful tools for screening HDAC inhibitors. Building on these results, we moved on and designed a dual-purpose fluorescent probe by introducing a diazirine photo-cross-linker into the probe. The resulting probe was not only capable of reporting enzymatic activity but also able to directly identify and capture the protein targets from the complex cellular environment. By combining a fluorometric method and in-gel fluorescence scanning technique, we found that epigenetic readers and erasers can be readily identified and differentiated using a single probe. This is not achievable with traditional photoaffinity probes. In light of the prominent properties and the diverse functions of this newly developed probe, we envision that it can provide a robust tool for functional analysis of HDACs and facilitate future drug discovery in epigenetics.

Pump-probe Kelvin-probe force microscopy: Principle of operation and resolution limits

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

Murawski, J.; Graupner, T.; Milde, P., E-mail: peter.milde@tu-dresden.de

Knowledge on surface potential dynamics is crucial for understanding the performance of modern-type nanoscale devices. We describe an electrical pump-probe approach in Kelvin-probe force microscopy that enables a quantitative measurement of dynamic surface potentials at nanosecond-time and nanometer-length scales. Also, we investigate the performance of pump-probe Kelvin-probe force microscopy with respect to the relevant experimental parameters. We exemplify a measurement on an organic field effect transistor that verifies the undisturbed functionality of our pump-probe approach in terms of simultaneous and quantitative mapping of topographic and electronic information at a high lateral and temporal resolution.

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.

Oligonucleotides as probes for studying polymerization reactions in dilute aqueous solution: II. Polycondensations

NASA Technical Reports Server (NTRS)

Kolb, V.; Orgel, L. E.

1995-01-01

We have prepared a [32P]-labeled oligonucleotide probe carrying a ureido (-NH-CO-NH2) function at its 3'-terminus. This labeled oligomer was used to study polycondensations of urea and formaldehyde and of various phenols and formaldehyde in aqueous solution. The formation of formaldehyde copolymers attached to the amido-function of the probe was monitored by gel electrophoresis. Our results are generally in agreement with those obtained using conventional techniques. Our method is suitable for monitoring potentially prebiotic polycondensation reactions involving formaldehyde.

Oligonucleotides as probes for studying polymerization reactions in dilute aqueous solution. 2: Polycondensations

NASA Technical Reports Server (NTRS)

Kolb, Vera; Orgel, Leslie E.

1995-01-01

We have prepared a (P-32)-labeled oligonucleotide probe carrying a ureido (-NH-CO-NH2) function at its 3'-terminus. This labeled oligomer was used to study polycondensations of urea and formaldehyde and of various phenols and formaldehyde in aqueous solution. The formation of formaldehyde copolymers attached to the amido-function of the probe was monitored by gel electrophoresis. Our results are generally in agreement with those obtained using conventional techniques. Our method is suitable for monitoring potentially prebiotic polycondensation reactions involving formaldehyde.

U-Shaped and Surface Functionalized Polymer Optical Fiber Probe for Glucose Detection.

PubMed

Azkune, Mikel; Ruiz-Rubio, Leire; Aldabaldetreku, Gotzon; Arrospide, Eneko; Pérez-Álvarez, Leyre; Bikandi, Iñaki; Zubia, Joseba; Vilas-Vilela, Jose Luis

2017-12-25

In this work we show an optical fiber evanescent wave absorption probe for glucose detection in different physiological media. High selectivity is achieved by functionalizing the surface of an only-core poly(methyl methacrylate) (PMMA) polymer optical fiber with phenilboronic groups, and enhanced sensitivity by using a U-shaped geometry. Employing a supercontinuum light source and a high-resolution spectrometer, absorption measurements are performed in the broadband visible light spectrum. Experimental results suggest the feasibility of such a fiber probe as a low-cost and selective glucose detector.

Teaching Special Education Teachers How to Conduct Functional Analysis in Natural Settings

ERIC Educational Resources Information Center

Erbas, Dilek; Tekin-Iftar, Elif; Yucesoy, Serife

2006-01-01

Effects of a training program utilized to teach how to conduct functional analysis process to teachers of children with developmental disabilities was examined. Furthermore, teachers' opinions regarding this process were investigated. A multiple probe design across subjects with probe conditions was used. Teacher training was in two phases. In the…

[Development of fluorescent probes for bone imaging in vivo ~Fluorescent probes for intravital imaging of osteoclast activity~.

PubMed

Minoshima, Masafumi; Kikuchi, Kazuya

Fluorescent molecules are widely used as a tool to directly visualize target biomolecules in vivo. Fluorescent probes have the advantage that desired function can be rendered based on rational design. For bone-imaging fluorescent probes in vivo, they should be delivered to bone tissue upon administration. Recently, a fluorescent probe for detecting osteoclast activity was developed. The fluorescent probe has acid-sensitive fluorescence property, specific delivery to bone tissue, and durability against laser irradiation, which enabled real-time intravital imaging of bone-resorbing osteoclasts for a long period of time.

Non-toxic fluorescent phosphonium probes to detect mitochondrial potential.

PubMed

Šarić, Ana; Crnolatac, Ivo; Bouillaud, Frédéric; Sobočanec, Sandra; Mikecin, Ana-Matea; Mačak Šafranko, Željka; Delgeorgiev, Todor; Piantanida, Ivo; Balog, Tihomir; Petit, Patrice X

2017-03-22

We evaluated our phosphonium-based fluorescent probes for selective staining of mitochondria. Currently used probes for monitoring mitochondrial membrane potential show varying degrees of interference with cell metabolism, photo-induced damage and probe binding. Here presented probes are characterised by highly efficient cellular uptake and specific accumulation in mitochondria. Fluorescent detection of the probes was accomplished using flow cytometry and confocal microscopy imaging of yeast and mammalian cells. Toxicity analysis (impedimetry-xCELLigence for the cellular proliferation and Seahorse technology for respiratory properties) confirms that these dyes exhibit no-toxicity on mitochondrial or cellular functioning even for long time incubation. The excellent chemical and photophysical stability of the dyes makes them promising leads toward improved fluorescent probes. Therefore, the probes described here offer to circumvent the problems associated with existing-probe's limitations.

Resistance Probes in the Science Laboratory Part I. The Thermistor Thermometer.

ERIC Educational Resources Information Center

Powers, Michael H.

1987-01-01

Describes the functioning of temperature transducers, or thermistors. Discusses the interface connections between thermistors and the game-port of several kinds of microcomputers. Demonstrates how to construct a thermistor probe and suggests several applications of the use of such probes in various scientific experiments. (TW)

Uprobe: a genome-wide universal probe resource for comparative physical mapping in vertebrates.

PubMed

Kellner, Wendy A; Sullivan, Robert T; Carlson, Brian H; Thomas, James W

2005-01-01

Interspecies comparisons are important for deciphering the functional content and evolution of genomes. The expansive array of >70 public vertebrate genomic bacterial artificial chromosome (BAC) libraries can provide a means of comparative mapping, sequencing, and functional analysis of targeted chromosomal segments that is independent and complementary to whole-genome sequencing. However, at the present time, no complementary resource exists for the efficient targeted physical mapping of the majority of these BAC libraries. Universal overgo-hybridization probes, designed from regions of sequenced genomes that are highly conserved between species, have been demonstrated to be an effective resource for the isolation of orthologous regions from multiple BAC libraries in parallel. Here we report the application of the universal probe design principal across entire genomes, and the subsequent creation of a complementary probe resource, Uprobe, for screening vertebrate BAC libraries. Uprobe currently consists of whole-genome sets of universal overgo-hybridization probes designed for screening mammalian or avian/reptilian libraries. Retrospective analysis, experimental validation of the probe design process on a panel of representative BAC libraries, and estimates of probe coverage across the genome indicate that the majority of all eutherian and avian/reptilian genes or regions of interest can be isolated using Uprobe. Future implementation of the universal probe design strategy will be used to create an expanded number of whole-genome probe sets that will encompass all vertebrate genomes.

High Temperature Ultrasonic Probe and Pulse-Echo Probe Mounting Fixture for Testing and Blind Alignment on Steam Pipes

NASA Technical Reports Server (NTRS)

Lih, Shyh-Shiuh (Inventor); Takano, Nobuyuki (Inventor); Lee, Hyeong Jae (Inventor); Bao, Xiaoqi (Inventor); Badescu, Mircea (Inventor); Bar-Cohen, Yoseph (Inventor); Sherrit, Stewart (Inventor); Ostlund, Patrick N. (Inventor)

2017-01-01

A high temperature ultrasonic probe and a mounting fixture for attaching and aligning the probe to a steam pipe using blind alignment. The high temperature ultrasonic probe includes a piezoelectric transducer having a high temperature. The probe provides both transmitting and receiving functionality. The mounting fixture allows the high temperature ultrasonic probe to be accurately aligned to the bottom external surface of the steam pipe so that the presence of liquid water in the steam pipe can be monitored. The mounting fixture with a mounted high temperature ultrasonic probe are used to conduct health monitoring of steam pipes and to track the height of condensed water through the wall in real-time.

Probing dimensionality using a simplified 4-probe method.

PubMed

Kjeldby, Snorre B; Evenstad, Otto M; Cooil, Simon P; Wells, Justin W

2017-10-04

4-probe electrical measurements have been in existence for many decades. One of the most useful aspects of the 4-probe method is that it is not only possible to find the resistivity of a sample (independently of the contact resistances), but that it is also possible to probe the dimensionality of the sample. In theory, this is straightforward to achieve by measuring the 4-probe resistance as a function of probe separation. In practice, it is challenging to move all four probes with sufficient precision over the necessary range. Here, we present an alternative approach. We demonstrate that the dimensionality of the conductive path within a sample can be directly probed using a modified 4-probe method in which an unconventional geometry is exploited; three of the probes are rigidly fixed, and the position of only one probe is changed. This allows 2D and 3D (and other) contributions the to resistivity to be readily disentangled. The required experimental instrumentation can be vastly simplified relative to traditional variable spacing 4-probe instruments.

Cpg-ODN, a TLR9 Agonist, Aggravates Myocardial Ischemia/Reperfusion Injury by Activation of TLR9-P38 MAPK Signaling.

PubMed

Xie, Liang; He, Songqing; Kong, Na; Zhu, Ying; Tang, Yi; Li, Jianhua; Liu, Zhengbing; Liu, Jing; Gong, Jianbin

2018-06-19

Toll-like receptors (TLRs) have been implicated in myocardial ischemia/ reperfusion (I/R) injury. We examined the effect of CpG-oligodeoxynucleotide (ODN) on myocardial I/R injury. Male Sprague-Dawley rats were treated with either CpG-ODN or control ODN 1 h prior to myocardial ischemia (30 min) followed by reperfusion. Rats treated with phosphate-buffered saline (PBS) served as I/R controls (n = 8/group). Infarct size was determined by 2,3,5-triphenyltetrazolium chloride and Evans blue straining. Cardiac function was examined by echocardiography before and up to 14 days after myocardial I/R. CpG-ODN administration significantly increased infarct size and reduced cardiac function and survival rate after myocardial I/R, compared to the PBS-treated I/R group. Control-ODN did not alter I/R-induced myocardial infarct size, cardiac dysfunction, and survival rate. Additionally, CpG-ODN promoted I/R-induced myocardial apoptosis and cleaved caspase-3 levels in the myocardium. CpG-ODN increased TLR9 activation and p38 phosphorylation in the myocardium. In vitro data also suggested that CpG-ODN treatment induced TLR9 activation and p38 phosphorylation. Importantly, p38 mitogen-activated protein kinase (MAPK) inhibition abolished CpG-ODN-induced cardiac injury. CpG-ODN, the TLR9 ligand, accelerates myocardial I/R injury. The mechanisms involve activation of the TLR9-p38 MAPK signaling pathway. © 2018 The Author(s). Published by S. Karger AG, Basel.

Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications

PubMed Central

Mo, Liuting; Lu, Chun-Hua; Fu, Ting

2016-01-01

Hydrogels are crosslinked hydrophilic polymers that can absorb a large amount of water. By their hydrophilic, biocompatible and highly tunable nature, hydrogels can be tailored for applications in bioanalysis and biomedicine. Of particular interest are DNA-based hydrogels owing to the unique features of nucleic acids. Since the discovery of DNA double helical structure, interest in DNA has expanded beyond its genetic role to applications in nanotechnology and materials science. In particular, DNA-based hydrogels present such remarkable features as stability, flexibility, precise programmability, stimuli-responsive DNA conformations, facile synthesis and modification. Moreover, functional nucleic acids (FNAs) have allowed the construction of hydrogels based on aptamers, DNAzymes, i-motif nanostructures, siRNAs and CpG oligodeoxynucleotides to provide additional molecular recognition, catalytic activities and therapeutic potential, making them key players in biological analysis and biomedical applications. To date, a variety of applications have been demonstrated with FNA-based hydrogels, including biosensing, environmental analysis, controlled drug release, cell adhesion and targeted cancer therapy. In this review, we focus on advances in the development of FNA-based hydrogels, which have fully incorporated both the unique features of FNAs and DNA-based hydrogels. We first introduce different strategies for constructing DNA-based hydrogels. Subsequently, various types of FNAs and the most recent developments of FNA-based hydrogels for bioanalytical and biomedical applications are described with some selected examples. Finally, the review provides an insight into the remaining challenges and future perspectives of FNA-based hydrogels. PMID:26758955

Dual-probe near-field fiber head with gap servo control for data storage applications.

PubMed

Fang, Jen-Yu; Tien, Chung-Hao; Shieh, Han-Ping D

2007-10-29

We present a novel fiber-based near-field optical head consisting of a straw-shaped writing probe and a flat gap sensing probe. The straw-shaped probe with a C-aperture on the end face exhibits enhanced transmission by a factor of 3 orders of magnitude over a conventional fiber probe due to a hybrid effect that excites both propagation modes and surface plasmon waves. In the gap sensing probe, the spacing between the probe and the disk surface functions as an external cavity. The high sensitivity of the output power to the change in the gap width is used as a feedback control signal. We characterize and design the straw-shaped writing probe and the flat gap sensing probe. The dual-probe system is installed on a conventional biaxial actuator to demonstrate the capability of flying over a disk surface with nanometer position precision.

Effects of Computer and Classroom Simulations to Teach Students with Various Exceptionalities to Locate Apparel Sizes

ERIC Educational Resources Information Center

Bramlett, Virginia; Ayres, Kevin M.; Douglas, Karen H.; Cihak, David F.

2011-01-01

This study evaluated the effects of simulation training to teach functional community skills to four students with developmental disabilities in middle school. A multiple probe across participants and multiple probe across behaviors allowed for an evaluation of a functional relation between simulation and skill acquisition. Students learned how to…

Probe-Hole Field Emission Microscope System Controlled by Computer

NASA Astrophysics Data System (ADS)

Gong, Yunming; Zeng, Haishan

1991-09-01

A probe-hole field emission microscope system, controlled by an Apple II computer, has been developed and operated successfully for measuring the work function of a single crystal plane. The work functions on the clean W(100) and W(111) planes are measured to be 4.67 eV and 4.45 eV, respectively.

Salience Is Only Briefly Represented: Evidence from Probe-Detection Performance

ERIC Educational Resources Information Center

Donk, Mieke; Soesman, Leroy

2010-01-01

Salient objects in the visual field tend to capture attention. The present study aimed to examine the time-course of salience effects using a probe-detection task. Eight experiments investigated how the salience of different orientation singletons affected probe reaction time as a function of stimulus onset asynchrony (SOA) between the…

Fiber-optic temperature probe system for inner body

NASA Astrophysics Data System (ADS)

Liu, Bo; Deng, Xing-Zhong; Cao, Wei; Cheng, Xianping; Xie, Tuqiang; Zhong, Zugen

1991-08-01

The authors have designed a fiber-optic temperature probe system that can quickly insert its probe into bodies to measure temperature. Its thermometer unit has the function of program- controlled zeroing. The single-chip microcomputer is used to control the whole system and process data. The sample system has been tested in a coal furnace.

Frequency correlation of probe waves backscattered from small scale ionospheric irregularities generated by high power HF radio waves

NASA Astrophysics Data System (ADS)

Puchkov, V. A.

2016-09-01

Aspect sensitive scattering of multi-frequency probe signals by artificial, magnetic field aligned density irregularities (with transverse size ∼ 1- 10 m) generated in the ionosphere by powerful radio waves is considered. Fluctuations of received signals depending on stochastic properties of the irregularities are calculated. It is shown that in the case of HF probe waves two mechanisms may contribute to the scattered signal fluctuations. The first one is due to the propagation of probe waves in the ionospheric plasma as in a randomly inhomogeneous medium. The second one lies in non-stationary stochastic behavior of irregularities which satisfy the Bragg conditions for the scattering geometry and therefore constitute centers of scattering. In the probe wave frequency band of the order of 10-100 MHz the second mechanism dominates which delivers opportunity to recover some properties of artificial irregularities from received signals. Correlation function of backscattered probe waves with close frequencies is calculated, and it is shown that detailed spatial distribution of irregularities along the scattering vector can be found experimentally from observations of this correlation function.

Indirect Validation of Probe Speed Data on Arterial Corridors

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

Eshragh, Sepideh; Young, Stanley E.; Sharifi, Elham

This study aimed to estimate the accuracy of probe speed data on arterial corridors on the basis of roadway geometric attributes and functional classification. It was assumed that functional class (medium and low) along with other road characteristics (such as weighted average of the annual average daily traffic, average signal density, average access point density, and average speed) were available as correlation factors to estimate the accuracy of probe traffic data. This study tested these factors as predictors of the fidelity of probe traffic data by using the results of an extensive validation exercise. This study showed strong correlations betweenmore » these geometric attributes and the accuracy of probe data when they were assessed by using average absolute speed error. Linear models were regressed to existing data to estimate appropriate models for medium- and low-type arterial corridors. The proposed models for medium- and low-type arterials were validated further on the basis of the results of a slowdown analysis. These models can be used to predict the accuracy of probe data indirectly in medium and low types of arterial corridors.« less

Coherence specific signal detection via chiral pump-probe spectroscopy.

PubMed

Holdaway, David I H; Collini, Elisabetta; Olaya-Castro, Alexandra

2016-05-21

We examine transient circular dichroism (TRCD) spectroscopy as a technique to investigate signatures of exciton coherence dynamics under the influence of structured vibrational environments. We consider a pump-probe configuration with a linearly polarized pump and a circularly polarized probe, with a variable angle θ between the two directions of propagation. In our theoretical formalism the signal is decomposed in chiral and achiral doorway and window functions. Using this formalism, we show that the chiral doorway component, which beats during the population time, can be isolated by comparing signals with different values of θ. As in the majority of time-resolved pump-probe spectroscopy, the overall TRCD response shows signatures of both excited and ground state dynamics. However, we demonstrate that the chiral doorway function has only a weak ground state contribution, which can generally be neglected if an impulsive pump pulse is used. These findings suggest that the pump-probe configuration of optical TRCD in the impulsive limit has the potential to unambiguously probe quantum coherence beating in the excited state. We present numerical results for theoretical signals in an example dimer system.

Dynamic pressure probe response tests for robust measurements in periodic flows close to probe resonating frequency

NASA Astrophysics Data System (ADS)

Ceyhun Şahin, Fatma; Schiffmann, Jürg

2018-02-01

A single-hole probe was designed to measure steady and periodic flows with high fluctuation amplitudes and with minimal flow intrusion. Because of its high aspect ratio, estimations showed that the probe resonates at a frequency two orders of magnitude lower than the fast response sensor cut-off frequencies. The high fluctuation amplitudes cause a non-linear behavior of the probe and available models are neither adequate for a quantitative estimation of the resonating frequencies nor for predicting the system damping. Instead, a non-linear data correction procedure based on individual transfer functions defined for each harmonic contribution is introduced for pneumatic probes that allows to extend their operating range beyond the resonating frequencies and linear dynamics. This data correction procedure was assessed on a miniature single-hole probe of 0.35 mm inner diameter which was designed to measure flow speed and direction. For the reliable use of such a probe in periodic flows, its frequency response was reproduced with a siren disk, which allows exciting the probe up to 10 kHz with peak-to-peak amplitudes ranging between 20%-170% of the absolute mean pressure. The effect of the probe interior design on the phase lag and amplitude distortion in periodic flow measurements was investigated on probes with similar inner diameters and different lengths or similar aspect ratios (L/D) and different total interior volumes. The results suggest that while the tube length consistently sets the resonance frequency, the internal total volume affects the non-linear dynamic response in terms of varying gain functions. A detailed analysis of the introduced calibration methodology shows that the goodness of the reconstructed data compared to the reference data is above 75% for fundamental frequencies up to twice the probe resonance frequency. The results clearly suggest that the introduced procedure is adequate to capture non-linear pneumatic probe dynamics and to reproduce time-resolved data far above probe resonant frequency.

Non-toxic fluorescent phosphonium probes to detect mitochondrial potential

NASA Astrophysics Data System (ADS)

Šarić, Ana; Crnolatac, Ivo; Bouillaud, Frédéric; Sobočanec, Sandra; Mikecin, Ana-Matea; Mačak Šafranko, Željka; Delgeorgiev, Todor; Piantanida, Ivo; Balog, Tihomir; Petit, Patrice X.

2017-03-01

We evaluated our phosphonium-based fluorescent probes for selective staining of mitochondria. Currently used probes for monitoring mitochondrial membrane potential show varying degrees of interference with cell metabolism, photo-induced damage and probe binding. Here presented probes are characterised by highly efficient cellular uptake and specific accumulation in mitochondria. Fluorescent detection of the probes was accomplished using flow cytometry and confocal microscopy imaging of yeast and mammalian cells. Toxicity analysis (impedimetry—xCELLigence for the cellular proliferation and Seahorse technology for respiratory properties) confirms that these dyes exhibit no-toxicity on mitochondrial or cellular functioning even for long time incubation. The excellent chemical and photophysical stability of the dyes makes them promising leads toward improved fluorescent probes. Therefore, the probes described here offer to circumvent the problems associated with existing-probe’s limitations.

Framework for reanalysis of publicly available Affymetrix® GeneChip® data sets based on functional regions of interest.

PubMed

Saka, Ernur; Harrison, Benjamin J; West, Kirk; Petruska, Jeffrey C; Rouchka, Eric C

2017-12-06

Since the introduction of microarrays in 1995, researchers world-wide have used both commercial and custom-designed microarrays for understanding differential expression of transcribed genes. Public databases such as ArrayExpress and the Gene Expression Omnibus (GEO) have made millions of samples readily available. One main drawback to microarray data analysis involves the selection of probes to represent a specific transcript of interest, particularly in light of the fact that transcript-specific knowledge (notably alternative splicing) is dynamic in nature. We therefore developed a framework for reannotating and reassigning probe groups for Affymetrix® GeneChip® technology based on functional regions of interest. This framework addresses three issues of Affymetrix® GeneChip® data analyses: removing nonspecific probes, updating probe target mapping based on the latest genome knowledge and grouping probes into gene, transcript and region-based (UTR, individual exon, CDS) probe sets. Updated gene and transcript probe sets provide more specific analysis results based on current genomic and transcriptomic knowledge. The framework selects unique probes, aligns them to gene annotations and generates a custom Chip Description File (CDF). The analysis reveals only 87% of the Affymetrix® GeneChip® HG-U133 Plus 2 probes uniquely align to the current hg38 human assembly without mismatches. We also tested new mappings on the publicly available data series using rat and human data from GSE48611 and GSE72551 obtained from GEO, and illustrate that functional grouping allows for the subtle detection of regions of interest likely to have phenotypical consequences. Through reanalysis of the publicly available data series GSE48611 and GSE72551, we profiled the contribution of UTR and CDS regions to the gene expression levels globally. The comparison between region and gene based results indicated that the detected expressed genes by gene-based and region-based CDFs show high consistency and regions based results allows us to detection of changes in transcript formation.

Criteria for the selection of focusing ultrasonic probes

NASA Technical Reports Server (NTRS)

Schlengermann, U.

1978-01-01

The principles of operation employed in the focusing of a sound field are considered, taking into account the use of solid and liquid coupling media. The focusing limits for a given transducer are investigated. As a diffraction phenomenon, focusing is a function of the system dimensions, the frequency, and the sound velocity. The frequency and the material used for the lenses are in most cases determined in accordance with considerations regarding sound propagation. Changes in the focus are therefore effected mainly by the selection of transducer and lens dimensions. The functions of the focusing factor for a normal immersion probe and a direct contact angle probe are represented in graphs. The deviation of the appropriate parametric values for an ultrasonic probe is illustrated with the aid of examples.

Dopamine-functionalized InP/ZnS quantum dots as fluorescence probes for the detection of adenosine in microfluidic chip.

PubMed

Ankireddy, Seshadri Reddy; Kim, Jongsung

2015-01-01

Microbeads are frequently used as solid supports for biomolecules such as proteins and nucleic acids in heterogeneous microfluidic assays. Chip-based, quantum dot (QD)-bead-biomolecule probes have been used for the detection of various types of DNA. In this study, we developed dopamine (DA)-functionalized InP/ZnS QDs (QDs-DA) as fluorescence probes for the detection of adenosine in microfluidic chips. The photoluminescence (PL) intensity of the QDs-DA is quenched by Zn(2+) because of the strong coordination interactions. In the presence of adenosine, Zn(2+) cations preferentially bind to adenosine, and the PL intensity of the QDs-DA is recovered. A polydimethylsiloxane-based microfluidic chip was fabricated, and adenosine detection was confirmed using QDs-DA probes.

Dopamine-functionalized InP/ZnS quantum dots as fluorescence probes for the detection of adenosine in microfluidic chip

PubMed Central

Ankireddy, Seshadri Reddy; Kim, Jongsung

2015-01-01

Microbeads are frequently used as solid supports for biomolecules such as proteins and nucleic acids in heterogeneous microfluidic assays. Chip-based, quantum dot (QD)-bead-biomolecule probes have been used for the detection of various types of DNA. In this study, we developed dopamine (DA)-functionalized InP/ZnS QDs (QDs-DA) as fluorescence probes for the detection of adenosine in microfluidic chips. The photoluminescence (PL) intensity of the QDs-DA is quenched by Zn2+ because of the strong coordination interactions. In the presence of adenosine, Zn2+ cations preferentially bind to adenosine, and the PL intensity of the QDs-DA is recovered. A polydimethylsiloxane-based microfluidic chip was fabricated, and adenosine detection was confirmed using QDs-DA probes. PMID:26347351

Characteristics of Ion Distribution Functions in Dipolarizing FluxBundles: THEMIS Event Studies

NASA Astrophysics Data System (ADS)

Runov, A.; Artemyev, A.; Birn, J.; Pritchett, P. L.; Zhou, X.

2016-12-01

Taking advantage of multi-point observations from repeating configuration of the Time History of Events and Macroscale Interactions during Substorms (THEMIS) fleet with probe separation of 1 to 2 Earth radii (RE) along X, Y, and Z in the geocentric solar magnetospheric system (GSM), we study ion distribution functions observed by the probes during three transient dipolarization events. Comparing observations by the multiple probes, we characterize changes in the ion distribution functions with respect to geocentric distance (X), cross-tail probe separation (Y), and levels of |Bx|, which characterize the distance from the neutral sheet. We examined 2-D and 1-D cuts of the 3-D velocity distribution functions by the {Vb,Vbxv} plane. The results indicate that the velocity distribution functions observed inside the dipolarizing flux bundles (DFB) close to the magnetic equator are often perpendicularly anisotropic for velocities Vth≤v≤2Vth, where Vth is the ion thermal velocity. Ions of higher energies (v>2Vth) are isotropic. Hence, interaction of DFBs and ambient ions may result in the perpendicular anisotropy of the injecting energetic ions, which is an important factor for plasma waves and instabilities excitation and further particle acceleration in the inner magnetosphere. We also compare the observations with the results of test-particles and PIC simulations.

Intercomparison of Microphysical Properties Derived from In-Situ Cloud and Remote Sensing Probes over the South East Atlantic Ocean

NASA Astrophysics Data System (ADS)

Miller, R.; McFarquhar, G. M.; Gupta, S.; Poellot, M.; O'Brien, J.; Delene, D. J.

2017-12-01

During the Observations of Aerosols Above Clouds and their Interactions (ORACLES) field campaigns, the NASA P3-Orion was equipped with in-situ probes measuring aerosol and cloud microphysical properties, while the NASA ER-2 was equipped with remote sensors retrieving cloud and aerosol quantities. During ORACLES 2017, the P-3 aircraft was equipped with two Clouds Droplet Probes (CDPs) sizing droplets with diameters (D) between 2 and 50µm. The two CDPs were mounted on pylons with different designs, the CDP on the newly designed left wing pylon positioned further below and ahead of the wing, whereas that on the right wing pylon directly below the wing. The P-3 was also equipped with a Cloud and Aerosol Spectrometer (CAS) sizing droplets with 0.51 µm < D < 50 µm, and three optical array probes: a 2D-stero probe (2DS) for 10 µm < D < 1280 µm; a High Volume Precipitation Sampler (HVPS-3), for 150 µm < D < 1.92 cm; and a Cloud Imaging Probe (CIP) for 25 µm < D < 1600 µm. In addition, a Phase Doppler Interferometer (PDI) for 0.5 µm < D < 2500 µm was included. In this presentation, the number distribution functions n(D) derived from different probes in their overlap ranges and bulk quantities, such as liquid water content (LWC), effective radius (re), total number concentration, extinction, skewness, dispersion and kurtosis derived by different probes over equivalent size ranges are compared. Additional comparison with bulk parameters (e.g., LWC measured by King and hot wire probes) and remotely sensed values are also made. The effect of the software package used to process the data is also examined by using two different packages, the National Center for Atmospheric Research Software for OAP Data Analysis (SODA2), and the University of Oklahoma/Illinois' Processing Software (UIOOPS) to process the optical array probe data. These intercomparisons, as a function of aircraft parameters and environmental conditions, help quantify uncertainties in measurements, improve our understanding of conditions under which the probes best function, assist in the development of a probe-independent best estimate of cloud microphysical parameters, and evaluate the quality of remote sensing retrievals. This in turn, will allow the use of these data sets to quantify cloud-aerosol relationships in the southeast Atlantic.

A reversible fluorescent probe based on C[double bond, length as m-dash]N isomerization for the selective detection of formaldehyde in living cells and in vivo.

PubMed

Song, Xinyu; Han, Xiaoyue; Yu, Fabiao; Zhang, Jinjin; Chen, Lingxin; Lv, Changjun

2018-01-15

Formaldehyde (FA) is an endogenously produced reactive carbonyl species (RCS) through biological metabolic processes whose concentration is closely related to human health and disease. Noninvasive and real-time detection of FA concentration in organisms is very important for revealing the physiological and pathological functions of FA. Herein, we design and synthesize a reversible fluorescent probe BOD-NH 2 for the detection of FA in living cells and in vivo. The probe is composed of two moieties: the BODIPY fluorophore and the primary amino group response unit. The probe undergoes an intracellular aldimine condensation reaction with FA and forms imine (C[double bond, length as m-dash]N) which will result in C[double bond, length as m-dash]N isomerization and rotation to turn-off the fluorescence of the probe. It is important that the probe can show a reversible response to FA. The probe BOD-NH 2 has been successfully applied for detecting and imaging FA in the cytoplasm of living cells. BOD-NH 2 is capable of detecting fluctuations in the levels of endogenous and exogenous FA in different types of living cells. The probe can be used to visualize the FA concentration in fresh hippocampus and the probe can further qualitatively evaluate the FA concentrations in ex vivo-dissected organs. Moreover, BOD-NH 2 can also be used for imaging in mice. The above applications make our new probe a potential chemical tool for the study of physiological and pathological functions of FA in cells and in vivo.

Improved Tumor Targeting and Longer Retention Time of NIR Fluorescent Probes Using Bioorthogonal Chemistry.

PubMed

Zhang, Xianghan; Wang, Bo; Zhao, Na; Tian, Zuhong; Dai, Yunpeng; Nie, Yongzhan; Tian, Jie; Wang, Zhongliang; Chen, Xiaoyuan

2017-01-01

The traditional labeling method for targeted NIR fluorescence probes requires directly covalent-bonded conjugation of targeting domains and fluorophores in vitro . Although this strategy works well, it is not sufficient for detecting or treating cancers in vivo , due to steric hindrance effects that relatively large fluorophore molecules exert on the configurations and physiological functions of specific targeting domains. The copper-free, "click-chemistry"-assisted assembly of small molecules in living systems may enhance tumor accumulation of fluorescence probes by improving the binding affinities of the targeting factors. Here, we employed a vascular homing peptide, GEBP11, as a targeting factor for gastric tumors, and we demonstrate its effectiveness for in vivo imaging via click-chemistry-mediated conjugation with fluorescence molecules in tumor xenograft mouse models. This strategy showed higher binding affinities than those of the traditional conjugation method, and our results showed that the tumor accumulation of click-chemistry-mediated probes are 11-fold higher than that of directly labeled probes. The tracking life was prolonged by 12-fold, and uptake of the probes into the kidney was reduced by 6.5-fold. For lesion tumors of different sizes, click-chemistry-mediated probes can achieve sufficient signal-to-background ratios (3.5-5) for in vivo detection, and with diagnostic sensitivity approximately 3.5 times that of traditional labeling probes. The click-chemistry-assisted detection strategy utilizes the advantages of "small molecule" probes while not perturbing their physiological functions; this enables tumor detection with high sensitivity and specific selectivity.

Resistivity Measurement by Dual-Configuration Four-Probe Method

NASA Astrophysics Data System (ADS)

Yamashita, Masato; Nishii, Toshifumi; Mizutani, Hiroya

2003-02-01

The American Society for Testing and Materials (ASTM) Committee has published a new technique for the measurement of resistivity which is termed the dual-configuration four-probe method. The resistivity correction factor is the function of only the data which are obtained from two different electrical configurations of the four probes. The measurement of resistivity and sheet resistance are performed for graphite rectangular plates and indium tin oxide (ITO) films by the conventional four-probe method and the dual-configuration four-probe method. It is demonstrated that the dual-configuration four-probe method which includes a probe array with equal separations of 10 mm can be applied to specimens having thicknesses up to 3.7 mm if a relative resistivity difference up to 5% is allowed.

Handheld scanning probes for optical coherence tomography: developments, applications, and perspectives

NASA Astrophysics Data System (ADS)

Duma, V.-F.; Demian, D.; Sinescu, C.; Cernat, R.; Dobre, G.; Negrutiu, M. L.; Topala, F. I.; Hutiu, Gh.; Bradu, A.; Podoleanu, A. G.

2016-03-01

We present the handheld scanning probes that we have recently developed in our current project for biomedical imaging in general and for Optical Coherence Tomography (OCT) in particular. OCT is an established, but dynamic imagistic technique based on laser interferometry, which offers micrometer resolutions and millimeters penetration depths. With regard to existing devices, the newly developed handheld probes are simple, light and relatively low cost. Their design is described in detail to allow for the reproduction in any lab, including for educational purposes. Two probes are constructed almost entirely from off-the-shelf components, while a third, final variant is constructed with dedicated components, in an ergonomic design. The handheld probes have uni-dimensional (1D) galvanometer scanners therefore they achieve transversal sections through the biological sample investigated - in contrast to handheld probes equipped with bi-dimensional (2D) scanners that can also achieve volumetric (3D) reconstructions of the samples. These latter handheld probes are therefore also discussed, as well as the possibility to equip them with galvanometer 2D scanners or with Risley prisms. For galvanometer scanners the optimal scanning functions studied in a series of previous works are pointed out; these functions offer a higher temporal efficiency/duty cycle of the scanning process, as well as artifact-free OCT images. The testing of the handheld scanning probes in dental applications is presented, for metal ceramic prosthesis and for teeth.

Formative Assessment Probes: Is It Made of Parts?: Scaffolding a Formative Assessment Probe

ERIC Educational Resources Information Center

Keeley, Page

2013-01-01

This column focuses on promoting learning through assessment. This month's issue explores structure and function as it relates to animals and plants. One of the disciplinary core ideas in "A Framework for K-12 Science Education" is LS1.A Structure and Function (NRC 2012). This disciplinary core idea is included in the "Next…

Behavioral and neural stability of attention bias to threat in healthy adolescents

PubMed Central

Britton, Jennifer C.; Sequeira, Stefanie; Ronkin, Emily G.; Chen, Gang; Bar-Haim, Yair; Shechner, Tomer; Ernst, Monique; Fox, Nathan A.; Leibenluft, Ellen; Pine, Daniel S.

2016-01-01

Considerable translational research on anxiety examines attention bias to threat and the efficacy of attention training in reducing symptoms. Imaging research on the stability of brain functions engaged by attention bias tasks could inform such research. Perturbed fronto-amygdala function consistently arises in attention bias research on adolescent anxiety. The current report examines the stability of the activation and functional connectivity of these regions on the dot-probe task. Functional magnetic resonance imaging (fMRI) activation and connectivity data were acquired with the dot-probe task in 39 healthy youth (f =18, Mean Age = 13.71 years, SD = 2.31) at two time points, separated by approximately nine weeks. Intraclass-correlations demonstrate good reliability in both neural activation for the ventrolateral PFC and task-specific connectivity for fronto-amygdala circuitry. Behavioral measures showed generally poor test-retest reliability. These findings suggest potential avenues for future brain imaging work by highlighting brain circuitry manifesting stable functioning on the dot-probe attention bias task. PMID:27129757

Ring-averaged ion velocity distribution function probe for laboratory magnetized plasma experiment

NASA Astrophysics Data System (ADS)

Kawamori, Eiichirou; Chen, Jinting; Lin, Chiahsuan; Lee, Zongmau

2017-10-01

Ring-averaged velocity distribution function of ions at a fixed guiding center position is a fundamental quantity in the gyrokinetic plasma physics. We have developed a diagnostic tool for the ring averaged velocity distribution function of ions for laboratory plasma experiments, which is named as the ring-averaged ion distribution function probe (RIDFP). The RIDFP is a set of ion collectors for different velocities. It is designed to be immersed in magnetized plasmas and achieves momentum selection of incoming ions by the selection of the ion Larmor radii. To nullify the influence of the sheath potential surrounding the RIDFP on the orbits of the incoming ions, the electrostatic potential of the RIDFP body is automatically adjusted to coincide with the space potential of the target plasma with the use of an emissive probe and a voltage follower. The developed RIDFP successfully measured the equilibrium ring-averaged velocity distribution function of a laboratory magnetized plasma, which was in accordance with the Maxwellian distribution having an ion temperature of 0.2 eV.

Ring-averaged ion velocity distribution function probe for laboratory magnetized plasma experiment.

PubMed

Kawamori, Eiichirou; Chen, Jinting; Lin, Chiahsuan; Lee, Zongmau

2017-10-01

Ring-averaged velocity distribution function of ions at a fixed guiding center position is a fundamental quantity in the gyrokinetic plasma physics. We have developed a diagnostic tool for the ring averaged velocity distribution function of ions for laboratory plasma experiments, which is named as the ring-averaged ion distribution function probe (RIDFP). The RIDFP is a set of ion collectors for different velocities. It is designed to be immersed in magnetized plasmas and achieves momentum selection of incoming ions by the selection of the ion Larmor radii. To nullify the influence of the sheath potential surrounding the RIDFP on the orbits of the incoming ions, the electrostatic potential of the RIDFP body is automatically adjusted to coincide with the space potential of the target plasma with the use of an emissive probe and a voltage follower. The developed RIDFP successfully measured the equilibrium ring-averaged velocity distribution function of a laboratory magnetized plasma, which was in accordance with the Maxwellian distribution having an ion temperature of 0.2 eV.

Red Fluorescent Carbon Nanoparticle-Based Cell Imaging Probe.

PubMed

Ali, Haydar; Bhunia, Susanta Kumar; Dalal, Chumki; Jana, Nikhil R

2016-04-13

Fluorescent carbon nanoparticle-based probes with tunable visible emission are biocompatible, environment friendly and most suitable for various biomedical applications. However, synthesis of red fluorescent carbon nanoparticles and their transformation into functional nanoparticles are very challenging. Here we report red fluorescent carbon nanoparticle-based nanobioconjugates of <25 nm hydrodynamic size and their application as fluorescent cell labels. Hydrophobic carbon nanoparticles are synthesized via high temperature colloid-chemical approach and transformed into water-soluble functional nanoparticles via coating with amphiphilic polymer followed by covalent linking with desired biomolecules. Following this approach, carbon nanoparticles are functionalized with polyethylene glycol, primary amine, glucose, arginine, histidine, biotin and folic acid. These functional nanoparticles can be excited with blue/green light (i.e., 400-550 nm) to capture their emission spanning from 550 to 750 nm. Arginine and folic acid functionalized nanoparticles have been demonstrated as fluorescent cell labels where blue and green excitation has been used for imaging of labeled cells. The presented method can be extended for the development of carbon nanoparticle-based other bioimaging probes.

Separation of Uncharged Oligodeoxynucleotide Analogs by Anion-Exchange Chromatography at High pH

NASA Technical Reports Server (NTRS)

Schmidt, Jurgen G.; Nielsen, Peter E.; Orgel, Leslie

1996-01-01

Ion-exchange chromatography is a well-established method for the analysis and purification of phosphodiester-linked oligonucleotides. If elution is carried out under alkaline conditions, the secondary structure of G- and C-rich oligomers is disrupted. Furthermore, elution times become more sensitive to the G and T content of the oligomer, because G and T are deprotonated at pH 10. In recent work on peptide-nucleic acids (PNAs) we noted that mixtures of PNA oligomers G(sub 4), G(Sub 6), G(sub 8), and G(sub 10) are readily separated by elution at pH 12 on an RPC-5 column. Here we show that this separation method is more generally applicable.

Immunoregulation of GVHD by triggering the innate immune system with CpG.

PubMed

Morecki, Shoshana; Slavin, Shimon

2009-08-01

Stimulation of Toll-like receptors by oligodeoxynucleotide sequences containing a CpG motif provides signals capable of triggering the innate and adaptive immune systems, thereby leading either to stimulation or suppression of immunoreactivities. Similar immunoregulatory capabilities are necessary for achieving the fine balance between engraftment and graft-versus-host disease required in the setup of allogeneic cell therapy. Ligation of CpG to its Toll-like receptors can be accomplished by treatment of the host or pretransplant treatment of the donor in vivo. These different strategies are presented in this review, which summarizes the attempts to maximize beneficial alloreactivity against malignant or other undesirable host cells, while controlling graft-versus-host disease.

Spermine moiety attached to the C-5 position of deoxyuridine enhances the duplex stability of the phosphorothioate DNA/complementary DNA and shows the susceptibility of the substrate to RNase H.

PubMed

Moriguchi, Tomohisa; Sakai, Hideaki; Suzuki, Hideo; Shinozuka, Kazuo

2008-09-01

Novel phosphorothioate-modified oligodeoxynucleotides (S-ODNs) containing a deoxyuridine derivative bearing a spermine moiety at the C-5 position were synthesized. The study of the thermal stability and the thermodynamic stability showed that the modified S-ODNs have been able to form the stable duplexes with the complementary DNA. It was also found that the duplex composed of the modified S-ODN and its complementary RNA strand is the substrate for Escherichia coli RNase H, and the cleavage of the RNA strand by the enzyme was almost similar as in the case of the unmodified one.

Nuclear receptor coactivators function in estrogen receptor- and progestin receptor-dependent aspects of sexual behavior in female rats

PubMed Central

Molenda-Figueira, Heather A.; Williams, Casey A.; Griffin, Andreana L.; Rutledge, Eric M.; Blaustein, Jeffrey D.; Tetel, Marc J.

2008-01-01

The ovarian hormones, estradiol (E) and progesterone (P) facilitate the expression of sexual behavior in female rats. E and P mediate many of these behavioral effects by binding to their respective intracellular receptors in specific brain regions. Nuclear receptor coactivators, including Steroid Receptor Coactivator-1 (SRC-1) and CREB Binding Protein (CBP), dramatically enhance ligand-dependent steroid receptor transcriptional activity in vitro. Previously, our lab has shown that SRC-1 and CBP modulate estrogen receptor (ER)-mediated induction of progestin receptor (PR) gene expression in the ventromedial nucleus of the hypothalamus (VMN) and hormone-dependent sexual receptivity in female rats. Female sexual behaviors can be activated by high doses of E alone in ovariectomized rats, and thus are believed to be ER-dependent. However, the full repertoire of female sexual behavior, in particular, proceptive behaviors such as hopping, darting and ear wiggling, are considered to be PR-dependent. In the present experiments, the function of SRC-1 and CBP in distinct ER- (Exp. 1) and PR- (Exp. 2) dependent aspects of female sexual behavior was investigated. In Exp. 1, infusion of antisense oligodeoxynucleotides to SRC-1 and CBP mRNA into the VMN decreased lordosis intensity in rats treated with E alone, suggesting that these coactivators modulate ER-mediated female sexual behavior. In Exp. 2, antisense to SRC-1 and CBP mRNA around the time of P administration reduced PR-dependent ear wiggling and hopping and darting. Taken together, these data suggest that SRC-1 and CBP modulate ER and PR action in brain and influence distinct aspects of hormone-dependent sexual behaviors. These findings support our previous studies and provide further evidence that SRC-1 and CBP function together to regulate ovarian hormone action in behaviorally-relevant brain regions. PMID:16769066

Study the friction behaviour of poly[2-(dimethylamino)ethyl methacrylate] brush with AFM probes in contact mechanics

NASA Astrophysics Data System (ADS)

Raftari, Maryam; Zhang, Zhenyu; Leggett, Graham J.; Geoghegan, Mark

2011-10-01

We have studied the frictional behaviour of grafted poly[2-(dimethylamino)ethyl methacrylate] (PDMAEMA) films using friction force microscopy (FFM). The films were prepared on native oxide-terminated silicon substrates using the technique of atom transfer radical polymerization (ATRP). We show that single asperity contact mechanics (Johnson-Kendall-Roberts(JKR) and Derjaguin-Muller-Toporov(DMT)) as well as a linear (Amontons) relation between applied load and frictional load depending on the pH of the FFM probe. Measurements were made using functionalized and unfunctionalized silicon nitride triangular probes. Functionalized probes included gold-coated probes, and ones coated with a self-assembled monolayer of dodecanethiol (DDT). The frictional behaviour between PDMAEMA and all tips immersed in pH from 3 to 11 are corresponded to the DMT or JKR model and are linear in pH=1, 2, and 12. These results show that contact mechanics of polyelectrolytes in water is complex and strongly dependent on the environmental pH.

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

EGR distribution and fluctuation probe based on CO2 measurements

DOEpatents

Parks, II, James E.; Partridge, Jr., William P.; Yoo, Ji Hyung

2015-06-30

A diagnostic system having a laser, an EGR probe, a detector and a processor. The laser may be a swept-.lamda. laser having a sweep range including a significant CO.sub.2 feature and substantially zero absorption regions. The sweep range may extend from about 2.708 .mu.m to about 2.7085 .mu.m. The processor may determine CO.sub.2 concentration as a function of the detector output signal. The processor may normalize the output signal as a function of the zero absorption regions. The system may include a plurality of EGR probes receiving light from a single laser. The system may include a separate detector for each probe. Alternatively, the system may combine the light returning from the different probes into a composite beam that is measured by a single detector. A unique modulation characteristic may be introduced into each light beam before combination so that the processor can discriminate between them in the composite beam.

Shock probes in a one-dimensional Katz-Lebowitz-Spohn model

NASA Astrophysics Data System (ADS)

Chatterjee, Sakuntala; Barma, Mustansir

2008-06-01

We consider shock probes in a one-dimensional driven diffusive medium with nearest-neighbor Ising interaction (KLS model). Earlier studies based on an approximate mapping of the present system to an effective zero-range process concluded that the exponents characterizing the decays of several static and dynamical correlation functions of the probes depend continuously on the strength of the Ising interaction. On the contrary, our numerical simulations indicate that over a substantial range of the interaction strength, these exponents remain constant and their values are the same as in the case of no interaction (when the medium executes an ASEP). We demonstrate this by numerical studies of several dynamical correlation functions for two probes and also for a macroscopic number of probes. Our results are consistent with the expectation that the short-ranged correlations induced by the Ising interaction should not affect the large time and large distance properties of the system, implying that scaling forms remain the same as in the medium with no interactions present.

HuMiChip: Development of a Functional Gene Array for the Study of Human Microbiomes

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

Tu, Q.; Deng, Ye; Lin, Lu

Microbiomes play very important roles in terms of nutrition, health and disease by interacting with their hosts. Based on sequence data currently available in public domains, we have developed a functional gene array to monitor both organismal and functional gene profiles of normal microbiota in human and mouse hosts, and such an array is called human and mouse microbiota array, HMM-Chip. First, seed sequences were identified from KEGG databases, and used to construct a seed database (seedDB) containing 136 gene families in 19 metabolic pathways closely related to human and mouse microbiomes. Second, a mother database (motherDB) was constructed withmore » 81 genomes of bacterial strains with 54 from gut and 27 from oral environments, and 16 metagenomes, and used for selection of genes and probe design. Gene prediction was performed by Glimmer3 for bacterial genomes, and by the Metagene program for metagenomes. In total, 228,240 and 801,599 genes were identified for bacterial genomes and metagenomes, respectively. Then the motherDB was searched against the seedDB using the HMMer program, and gene sequences in the motherDB that were highly homologous with seed sequences in the seedDB were used for probe design by the CommOligo software. Different degrees of specific probes, including gene-specific, inclusive and exclusive group-specific probes were selected. All candidate probes were checked against the motherDB and NCBI databases for specificity. Finally, 7,763 probes covering 91.2percent (12,601 out of 13,814) HMMer confirmed sequences from 75 bacterial genomes and 16 metagenomes were selected. This developed HMM-Chip is able to detect the diversity and abundance of functional genes, the gene expression of microbial communities, and potentially, the interactions of microorganisms and their hosts.« less

Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays.

PubMed

Kimura, Yasumasa; Soma, Takahiro; Kasahara, Naoko; Delobel, Diane; Hanami, Takeshi; Tanaka, Yuki; de Hoon, Michiel J L; Hayashizaki, Yoshihide; Usui, Kengo; Harbers, Matthias

2016-01-01

Analytical PCR experiments preferably use internal probes for monitoring the amplification reaction and specific detection of the amplicon. Such internal probes have to be designed in close context with the amplification primers, and may require additional considerations for the detection of genetic variations. Here we describe Edesign, a new online and stand-alone tool for designing sets of PCR primers together with an internal probe for conducting quantitative real-time PCR (qPCR) and genotypic experiments. Edesign can be used for selecting standard DNA oligonucleotides like for instance TaqMan probes, but has been further extended with new functions and enhanced design features for Eprobes. Eprobes, with their single thiazole orange-labelled nucleotide, allow for highly sensitive genotypic assays because of their higher DNA binding affinity as compared to standard DNA oligonucleotides. Using new thermodynamic parameters, Edesign considers unique features of Eprobes during primer and probe design for establishing qPCR experiments and genotyping by melting curve analysis. Additional functions in Edesign allow probe design for effective discrimination between wild-type sequences and genetic variations either using standard DNA oligonucleotides or Eprobes. Edesign can be freely accessed online at http://www.dnaform.com/edesign2/, and the source code is available for download.

Non-invasive diagnostic system and its opto-mechanical probe for combining confocal Raman spectroscopy and optical coherence tomography.

PubMed

Klemes, Jan; Kotzianova, Adela; Pokorny, Marek; Mojzes, Peter; Novak, Jindrich; Sukova, Lada; Demuth, Jaroslav; Vesely, Jaroslav; Sasek, Ladislav; Velebny, Vladimir

2017-11-01

Non-invasive optical diagnostic methods allow important information about studied systems to be obtained in a non-destructive way. Complete diagnosis requires information about the chemical composition as well as the morphological structure of a sample. We report on the development of an opto-mechanical probe that combines Raman spectroscopy (RS) and optical coherence tomography (OCT), two methods that provide all the crucial information needed for a non-invasive diagnosis. The aim of this paper is to introduce the technical design, construction and optimization of a dual opto-mechanical probe combining two in-house developed devices for confocal RS and OCT. The unique benefit of the probe is a gradual acquisition of OCT and RS data, which allows to use the acquired OCT images to pinpoint locations of interest for RS measurements. The parameters and the correct functioning of the probe were verified by RS scanning of various samples (silicon wafer and ex vivo tissue) based on their OCT images - lateral as well as depth scanning was performed. Both the OCT and RS systems were developed, optimized and tested with the ultimate aim of verifying the functionality of the probe. Picture: Schematic illustration and visualization of the developed RS-OCT probe. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays

PubMed Central

Kasahara, Naoko; Delobel, Diane; Hanami, Takeshi; Tanaka, Yuki; de Hoon, Michiel J. L.; Hayashizaki, Yoshihide; Usui, Kengo; Harbers, Matthias

2016-01-01

Analytical PCR experiments preferably use internal probes for monitoring the amplification reaction and specific detection of the amplicon. Such internal probes have to be designed in close context with the amplification primers, and may require additional considerations for the detection of genetic variations. Here we describe Edesign, a new online and stand-alone tool for designing sets of PCR primers together with an internal probe for conducting quantitative real-time PCR (qPCR) and genotypic experiments. Edesign can be used for selecting standard DNA oligonucleotides like for instance TaqMan probes, but has been further extended with new functions and enhanced design features for Eprobes. Eprobes, with their single thiazole orange-labelled nucleotide, allow for highly sensitive genotypic assays because of their higher DNA binding affinity as compared to standard DNA oligonucleotides. Using new thermodynamic parameters, Edesign considers unique features of Eprobes during primer and probe design for establishing qPCR experiments and genotyping by melting curve analysis. Additional functions in Edesign allow probe design for effective discrimination between wild-type sequences and genetic variations either using standard DNA oligonucleotides or Eprobes. Edesign can be freely accessed online at http://www.dnaform.com/edesign2/, and the source code is available for download. PMID:26863543

Work function of few layer graphene covered nickel thin films measured with Kelvin probe force microscopy

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

Eren, B.; Material Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720; Gysin, U.

2016-01-25

Few layer graphene and graphite are simultaneously grown on a ∼100 nm thick polycrystalline nickel film. The work function of few layer graphene/Ni is found to be 4.15 eV with a variation of 50 meV by local measurements with Kelvin probe force microscopy. This value is lower than the work function of free standing graphene due to peculiar electronic structure resulting from metal 3d-carbon 2p(π) hybridization.

Design strategies of fluorescent probes for selective detection among biothiols.

PubMed

Niu, Li-Ya; Chen, Yu-Zhe; Zheng, Hai-Rong; Wu, Li-Zhu; Tung, Chen-Ho; Yang, Qing-Zheng

2015-10-07

Simple thiol derivatives, such as cysteine (Cys), homocysteine (Hcy), and glutathione (GSH), play key roles in biological processes, and the fluorescent probes to detect such thiols in vivo selectively with high sensitivity and fast response times are critical for understanding their numerous functions. However, the similar structures and reactivities of these thiols pose considerable challenges to the development of such probes. This review focuses on various strategies for the design of fluorescent probes for the selective detection of biothiols. We classify the fluorescent probes for discrimination among biothiols according to reaction types between the probes and thiols such as cyclization with aldehydes, conjugate addition-cyclization with acrylates, native chemical ligation, and aromatic substitution-rearrangement.

Human Herpesvirus-8-Transformed Endothelial Cells Have Functionally Activated Vascular Endothelial Growth Factor/Vascular Endothelial Growth Factor Receptor

PubMed Central

Masood, Rizwan; Cesarman, Ethel; Smith, D. Lynne; Gill, Parkash S.; Flore, Ornella

2002-01-01

Kaposi’s sarcoma is a vascular tumor commonly associated with human immunodeficiency virus (HIV)-1 and human herpesvirus (HHV-8) also known as Kaposi’s sarcoma-associated herpesvirus. The principal features of this tumor are abnormal proliferation of vascular structures lined with spindle-shaped endothelial cells. HHV-8 may transform a subpopulation of endothelial cells in vitro via viral and cellular gene expression. We hypothesized that among the cellular genes, vascular endothelial growth factors (VEGFs) and their cognate receptors may be involved in viral-mediated transformation. We have shown that HHV-8-transformed endothelial cells (EC-HHV-8) express higher levels of VEGF, VEGF-C, VEGF-D, and PlGF in addition to VEGF receptors-1, -2, and -3. Furthermore, antibodies to VEGF receptor-2 inhibited cell proliferation and viability. Similarly, inhibition of VEGF gene expression with antisense oligonucleotides inhibited EC-HHV-8 cell proliferation/viability. The growth and viability of primary endothelial cells and a fibroblast cell line however were unaffected by either the VEGF receptor-2 antibody or the VEGF antisense oligodeoxynucleotides. VEGF and VEGF receptors are thus induced in EC-HHV-8 and participate in the transformation. Inhibitors of VEGF may thus modulate the disease process during development and progression. PMID:11786394

A novel fusion protein domain III-capsid from dengue-2, in a highly aggregated form, induces a functional immune response and protection in mice

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

Valdes, Iris, E-mail: iris.valdes@cigb.edu.c; Bernardo, Lidice; Gil, Lazaro

Based on the immunogenicity of domain III from the Envelope protein of dengue virus as well as the proven protective capacity of the capsid antigen, we have designed a novel domain III-capsid chimeric protein with the goal of obtaining a molecule potentially able to induce both humoral and cell-mediated immunity (CMI). After expression of the recombinant gene in Escherichia coli, the domain III moiety retained its antigenicity as evaluated with anti-dengue sera. In order to explore alternatives for modulating the immunogenicity of the protein, it was mixed with oligodeoxynucleotides in order to obtain particulated aggregates and then immunologically evaluated inmore » mice in comparison with non-aggregated controls. Although the humoral immune response induced by both forms of the protein was equivalent, the aggregated variant resulted in a much stronger CMI as measured by in vitro IFN-gamma secretion and protection experiments, mediated by CD4{sup +} and CD8{sup +} cells. The present work provides additional evidence in support for a crucial role of CMI in protection against dengue virus and describes a novel vaccine candidate against the disease based on a recombinant protein that can stimulate both arms of the acquired immune system.« less

Ultrafast scanning probe microscopy

DOEpatents

Weiss, S.; Chemla, D.S.; Ogletree, D.F.; Botkin, D.

1995-05-16

An ultrafast scanning probe microscopy method is described for achieving subpicosecond-temporal resolution and submicron-spatial resolution of an observation sample. In one embodiment of the present claimed invention, a single short optical pulse is generated and is split into first and second pulses. One of the pulses is delayed using variable time delay means. The first pulse is then directed at an observation sample located proximate to the probe of a scanning probe microscope. The scanning probe microscope produces probe-sample signals indicative of the response of the probe to characteristics of the sample. The second pulse is used to modulate the probe of the scanning probe microscope. The time delay between the first and second pulses is then varied. The probe-sample response signal is recorded at each of the various time delays created between the first and second pulses. The probe-sample response signal is then plotted as a function of time delay to produce a cross-correlation of the probe sample response. In so doing, the present invention provides simultaneous subpicosecond-temporal resolution and submicron-spatial resolution of the sample. 6 Figs.

Ultrafast scanning probe microscopy

DOEpatents

Weiss, Shimon; Chemla, Daniel S.; Ogletree, D. Frank; Botkin, David

1995-01-01

An ultrafast scanning probe microscopy method for achieving subpicosecond-temporal resolution and submicron-spatial resolution of an observation sample. In one embodiment of the present claimed invention, a single short optical pulse is generated and is split into first and second pulses. One of the pulses is delayed using variable time delay means. The first pulse is then directed at an observation sample located proximate to the probe of a scanning probe microscope. The scanning probe microscope produces probe-sample signals indicative of the response of the probe to characteristics of the sample. The second pulse is used to modulate the probe of the scanning probe microscope. The time delay between the first and second pulses is then varied. The probe-sample response signal is recorded at each of the various time delays created between the first and second pulses. The probe-sample response signal is then plotted as a function of time delay to produce a cross-correlation of the probe sample response. In so doing, the present invention provides simultaneous subpicosecond-temporal resolution and submicron-spatial resolution of the sample.

Highly specific noninvasive photoacoustic and positron emission tomography of brain plaque with functionalized croconium dye labeled by a radiotracer† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc04798j Click here for additional data file.

PubMed Central

Liu, Yajing; Yang, Yanping; Sun, Mingjian; Cui, Mengchao; Fu, Ying; Lin, Yu

2017-01-01

Highly-efficient targeting probes are desirable for disease diagnosis and functional imaging. However, most of the current near-infrared (NIR) probes suffer from low signal conversion, insufficient photostability, poor probe specificity, and limited functions. Herein, an NIR ultrahigh absorbing croconium dye for amyloid (CDA) was designed and synthesized to specifically bind to cerebrovascular amyloid without antibody linkage. This unique CDA is able to strongly bind the hydrophobic channels of amyloid beta (Aβ) fiber with a very strong binding energy of –9.3 kcal mol–1. Our experimental results demonstrate that the amphipathic dye with an intense absorption peak at 800 nm generated a significant local temperature surge under low-power laser irradiation. Compared with representative prominent indocyanine green, Prussian blue, and gold nanorods, this probe can produce the strongest photoacoustic signal based on the same mass concentration. Labeled with radioactive 18F, this multifunctional probe allowed for the ultrasensitive photoacoustic tomography (PAT)/positron emission tomography (PET)/fluorescence imaging of Aβ plaques in the brain cortex. Featured with high spatial resolution and optical specificity, PAT was intrinsically suitable for imaging pathological sites on cortical vessels, whereas PET revealed whole-body anatomy with quantitative biodistribution information. Our study shows that a CDA-based functionalized dye aided with PAT and PET is capable of plaque diagnosis and localization. PMID:28451353

Feasibility, strategy, methodology, and analysis of probe measurements in plasma under high gas pressure

NASA Astrophysics Data System (ADS)

Demidov, V. I.; Koepke, M. E.; Kurlyandskaya, I. P.; Malkov, M. A.

2018-02-01

This paper reviews existing theories for interpreting probe measurements of electron distribution functions (EDF) at high gas pressure when collisions of electrons with atoms and/or molecules near the probe are pervasive. An explanation of whether or not the measurements are realizable and reliable, an enumeration of the most common sources of measurement error, and an outline of proper probe-experiment design elements that inherently limit or avoid error is presented. Additionally, we describe recent expanded plasma-condition compatibility for EDF measurement, including in applications of large wall probe plasma diagnostics. This summary of the authors’ experiences gained over decades of practicing and developing probe diagnostics is intended to inform, guide, suggest, and detail the advantages and disadvantages of probe application in plasma research.

Low-Virtuality Leptoproduction of Open-Charm as a Probe of the Gluon Sivers Function

NASA Astrophysics Data System (ADS)

Godbole, Rohini M.; Kaushik, Abhiram; Misra, Anuradha

2018-05-01

We propose low-virtuality leptoproduction of open-charm, p^\\uparrow l→ D^0+X, as a probe of the gluon Sivers function (GSF). At leading-order, this process directly probes the gluon content of the proton, making detection of a trasverse single-spin asymmetry in the process a clear indication of a non-zero GSF. Considering the kinematics of the proposed future Electron-Ion Collider, we present predictions for asymmetry using fits of the GSF available in literature. We also study the asymmetry at the level of muons produced in D-meson decays and find that the asymmetry is preserved therein as well.

nextPARS: parallel probing of RNA structures in Illumina

PubMed Central

Saus, Ester; Willis, Jesse R.; Pryszcz, Leszek P.; Hafez, Ahmed; Llorens, Carlos; Himmelbauer, Heinz

2018-01-01

RNA molecules play important roles in virtually every cellular process. These functions are often mediated through the adoption of specific structures that enable RNAs to interact with other molecules. Thus, determining the secondary structures of RNAs is central to understanding their function and evolution. In recent years several sequencing-based approaches have been developed that allow probing structural features of thousands of RNA molecules present in a sample. Here, we describe nextPARS, a novel Illumina-based implementation of in vitro parallel probing of RNA structures. Our approach achieves comparable accuracy to previous implementations, while enabling higher throughput and sample multiplexing. PMID:29358234

Using a biased qubit to probe complex systems

NASA Astrophysics Data System (ADS)

Pollock, Felix A.; Checińska, Agata; Pascazio, Saverio; Modi, Kavan

2016-09-01

Complex mesoscopic systems play increasingly important roles in modern science, from understanding biological functions at the molecular level to designing solid-state information processing devices. The operation of these systems typically depends on their energetic structure, yet probing their energy landscape can be extremely challenging; they have many degrees of freedom, which may be hard to isolate and measure independently. Here, we show that a qubit (a two-level quantum system) with a biased energy splitting can directly probe the spectral properties of a complex system, without knowledge of how they couple. Our work is based on the completely positive and trace-preserving map formalism, which treats any unknown dynamics as a "black-box" process. This black box contains information about the system with which the probe interacts, which we access by measuring the survival probability of the initial state of the probe as function of the energy splitting and the process time. Fourier transforming the results yields the energy spectrum of the complex system. Without making assumptions about the strength or form of its coupling, our probe could determine aspects of a complex molecule's energy landscape as well as, in many cases, test for coherent superposition of its energy eigenstates.

Plasma potential and electron temperature evaluated by ball-pen and Langmuir probes in the COMPASS tokamak

NASA Astrophysics Data System (ADS)

Dimitrova, M.; Popov, Tsv K.; Adamek, J.; Kovačič, J.; Ivanova, P.; Hasan, E.; López-Bruna, D.; Seidl, J.; Vondráček, P.; Dejarnac, R.; Stöckel, J.; Imríšek, M.; Panek, R.; the COMPASS Team

2017-12-01

The radial distributions of the main plasma parameters in the scrape-off-layer of the COMPASS tokamak are measured during L-mode and H-mode regimes by using both Langmuir and ball-pen probes mounted on a horizontal reciprocating manipulator. The radial profile of the plasma potential derived previously from Langmuir probes data by using the first derivative probe technique is compared with data derived using ball-pen probes. A good agreement can be seen between the data acquired by the two techniques during the L-mode discharge and during the H-mode regime within the inter-ELM periods. In contrast with the first derivative probe technique, the ball-pen probe technique does not require a swept voltage and, therefore, the temporal resolution is only limited by the data acquisition system. In the electron temperature evaluation, in the far scrape-off layer and in the limiter shadow, where the electron energy distribution is Maxwellian, the results from both techniques match well. In the vicinity of the last closed flux surface, where the electron energy distribution function is bi-Maxwellian, the ball-pen probe technique results are in agreement with the high-temperature components of the electron distribution only. We also discuss the application of relatively large Langmuir probes placed in parallel and perpendicularly to the magnetic field lines to studying the main plasma parameters. The results obtained by the two types of the large probes agree well. They are compared with Thomson scattering data for electron temperatures and densities. The results for the electron densities are compared also with the results from ASTRA code calculation of the electron source due to the ionization of the neutrals by fast electrons and the origin of the bi-Maxwellian electron energy distribution function is briefly discussed.

Methods of epigenome editing for probing the function of genomic imprinting.

PubMed

Rienecker, Kira DA; Hill, Matthew J; Isles, Anthony R

2016-10-01

The curious patterns of imprinted gene expression draw interest from several scientific disciplines to the functional consequences of genomic imprinting. Methods of probing the function of imprinting itself have largely been indirect and correlational, relying heavily on conventional transgenics. Recently, the burgeoning field of epigenome editing has provided new tools and suggested strategies for asking causal questions with site specificity. This perspective article aims to outline how these new methods may be applied to questions of functional imprinting and, with this aim in mind, to suggest new dimensions for the expansion of these epigenome-editing tools.

GeoChip 3.0 as a high-thoughput tool for analyzing microbial community composition, structure, and functional activity

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

He, Z.; Deng, Y.; Van Nostrand, J.D.

A new generation of functional gene arrays (FGAs; GeoChip 3.0) has been developed, with {approx}28,000 probes covering approximately 57,000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance and organic contaminant degradation. GeoChip 3.0 also has several other distinct features, such as a common oligo reference standard (CORS) for data normalization and comparison, a software package for data management and future updating and the gyrB gene for phylogenetic analysis. Computational evaluation of probe specificity indicated that all designed probes would have a high specificity to their corresponding targets.more » Experimental analysis with synthesized oligonucleotides and genomic DNAs showed that only 0.0036-0.025% false-positive rates were observed, suggesting that the designed probes are highly specific under the experimental conditions examined. In addition, GeoChip 3.0 was applied to analyze soil microbial communities in a multifactor grassland ecosystem in Minnesota, USA, which showed that the structure, composition and potential activity of soil microbial communities significantly changed with the plant species diversity. As expected, GeoChip 3.0 is a high-throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning.« less

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.

Dual-Reactable Fluorescent Probes for Highly Selective and Sensitive Detection of Biological H2 S.

PubMed

Wei, Chao; Wang, Runyu; Zhang, Changyu; Xu, Guoce; Li, Yanyan; Zhang, Qiang-Zhe; Li, Lu-Yuan; Yi, Long; Xi, Zhen

2016-05-06

Hydrogen sulfide (H2 S) is an important endogenous signaling molecule with a variety of biological functions. Development of fluorescent probes for highly selective and sensitive detection of H2 S is necessary. We show here that dual-reactable fluorescent H2 S probes could react with higher selectivity than single-reactable probes. One of the dual-reactable probes gives more than 4000-fold turn-on response when reacting with H2 S, the largest response among fluorescent H2 S probes reported thus far. In addition, the probe could be used for high-throughput enzymatic assays and for the detection of Cys-induced H2 S in cells and in zebrafish. These dual-reactable probes hold potential for highly selective and sensitive detection of H2 S in biological systems. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Antisense oligodeoxynucleotide inhibition as a potent diagnostic tool for gene function in plant biology

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

Jansson, Christer; Sun, Chuanxin; Ghebramedhin, Haile

Antisense oligodeoxynucleotide (ODN) inhibition emerges as an effective means for probing gene function in plant cells. Employing this method we have established the importance of the SUSIBA2 transcription factor for regulation of starch synthesis in barley endosperm, and arrived at a model for the role of the SUSIBAs in sugar signaling and source-sink commutation during cereal endosperm development. In this addendum we provide additional data demonstrating the suitability of the antisense ODN technology in studies on starch branching enzyme activities in barley leaves. We also comment on the mechanism for ODN uptake in plant cells. Antisense ODNs are short (12-25more » nt-long) stretches of single-stranded ODNs that hybridize to the cognate mRNA in a sequence-specific manner, thereby inhibiting gene expression. They are naturally occurring in both prokaryotes and eukaryotes where they partake in gene regulation and defense against viral infection. The mechanisms for antisense ODN inhibition are not fully understood but it is generally considered that the ODN either sterically interferes with translation or promotes transcript degradation by RNase H activation. The earliest indication of the usefulness of antisense ODN technology for the purposes of molecular biology and medical therapy was the demonstration in 1978 that synthetic ODNs complementary to Raos sarcoma virus could inhibit virus replication in tissue cultures of chick embryo fibroblasts. Since then the antisense ODN technology has been widely used in animal sciences and as an important emerging therapeutic approach in clinical medicine. However, antisense ODN inhibition has been an under-exploited strategy for plant tissues, although the prospects for plant cells in suspension cultures to take up single-stranded ODNs was reported over a decade ago. In 2001, two reports from Malho and coworker demonstrated the use of cationic-complexed antisense ODNs to suppress expression of genes encoding pollen-signaling proteins in pollen tubes from the lilly Agapanthus umbellatus. For the uptake of DNA pollen tubes represent a unique system since the growing tip is surrounded by a loose matrix of hemicellulose and pectins, exposing the plasma membrane7 and the first uptake of ODNs by pollen tubes was reported as early as 1994. A breakthrough in the employment of antisense ODN inhibition as a powerful approach in plant biology was recently presented through our work on intact barley leaves. As was illustrated by confocal microscopy and fluorescently labeled ODNs, naked ODNs were taken up through the leaf petiole and efficiently imported into the plant cell and the nucleus. The work portrayed in that study demonstrate the applicability of antisense ODN inhibition in plant biology, e.g. as a rapid antecedent to time-consuming transgenic studies, and that it operates through RNase H degradation. We employed the antisense ODN strategy to demonstrate the importance of the SUSIBA2 transcription factor in regulation of starch synthesis, and to depict a possible mechanism for sugar signaling in plants and how it might confer endosperm-specific gene expression during seed development. We also described the employment of the antisense ODN strategy for studies on in vitro spike cultures of barley. Here we present further evidence as to the value of the antisense ODN approach in plant biology by following the effects on starch branching enzyme (SBE) accumulation in barley leaves after suppression of individual SBE genes. In agreement with transcript analyses of SBE expression in barley leaves, a zymogram assay (Fig. 1) revealed that sucrose treatment of barley leaves increased the number of SBE activity bands as compared to sorbitol treatment. In the presence of antisense SBEI or SBEIIA ODNs, zymograms of sucrose-treated leaves displayed only a subset of these activities with bands in the top portion of the zymogram gel missing or diminished. With antisense SBEIIB ODN, all activity bands in the top portion of the gel as well as the lowest band were absent. Based on these data we provide a tentative annotation for the various SBE activity bands. In animal experiments, naked ODNs are usually not taken up by the cells since both the ODNs and the outside of the plasma membrane carry a net negative charge. Thus the uptake of naked ODNs into barley leaf cells was surprising and called for an explanation. As demonstrated in our subsequent paper, the answer seems to be that the ODNs slip into the cells through sugar translocators as they are activated in the presence of the appropriate sugar (Fig. 2). Whether it is the structural resemblance between the sugar (deoxyribose) backbone of the ODNs and the transported sugars that allows for the ODNs to be transferred, or if other mechanisms are involved, remains to be elucidated.« less

Immune response in domestic ducks following intradermal delivery of inactivated vaccine against H5N1 highly pathogenic avian influenza virus adjuvanted with oligodeoxynucleotides containing CpG motifs.

PubMed

Yuk, Seong-Su; Lee, Dong-Hun; Park, Jae-Keun; To, Eredene-Ochir; Kwon, Jung-Hoon; Noh, Jin-Yong; Gomis, Susantha; Song, Chang-Seon

2015-08-01

Ducks are a natural reservoir for H5N1 highly pathogenic avian influenza (HPAI) viruses, which produces a range of clinical outcomes from asymptomatic infections to severe disease with mortality. Vaccination against HPAI is one of the few methods available for controlling avian influenza virus (AIV) infection in domestic ducks; therefore, it is necessary to improve vaccine efficacy against HPAI in domestic ducks. However, few studies have focused on enhancing the immune response by testing alternative administration routes and adjuvants. While attempting to maximize the efficacy of a vaccine, it is important to select an appropriate vaccine delivery route and adjuvant to elicit an enhanced immune response. Although several studies have indicated that the vaccination of ducks against HPAI viruses has offered protection against lethal virus challenge, the immunogenicity of the vaccine still requires improvement. In this study, we characterized the immune response following a novel vaccination strategy against H5N1 HPAI virus in domestic ducks. Our novel intradermal delivery system and the application of the cytosine-phosphodiester-guanine (CpG) oligodeoxynucleotide (ODN) adjuvant allowed us to obtain information regarding the sustained vaccine immunity. Compared with the intramuscular route of vaccination, the intradermal route resulted in higher antibody titer as well as lower antibody deviation following secondary vaccination. In addition, the use of a CpG-ODN adjuvant had a dose-sparing effect on antibody titer. Furthermore, when a high dose of antigen was used, the CpG-ODN-adjuvanted vaccine maintained a high mean antibody titer. This data demonstrates that intradermal immunization combined with administration of CpG-ODN as an adjuvant may be a promising strategy for improving vaccine efficacy in domestic ducks. © 2015 Poultry Science Association Inc.

Sensitization of B-cell chronic lymphocytic leukemia cells to recombinant immunotoxin by immunostimulatory phosphorothioate oligodeoxynucleotides.

PubMed

Decker, Thomas; Hipp, Susanne; Kreitman, Robert J; Pastan, Ira; Peschel, Christian; Licht, Thomas

2002-02-15

A recombinant anti-CD25 immunotoxin, LMB-2, has shown clinical efficacy in hairy cell leukemia and T-cell neoplasms. Its activity in B-cell chronic lymphocytic leukemia (B-CLL) is inferior but might be improved if B-CLL cells expressed higher numbers of CD25 binding sites. It was recently reported that DSP30, a phosphorothioate CpG-oligodeoxynucleotide (CpG-ODN) induces immunogenicity of B-CLL cells by up-regulation of CD25 and other antigens. The present study investigated the antitumor activity of LMB-2 in the presence of DSP30. To this end, B-CLL cells from peripheral blood of patients were isolated immunomagnetically to more than 98% purity. Incubation with DSP30 for 48 hours augmented CD25 expression in 14 of 15 B-CLL samples, as assessed by flow cytometry. DSP30 increased LMB-2 cytotoxicity dose dependently whereas a control ODN with no CpG motif did not. LMB-2 displayed no antitumor cell activity in the absence of CpG-ODN as determined colorimetrically with an (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium, inner salt (MTS) assay. In contrast, B-CLL growth was inhibited in 12 of 13 samples with 50% inhibition concentrations (IC(50)) in the range of LMB-2 plasma levels achieved in clinical studies. Two samples were not evaluable because of spontaneous B-CLL cell death in the presence of DSP30. Control experiments with an immunotoxin that does not recognize hematopoietic cells, and an anti-CD22 immunotoxin, confirmed that sensitization to LMB-2 was specifically due to up-regulation of CD25. LMB-2 was much less toxic to normal B and T lymphocytes compared with B-CLL cells. In summary, immunostimulatory CpG-ODNs efficiently sensitize B-CLL cells to a recombinant immunotoxin by modulation of its target. This new treatment strategy deserves further attention.

Translesion synthesis past equine estrogen-derived 2'-deoxycytidine DNA adducts by human DNA polymerases eta and kappa.

PubMed

Suzuki, Naomi; Yasui, Manabu; Santosh Laxmi, Y R; Ohmori, Haruo; Hanaoka, Fumio; Shibutani, Shinya

2004-09-07

Estrogen replacement therapy (ERT), composed of equilenin, is associated with increased risk of breast, ovarian, and endometrial cancers. Several diastereoisomers of unique dC and dA DNA adducts were derived from 4-hydroxyequilenin (4-OHEN), a metabolite of equilenin, and have been detected in women receiving ERT. To explore the miscoding property of 4-OHEN-dC adduct, site-specifically modified oligodeoxynucleotides (Pk-1, Pk-2, Pk-3, and Pk-4) containing a single diastereoisomer of 4-OHEN-dC were prepared by a postsynthetic method. Among them, major 4-OHEN-dC-modified oligodeoxynucleotides (Pk-3 and Pk-4) were used to prepare the templates for primer extension reactions catalyzed by DNA polymerase (pol) alpha, pol eta, and pol kappa. Primer extension was retarded one base prior to the lesion and opposite the lesion; stronger blockage was observed with pol alpha, while with human pol eta or pol kappa, a fraction of the primers was extended past the lesion. Steady-state kinetic studies showed that both pol kappa and pol eta inserted dCMP and dAMP opposite the 4-OHEN-dC and extended past the lesion. Never or less-frequently, dGMP, the correct base, was inserted opposite the lesion. The relative bypass frequency past the 4-OHEN-dC lesion with pol eta was at least 3 orders of magnitude higher than that for pol kappa, as observed for primer extension reactions. The bypass frequency past the dA.4-OHEN-dC adduct in Pk-4 was 2 orders of magnitude more efficient than that past the adduct in Pk-3. Thus, 4-OHEN-dC is a highly miscoding lesion capable of generating C --> T transitions and C --> G transversions. The miscoding frequency and specificity of 4-OHEN-dC were strikingly influenced by the adduct stereochemistry and DNA polymerase used.

Randomized phase 2/3 trial of CpG oligodeoxynucleotide PF-3512676 alone or with dacarbazine for patients with unresectable stage III and IV melanoma.

PubMed

Weber, Jeffrey S; Zarour, Hassan; Redman, Bruce; Trefzer, Uwe; O'Day, Steven; van den Eertwegh, Alfons J M; Marshall, Ernest; Wagner, Stefan

2009-09-01

The primary objective of this phase 2 study was to assess the objective response rate (complete response [CR] + partial responses [PR]), by Response Evaluation Criteria in Solid Tumors, of PF-3512676, a CpG oligodeoxynucleotide, alone in 2 doses or in combination with dacarbazine (DTIC) in patients with unresectable stage IIIB/C or stage IV malignant melanoma, with the aim of selecting an arm to take forward to a phase 3 portion of the study. A total of 184 patients were randomized to 1 of 4 treatments: PF-3512676 10 mg (low dose), at 40 mg (high dose), 40 mg plus DTIC (850 mg/m(2)), or DTIC (850 mg/m(2)) alone. Patients received PF-3512676 subcutaneously weekly in a 3-week cycle and received DTIC intravenously on the first week of the cycle. The objective response rate (PR or CR, confirmed or unconfirmed) in the 40 mg + DTIC arm was 16% (7 patients) compared with 8% (3 patients) with DTIC alone. One (2%) patient in the 10-mg and 0 patients in the 40-mg arms achieved an objective response. Best response of CR or PR or stable disease (SD), with no minimum duration defined for SD, was achieved by 15 (33%) patients in the 40 mg + DTIC arm, 15 (38%) patients in the DTIC-only arm, 8 (17%) patients in the 10-mg arm, and 9 (20%) patients in the 40-mg arm. The most frequently reported adverse events were classified as local injection site reactions or systemic flu-like symptoms, specifically fatigue, rigors, and pyrexia. PF-3512676 at the doses used was generally well tolerated. The modest objective response rates observed in all arms did not warrant continuation to the phase 3 portion of the study.

Oligonucleotide treatment causes flax β-glucanase up-regulation via changes in gene-body methylation.

PubMed

Wojtasik, Wioleta; Kulma, Anna; Boba, Aleksandra; Szopa, Jan

2014-10-05

Nowadays, the challenge for biotechnology is to develop tools for agriculture and industry to provide plants characterized by productivity and quality that will satisfy the growing demand for different kinds of natural products. To meet the challenge, the generation and application of genetically modified plants is justified. However, the strong social resistance to genetically modified organisms and restrictive regulations in European Union countries necessitated the development of a new technology for new plant types generation which uses the knowledge resulting from analysis of genetically modified plants to generate favourably altered plants while omitting the introduction of heterologous genes to their genome. Four-year experiments led to the development of a technology inducing heritable epigenetic gene activation without transgenesis. The method comprises the induction of changes in methylation/demethylation of the endogenous gene by the plant's treatment with short oligodeoxynucleotides antisense to the coding region. In vitro cultured plants and F3 generation flax plants overproducing the β-1,3-glucanase gene (EMO-βGlu flax) were characterized by up-regulation of β-glucanase and chitinase genes, decreases in the methylation of CCGG sequences in the β-glucanase gene and in total DNA methylation and, more importantly, reasonable resistance against Fusarium infection. In addition, EMO-βGlu flax obtained by this technology showed similar features as those obtained by genetic engineering. To our best knowledge, this is the first report on plant gene activation by treatment with oligodeoxynucleotides homologous to the coding region of the gene. Apart from the evident effectiveness, the most important issue is that the EMO method allows generation of favourably altered plants, whose cultivation makes the plant producer independent from the complicated procedure of obtaining an agreement on GMO release into the environment and whose products might be more easily introduced to the global market.

Interleukin-12- and Gamma Interferon-Dependent Protection against Malaria Conferred by CpG Oligodeoxynucleotide in Mice

PubMed Central

Gramzinski, Robert A.; Doolan, Denise L.; Sedegah, Martha; Davis, Heather L.; Krieg, Arthur M.; Hoffman, Stephen L.

2001-01-01

Unmethylated CpG dinucleotides in bacterial DNA or synthetic oligodeoxynucleotides (ODNs) cause B-cell proliferation and immunoglobulin secretion, monocyte cytokine secretion, and activation of natural killer (NK) cell lytic activity and gamma interferon (IFN-γ) secretion in vivo and in vitro. The potent Th1-like immune activation by CpG ODNs suggests a possible utility for enhancing innate immunity against infectious pathogens. We therefore investigated whether the innate immune response could protect against malaria. Treatment of mice with CpG ODN 1826 (TCCATGACGTTCCTGACGTT, with the CpG dinucleotides underlined) or 1585 (ggGGTCAACGTTGAgggggG, with g representing diester linkages and phosphorothioate linkages being to the right of lowercase letters) in the absence of antigen 1 to 2 days prior to challenge with Plasmodium yoelii sporozoites conferred sterile protection against infection. A higher level of protection was consistently induced by CpG ODN 1826 compared with CpG ODN 1585. The protective effects of both CpG ODNs were dependent on interleukin-12, as well as IFN-γ. Moreover, CD8+ T cells (but not CD4+ T cells), NK cells, and nitric oxide were implicated in the CpG ODN 1585-induced protection. These data establish that the protective mechanism induced by administration of CpG ODN 1585 in the absence of parasite antigen is similar in nature to the mechanism induced by immunization with radiation-attenuated P. yoelii sporozoites or with plasmid DNA encoding preerythrocytic-stage P. yoelii antigens. We were unable to confirm whether CD8+ T cells, NK cells, or nitric oxide were required for the CpG ODN 1826-induced protection, but this may reflect differences in the potency of the ODNs rather than a real difference in the mechanism of action of the two ODNs. This is the first report that stimulation of the innate immune system by CpG immunostimulatory motifs can confer sterile protection against malaria. PMID:11179339

CpG oligodeoxynucleotide induces apoptosis and cell cycle arrest in A20 lymphoma cells via TLR9-mediated pathways.

PubMed

Qi, Xu-Feng; Zheng, Li; Kim, Cheol-Su; Lee, Kyu-Jae; Kim, Dong-Heui; Cai, Dong-Qing; Qin, Jun-Wen; Yu, Yan-Hong; Wu, Zheng; Kim, Soo-Ki

2013-07-01

Recent studies have suggested that the anti-cancer activity of CpG-oligodeoxynucleotides (CpG-ODNs) is owing to their immunomodulatory effects in tumor-bearing host. The purpose of this study is to investigate the directly cytotoxic activity of KSK-CpG, a novel CpG-ODN with an alternative CpG motif, against A20 and EL4 lymphoma cells in comparison with previously used murine CpG motif (1826-CpG). To evaluate the potential cytotoxic effects of KSK-CpG on lymphoma cells, cell viability assay, confocal microscopy, flow cytometry, DNA fragmentation, Western blotting, and reverse transcription-polymerase chain reaction (RT-PCR) analysis were used. We found that KSK-CpG induced direct cytotoxicity in A20 lymphoma cells, but not in EL4 lymphoma cells, at least in part via TLR9-mediated pathways. Apoptotic cell death was demonstrated to play an important role in CpG-ODNs-induced cytotoxicity. In addition, both mitochondrial membrane potential decrease and G1-phase arrest were involved in KSK-CpG-induced apoptosis in A20 cells. The activities of apoptotic molecules such as caspase-3, PARP, and Bax were increased, but the activation of p27 Kip1 and ERK were decreased in KSK-CpG-treated A20 cells. Furthermore, autocrine IFN-γ partially contributed to apoptotic cell death in KSK-CpG-treated A20 cells. Collectively, our findings suggest that KSK-CpG induces apoptotic cell death in A20 lymphoma cells at least in part by inducing G1-phase arrest and autocrine IFN-γ via increasing TLR9 expression, without the need for immune system of tumor-bearing host. This new understanding supports the development of TLR9-targeted therapy with CpG-ODN as a direct therapeutic agent for treating B lymphoma. Copyright © 2013 Elsevier Ltd. All rights reserved.

Modification of the plasma clearance and liver uptake of steroid ester-conjugated oligodeoxynucleotides by association with (lactosylated) low-density lipoprotein.

PubMed

Rump, E T; de Vrueh, R L; Manoharan, M; Waarlo, I H; van Veghel, R; Biessen, E A; van Berkel, T J; Bijsterbosch, M K

2000-06-01

Low-density lipoprotein (LDL) has been proposed as carrier for the selective delivery of anticancer drugs to tumor cells. We reported earlier the association of several lipidic steroid-conjugated anticancer oligodeoxynucleotides (ODNs) with LDL. In the present study, we determined the stability of these complexes. When the complexes were incubated with a mixture of high-density lipoprotein and albumin, or with rat plasma, the oleoyl steroid-conjugated ODNs appeared to be more stably associated with LDL than the cholesteryl-conjugated ODN. Intravenously injected free lipid-ODNs were very rapidly cleared from the circulation of rats. The area under the curve (AUC) of the lipid-ODNs in plasma was <0.4 microg x min/mL. After complexation with LDL, plasma clearance of the lipid-ODNs was delayed. This was most evident for ODN-5, the ODN conjugated with the oleoyl ester of lithocholic acid (AUC = 6.82 +/- 1.34 microg x min/mL). The AUC of ODN-4, a cholesteryl-conjugated ODN, was 1.49 +/- 0.37 microg x min/mL. In addition, the liver uptake of the LDL-complexed lipid-ODNs was reduced. The lipid-ODNs were also administered as a complex with lactosylated LDL, a modified LDL particle that is selectively taken up by the liver. A high proportion of ODN-5 was transported to the liver along with lactosylated LDL (69.1 +/- 8.1% of the dose at 15 min after injection), whereas much less ODN-4 was transported (36.6 +/- 0.1% of the dose at 15 min after injection). We conclude that the oleoyl ester of lithocholic acid is a more potent lipid anchor than the other steroid lipid anchors. Because of the stable association, the oleoyl ester of lithocholic acid is an interesting candidate for tumor targeting of anticancer ODNs with lipoproteins.

Neonate intestinal immune response to CpG oligodeoxynucleotide stimulation.

PubMed

Lacroix-Lamandé, Sonia; Rochereau, Nicolas; Mancassola, Roselyne; Barrier, Mathieu; Clauzon, Amandine; Laurent, Fabrice

2009-12-14

The development of mucosal vaccines is crucial to efficiently control infectious agents for which mucosae are the primary site of entry. Major drawbacks of these protective strategies are the lack of effective mucosal adjuvant. Synthetic oligodeoxynucleotides that contain several unmethylated cytosine-guanine dinucleotide (CpG-ODN) motifs are now recognized as promising adjuvants displaying mucosal adjuvant activity through direct activation of TLR9-expressing cells. However, little is known about the efficacy of these molecules in stimulating the intestinal immune system in neonates. First, newborn mice received CpG-ODN orally, and the intestinal cytokine and chemokine response was measured. We observed that oral administration of CpG-ODN induces CXC and CC chemokine responses and a cellular infiltration in the intestine of neonates as detected by immunohistochemistry. We next compared the efficiency of the oral route to intraperitoneal administration in stimulating the intestinal immune responses of both adults and neonates. Neonates were more responsive to TLR9-stimulation than adults whatever the CpG-ODN administration route. Their intestinal epithelial cells (IECs) indirectly responded to TLR9 stimulation and contributed to the CXC chemokine response, whereas other TLR9-bearing cells of the lamina-propria produced CC chemokines and Th1-type cytokines. Moreover, we showed that the intestine of adult exhibited a significantly higher level of IL10 at homeostasis than neonates, which might be responsible for the unresponsiveness to TLR9-stimulation, as confirmed by our findings in IL10-deficient mice. This is the first report that deciphers the role played by CpG-ODN in the intestine of neonates. This work clearly demonstrates that an intraperitoneal administration of CpG-ODN is more efficient in neonates than in adults to stimulate an intestinal chemokine response due to their lower IL-10 intestinal level. In addition we report the efficiency of the oral route at inducing intestinal chemokine responses in neonate that might be taken into consideration for further vaccine development against neonatal diseases.

Enhanced immune response to gastric cancer specific antigen Peptide by coencapsulation with CpG oligodeoxynucleotides in nanoemulsion.

PubMed

Shi, Rui; Hong, Liu; Wu, Daocheng; Ning, Xiaoxuan; Chen, Yu; Lin, Tao; Fan, Daiming; Wu, Kaichun

2005-02-01

CpG oligodeoxynucleotides (CpG ODN) have been shown to have potent adjuvant activity for a wide range of antigens. Of particular interest is their improved activity when closely associated with the antigen. The purpose of this study is to construct a nanovaccine coencapsulated with a gastric cancer specific antigen MG7 mimotope peptide and adjuvant CpG ODN 1645 using new nanotechnology as nanoemulsion and evaluate its immunocompetence. Nanoemulsion vaccine was prepared using magnetic ultrasound methods. BALB/c mice were immunized and the in vivo effectiveness was evaluated using tumor challenge assay. It was shown that the tumor masses formed in the mice immunized with coencapsulated nanovaccine (0.0825 g) markedly smaller (P < 0.01) than those formed in the mice immunized with nanovaccine encapsulated with antigen peptide alone (0.4465 g). A tumor inhibiting rate as high as 82.5% of the coencapsulated nanovaccine was obtained, while nanovaccine encapsulated with peptide only could not achieve the same effect (28.5%) (P < 0.01). Enzyme-linked immunospot assay (ELISPOT) showed that immunization using MG7 mimotope peptide coencapsulated with CpG ODN within the same nanoemulsion enhanced the frequency of splenocytes secreting IFN-gamma significantly (P < 0.01) when compared with immunization using MG7 peptide encapsulated in nanoemulsion alone (197spots/1 x 10(6) vs. 73 spots/1 x 10(6)). Cellular ELISA indicated that serum titer of antibody against MG7-Ag was significantly higher (P < 0.01) in mice immunized with coencapsulation form nanovaccine (0.7884) than that in the group immunized with nanovaccine encapsulated with MG7 peptide alone (0.3616). Using intracellular flow cytometric analysis, it was found that the IFN-gamma response was contributed by CD4+ T-cells. Our experiments suggest that a vaccinal approach using nano-delivery system carrying in tumoral epitope and CpG ODN as adjuvant may have important implications for cancer therapy.

Functional Scanning Probe Imaging of Nanostructured Solar Energy Materials.

PubMed

Giridharagopal, Rajiv; Cox, Phillip A; Ginger, David S

2016-09-20

From hybrid perovskites to semiconducting polymer/fullerene blends for organic photovoltaics, many new materials being explored for energy harvesting and storage exhibit performance characteristics that depend sensitively on their nanoscale morphology. At the same time, rapid advances in the capability and accessibility of scanning probe microscopy methods over the past decade have made it possible to study processing/structure/function relationships ranging from photocurrent collection to photocarrier lifetimes with resolutions on the scale of tens of nanometers or better. Importantly, such scanning probe methods offer the potential to combine measurements of local structure with local function, and they can be implemented to study materials in situ or devices in operando to better understand how materials evolve in time in response to an external stimulus or environmental perturbation. This Account highlights recent advances in the development and application of scanning probe microscopy methods that can help address such questions while filling key gaps between the capabilities of conventional electron microscopy and newer super-resolution optical methods. Focusing on semiconductor materials for solar energy applications, we highlight a range of electrical and optoelectronic scanning probe microscopy methods that exploit the local dynamics of an atomic force microscope tip to probe key properties of the solar cell material or device structure. We discuss how it is possible to extract relevant device properties using noncontact scanning probe methods as well as how these properties guide materials development. Specifically, we discuss intensity-modulated scanning Kelvin probe microscopy (IM-SKPM), time-resolved electrostatic force microscopy (trEFM), frequency-modulated electrostatic force microscopy (FM-EFM), and cantilever ringdown imaging. We explain these developments in the context of classic atomic force microscopy (AFM) methods that exploit the physics of cantilever motion and photocarrier generation to provide robust, nanoscale measurements of materials physics that are correlated with device operation. We predict that the multidimensional data sets made possible by these types of methods will become increasingly important as advances in data science expand capabilities and opportunities for image correlation and discovery.

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

Application of FRET Technology to the In Vivo Evaluation of Therapeutic Nucleic Acids (ANTs)

NASA Astrophysics Data System (ADS)

Benítez-Hess, María Luisa; Alvarez-Salas, Luis Marat

2007-02-01

Developing applications for therapeutic nucleic acids (TNAs) (i.e. ribozymes, antisense oligodeoxynucleotides (AS-ODNs), siRNA and aptamers) requires a reporter system designed to rapidly evaluate their in vivo effect. To this end we designed a reporter system based on the fluorescence resonance energy transfer (FRET) engineered to release the FRET effect produced by two green fluorescent protein (GFP) variants linked by a TNA target site. Because the FRET effect occurs instantaneously when two fluorophores are very close to each other (>100nm) stimulating emission of the acceptor fluorophore by the excitation of the donor fluorophore it has been widely use to reveal interactions between molecules. The present system (FRET2) correlates the FRET effect with the in vivo activity of distinct types of TNAs based on a model consisting of RNA from human papillomavirus type 16 (HPV-16) previously shown accessible to TNAs. HPV-16 is the most common papillomavirus associated with cervical cancer, the leading cause of death by cancer in México. The FRET2 system was first tested in vitro and then used in bacteria in which transcription is linked to translation allowing controlled expression and rapid evaluation of the FRET2 protein. To assure accessibility of the target mRNA to TNAs, the FRET2 mRNA was probed by RNaseH assays prior FRET testing. The fluorescence features of the FRET2 system was tested with different FRET-producing GFP donor-acceptor pairs leading to selection of green (donor) and yellow (acceptor) variants of GFP as the most efficient. Modifications in aminoacid composition and linker length of the target sequence did not affect FRET efficiency. In vivo AS-ODN-mediated destruction of the chimerical FRET2 reporter mRNA resulted in the recovery of GFP fluorescent spectrum in a concentration and time dependent manner. Reported anti-HPV ribozymes were also tested with similar results. Therefore, we conclude that the FRET effect can be a useful tool in the development of TNAs.

Failure analysis on false call probe pins of microprocessor test equipment

NASA Astrophysics Data System (ADS)

Tang, L. W.; Ong, N. R.; Mohamad, I. S. B.; Alcain, J. B.; Retnasamy, V.

2017-09-01

A study has been conducted to investigate failure analysis on probe pins of test modules for microprocessor. The `health condition' of the probe pin is determined by the resistance value. A test module of 5V power supplied from Arduino UNO with "Four-wire Ohm measurement" method is implemented in this study to measure the resistance of the probe pins of a microprocessor. The probe pins from a scrapped computer motherboard is used as the test sample in this study. The functionality of the test module was validated with the pre-measurement experiment via VEE Pro software. Lastly, the experimental work have demonstrated that the implemented test module have the capability to identify the probe pin's `health condition' based on the measured resistance value.

Potential of an emissive cylindrical probe in plasma.

PubMed

Fruchtman, A; Zoler, D; Makrinich, G

2011-08-01

The floating potential of an emissive cylindrical probe in a plasma is calculated for an arbitrary ratio of Debye length to probe radius and for an arbitrary ion composition. In their motion to the probe the ions are assumed to be collisionless. For a small Debye length, a two-scale analysis for the quasineutral plasma and for the sheath provides analytical expressions for the emitted and collected currents and for the potential as functions of a generalized mass ratio. For a Debye length that is not small, it is demonstrated that, as the Debye length becomes larger, the probe potential approaches the plasma potential and that the ion density near the probe is not smaller but rather is larger than it is in the plasma bulk.

Image simulation for electron energy loss spectroscopy

DOE PAGES

Oxley, Mark P.; Pennycook, Stephen J.

2007-10-22

In this paper, aberration correction of the probe forming optics of the scanning transmission electron microscope has allowed the probe-forming aperture to be increased in size, resulting in probes of the order of 1 Å in diameter. The next generation of correctors promise even smaller probes. Improved spectrometer optics also offers the possibility of larger electron energy loss spectrometry detectors. The localization of images based on core-loss electron energy loss spectroscopy is examined as function of both probe-forming aperture and detector size. The effective ionization is nonlocal in nature, and two common local approximations are compared to full nonlocal calculations.more » Finally, the affect of the channelling of the electron probe within the sample is also discussed.« less

Development of a BODIPY-based ratiometric fluorescent probe for hypochlorous acid and its application in living cells.

PubMed

Wang, Xuzhe; Zhou, Li; Qiang, Fei; Wang, Feiyi; Wang, Rui; Zhao, Chunchang

2016-03-10

A BODIPY-based ratiometric fluorescent probe for HOCl has been designed based on the transduction of thioether to sulfoxide function. This probe features a marked absorption and emission blue-shift upon the HOCl-promoted rapid transduction, enabling the highly selective and ratiometric detection. In addition, the probe works excellently within a wide pH range of 4-10, addressing the existing pH dependency issue. Living cells studies demonstrate that the probe is cell membrane permeable and can be employed successfully to image endogenous HOCl generation in macrophage cells. Copyright © 2016 Elsevier B.V. All rights reserved.

Synthetic-Molecule/Protein Hybrid Probe with Fluorogenic Switch for Live-Cell Imaging of DNA Methylation.

PubMed

Hori, Yuichiro; Otomura, Norimichi; Nishida, Ayuko; Nishiura, Miyako; Umeno, Maho; Suetake, Isao; Kikuchi, Kazuya

2018-02-07

Hybrid probes consisting of synthetic molecules and proteins are powerful tools for detecting biological molecules and signals in living cells. To date, most targets of the hybrid probes have been limited to pH and small analytes. Although biomacromolecules are essential to the physiological function of cells, the hybrid-probe-based approach has been scarcely employed for live-cell detection of biomacromolecules. Here, we developed a hybrid probe with a chemical switch for live-cell imaging of methylated DNA, an important macromolecule in the repression of gene expression. Using a protein labeling technique, we created a hybrid probe containing a DNA-binding fluorogen and a methylated-DNA-binding domain. The hybrid probe enhanced fluorescence intensity upon binding to methylated DNA and successfully monitored methylated DNA during mitosis. The hybrid probe offers notable advantages absent from probes based on small molecules or fluorescent proteins and is useful for live-cell analyses of epigenetic phenomena and diseases related to DNA methylation.

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

PubMed Central

Rutenberg-Schoenberg, Michael; Simon, Matthew D.

2015-01-01

The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5’-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function. PMID:26646615

Accuracy enhancement of point triangulation probes for linear displacement measurement

NASA Astrophysics Data System (ADS)

Kim, Kyung-Chan; Kim, Jong-Ahn; Oh, SeBaek; Kim, Soo Hyun; Kwak, Yoon Keun

2000-03-01

Point triangulation probes (PTBs) fall into a general category of noncontact height or displacement measurement devices. PTBs are widely used for their simple structure, high resolution, and long operating range. However, there are several factors that must be taken into account in order to obtain high accuracy and reliability; measurement errors from inclinations of an object surface, probe signal fluctuations generated by speckle effects, power variation of a light source, electronic noises, and so on. In this paper, we propose a novel signal processing algorithm, named as EASDF (expanded average square difference function), for a newly designed PTB which is composed of an incoherent source (LED), a line scan array detector, a specially selected diffuse reflecting surface, and several optical components. The EASDF, which is a modified correlation function, is able to calculate displacement between the probe and the object surface effectively even if there are inclinations, power fluctuations, and noises.

A reversible fluorescent probe for real-time live-cell imaging and quantification of endogenous hydropolysulfides.

PubMed

Umezawa, Keitaro; Kamiya, Mako; Urano, Yasuteru

2018-05-23

The chemical biology of reactive sulfur species, including hydropolysulfides, has been a subject undergoing intense study in recent years, but further understanding of their 'intact' function in living cells has been limited due to a lack of appropriate analytical tools. In order to overcome this limitation, we developed a new type of fluorescent probe which reversibly and selectively reacts to hydropolysulfides. The probe enables live-cell visualization and quantification of endogenous hydropolysulfides without interference from intrinsic thiol species such as glutathione. Additionally, real-time reversible monitoring of oxidative-stress-induced fluctuation of intrinsic hydropolysulfides has been achieved with a temporal resolution in the order of seconds, a result which has not yet been realized using conventional methods. These results reveal the probe's versatility as a new fluorescence imaging tool to understand the function of intracellular hydropolysulfides. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optimizing the specificity of nucleic acid hybridization.

PubMed

Zhang, David Yu; Chen, Sherry Xi; Yin, Peng

2012-01-22

The specific hybridization of complementary sequences is an essential property of nucleic acids, enabling diverse biological and biotechnological reactions and functions. However, the specificity of nucleic acid hybridization is compromised for long strands, except near the melting temperature. Here, we analytically derived the thermodynamic properties of a hybridization probe that would enable near-optimal single-base discrimination and perform robustly across diverse temperature, salt and concentration conditions. We rationally designed 'toehold exchange' probes that approximate these properties, and comprehensively tested them against five different DNA targets and 55 spurious analogues with energetically representative single-base changes (replacements, deletions and insertions). These probes produced discrimination factors between 3 and 100+ (median, 26). Without retuning, our probes function robustly from 10 °C to 37 °C, from 1 mM Mg(2+) to 47 mM Mg(2+), and with nucleic acid concentrations from 1 nM to 5 µM. Experiments with RNA also showed effective single-base change discrimination.

Active Plasma Resonance Spectroscopy: Evaluation of a fluiddynamic-model of the planar multipole resonance probe using functional analytic methods

NASA Astrophysics Data System (ADS)

Friedrichs, Michael; Brinkmann, Ralf Peter; Oberrath, Jens

2016-09-01

Measuring plasma parameters, e.g. electron density and electron temperature, is an important procedure to verify the stability and behavior of a plasma process. For this purpose the multipole resonance probe (MRP) represents a satisfying solution to measure the electron density. However the influence of the probe on the plasma through its physical presence makes it unattractive for some processes in industrial application. A solution to combine the benefits of the spherical MRP with the ability to integrate the probe into the plasma reactor is introduced by the planar model of the MRP. By coupling the model of the cold plasma with the maxwell equations for electrostatics an analytical model for the admittance of the plasma is derivated, adjusted to cylindrical geometry and solved analytically for the planar MRP using functional analytic methods.

Investigation of static and dynamic behavior of functionally graded piezoelectric actuated Poly-Si micro cantilever probe

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

Pandey, Vibhuti Bhushan; Parashar, Sandeep Kumar, E-mail: skparashar@rtu.ac.in

In the present paper a novel functionally graded piezoelectric (FGP) actuated Poly-Si micro cantilever probe is proposed for atomic force microscope. The shear piezoelectric coefficient d{sub 15} has much higher value than coupling coefficients d{sub 31} and d{sub 33}, hence in the present work the micro cantilever beam actuated by d{sub 15} effect is utilized. The material properties are graded in the thickness direction of actuator by a simple power law. A three dimensional finite element analysis has been performed using COMSOL Multiphysics® (version 4.2) software. Tip deflection and free vibration analysis for the micro cantilever probe has been done.more » The results presented in the paper shall be useful in the design of micro cantilever probe and their subsequent utilization in atomic force microscopes.« less

Genetic Incorporation of Twelve meta-Substituted Phenylalanine Derivatives Using A Single Pyrrolysyl-tRNA Synthetase

PubMed Central

Wang, Yane-Shih; Fang, Xinqiang; Chen, Hsueh-Ying; Wu, Bo; Wang, Zhiyong U.; Hilty, Christian; Liu, Wenshe R.

2012-01-01

When coexpressed with its cognate amber suppressing tRNACUAPyl, a pyrrolysyl-tRNA synthetase mutant N346A/C348A is able to genetically incorporate twelve meta-substituted phenylalanine derivatives into proteins site-specifically at amber mutation sites in Escherichia coli. These genetically encoded noncanonical amino acids resemble phenylalanine in size and contain diverse bioorthogonal functional groups such as halide, trifluoromethyl, nitrile, nitro, ketone, alkyne, and azide moieties. The genetic installation of these functional groups in proteins provides multiple ways to site-selectively label proteins with biophysical and biochemical probes for their functional investigations. We demonstrate that a genetically incorporated trifluoromethyl group can be used as a sensitive 19F NMR probe to study protein folding/unfolding, and that genetically incorporated reactive functional groups such as ketone, alkyne, and azide moieties can be applied to site-specifically label proteins with florescent probes. This critical discovery allows the synthesis of proteins with diverse bioorthogonal functional groups for a variety of basic studies and biotechnology development using a single recombinant expression system. PMID:23138887

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

Picosecond excite-and-probe absorption measurement of the 4T2 state nonradiative lifetime in ruby

NASA Technical Reports Server (NTRS)

Gayen, S. K.; Wang, W. B.; Petricevic, V.; Dorsinville, R.; Alfano, R. R.

1985-01-01

In a picosecond excite-and-probe absorption measurement, a 527-nm picosecond pulse excites the 4T2 state of the Cr(3+) ion in ruby and a 3.4-micron picosecond probe pulse monitors the growth and decay of population in the 2E state as a function of pump-probe delay. From the growth of population in the metastable 2E state, an upper limit of 7 ps for the nonradiative lifetime of the 4T2 state is determined.

Effects of computer-based training on procedural modifications to standard functional analyses.

PubMed

Schnell, Lauren K; Sidener, Tina M; DeBar, Ruth M; Vladescu, Jason C; Kahng, SungWoo

2018-01-01

Few studies have evaluated methods for training decision-making when functional analysis data are undifferentiated. The current study evaluated computer-based training to teach 20 graduate students to arrange functional analysis conditions, analyze functional analysis data, and implement procedural modifications. Participants were exposed to training materials using interactive software during a 1-day session. Following the training, mean scores on the posttest, novel cases probe, and maintenance probe increased for all participants. These results replicate previous findings during a 1-day session and include a measure of participant acceptability of the training. Recommendations for future research on computer-based training and functional analysis are discussed. © 2017 Society for the Experimental Analysis of Behavior.

GeoChip 3.0: A High Throughput Tool for Analyzing Microbial Community, Composition, Structure, and Functional Activity

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

He, Zhili; Deng, Ye; Nostrand, Joy Van

2010-05-17

Microarray-based genomic technology has been widely used for microbial community analysis, and it is expected that microarray-based genomic technologies will revolutionize the analysis of microbial community structure, function and dynamics. A new generation of functional gene arrays (GeoChip 3.0) has been developed, with 27,812 probes covering 56,990 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance, and organic contaminant degradation. Those probes were derived from 2,744, 140, and 262 species for bacteria, archaea, and fungi, respectively. GeoChip 3.0 has several other distinct features, such as a common oligomore » reference standard (CORS) for data normalization and comparison, a software package for data management and future updating, and the gyrB gene for phylogenetic analysis. Our computational evaluation of probe specificity indicated that all designed probes had a high specificity to their corresponding targets. Also, experimental analysis with synthesized oligonucleotides and genomic DNAs showed that only 0.0036percent-0.025percent false positive rates were observed, suggesting that the designed probes are highly specific under the experimental conditions examined. In addition, GeoChip 3.0 was applied to analyze soil microbial communities in a multifactor grassland ecosystem in Minnesota, USA, which demonstrated that the structure, composition, and potential activity of soil microbial communities significantly changed with the plant species diversity. All results indicate that GeoChip 3.0 is a high throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning. To our knowledge, GeoChip 3.0 is the most comprehensive microarrays currently available for studying microbial communities associated with geobiochemical cycling, global climate change, bioenergy, agricuture, land use, ecosystem management, environmental cleanup and restoration, bioreactor systems, and human health.« less

Method and apparatus for optical temperature measurement

DOEpatents

O'Rourke, P.E.; Livingston, R.R.; Prather, W.S.

1994-09-20

A temperature probe and a method for using said probe for temperature measurements based on changes in light absorption by the probe are disclosed. The probe comprises a first and a second optical fiber that carry light to and from the probe, and a temperature sensor material, the absorbance of which changes with temperature, through which the light is directed. Light is directed through the first optical fiber, passes through the temperature sensor material, and is transmitted by a second optical fiber from the material to a detector. Temperature-dependent and temperature-independent factors are derived from measurements of the transmitted light intensity. For each sensor material, the temperature T is a function of the ratio, R, of these factors. The temperature function f(R) is found by applying standard data analysis techniques to plots of T versus R at a series of known temperatures. For a sensor having a known temperature function f(R) and known characteristic and temperature-dependent factors, the temperature can be computed from a measurement of R. Suitable sensor materials include neodymium-doped borosilicate glass, accurate to [+-]0.5 C over an operating temperature range of about [minus]196 C to 400 C; and a mixture of D[sub 2]O and H[sub 2]O, accurate to [+-]0.1 C over an operating range of about 5 C to 90 C. 13 figs.

Method and apparatus for optical temperature measurement

DOEpatents

O'Rourke, Patrick E.; Livingston, Ronald R.; Prather, William S.

1994-01-01

A temperature probe and a method for using said probe for temperature measurements based on changes in light absorption by the probe. The probe comprises a first and a second optical fiber that carry light to and from the probe, and a temperature sensor material, the absorbance of which changes with temperature, through which the light is directed. Light is directed through the first optical fiber, passes through the temperature sensor material, and is transmitted by a second optical fiber from the material to a detector. Temperature-dependent and temperature-independent factors are derived from measurements of the transmitted light intensity. For each sensor material, the temperature T is a function of the ratio, R, of these factors. The temperature function f(R) is found by applying standard data analysis techniques to plots of T versus R at a series of known temperatures. For a sensor having a known temperature function f(R) and known characteristic and temperature-dependent factors, the temperature can be computed from a measurement of R. Suitable sensor materials include neodymium-doped boresilicate glass, accurate to .+-.0.5.degree. C. over an operating temperature range of about -196.degree. C. to 400.degree. C.; and a mixture of D.sub.2 O and H.sub.2 O, accurate to .+-.0.1.degree. C. over an operating range of about 5.degree. C. to 90.degree. C.

The local work function: Concept and implications

NASA Astrophysics Data System (ADS)

Wandelt, K.

1997-02-01

The term 'local work function' is now widely applied. The present work discusses the common physical basis of 'photoemission of adsorbed xenon (PAX)' and 'two-photon photonemissionspectroscopy of image potential states' as local work function probes. New examples with bimetallic and defective surfaces are presented which demonstrate the capability of PAX measurements for the characterization of heterogeneous surfaces on an atomic scale. Finally, implications of the existence of short-range variations of the surface potential at surface steps are addressed. In particular, dynamical work function change measurements are a sensitive probe for the step-density at surfaces and, as such, a powerful in-situ method to monitor film growth.

Accurate Detection of Adenylation Domain Functions in Nonribosomal Peptide Synthetases by an Enzyme-linked Immunosorbent Assay System Using Active Site-directed Probes for Adenylation Domains.

PubMed

Ishikawa, Fumihiro; Miyamoto, Kengo; Konno, Sho; Kasai, Shota; Kakeya, Hideaki

2015-12-18

A significant gap exists between protein engineering and enzymes used for the biosynthesis of natural products, largely because there is a paucity of strategies that rapidly detect active-site phenotypes of the enzymes with desired activities. Herein, we describe a proof-of-concept study of an enzyme-linked immunosorbent assay (ELISA) system for the adenylation (A) domains in nonribosomal peptide synthetases (NRPSs) using a combination of active site-directed probes coupled to a 5'-O-N-(aminoacyl)sulfamoyladenosine scaffold with a biotin functionality that immobilizes probe molecules onto a streptavidin-coated solid support. The recombinant NRPSs have a C-terminal His-tag motif that is targeted by an anti-6×His mouse antibody as the primary antibody and a horseradish peroxidase-linked goat antimouse antibody as the secondary antibody. These probes can selectively capture the cognate A domains by ligand-directed targeting. In addition, the ELISA technique detected A domains in the crude cell-free homogenates from the Escherichia coli expression systems. When coupled with a chromogenic substrate, the antibody-based ELISA technique can visualize probe-protein binding interactions, which provides accurate readouts of the A-domain functions in NRPS enzymes. To assess the ELISA-based engineering of the A domains of NRPSs, we reprogramed 2,3-dihydroxybenzoic acid (DHB)-activating enzyme EntE toward salicylic acid (Sal)-activating enzymes and investigated a correlation between binding properties for probe molecules and enzyme catalysts. We generated a mutant of EntE that displayed negligible loss in the kcat/Km value with the noncognate substrate Sal and a corresponding 48-fold decrease in the kcat/Km value with the cognate substrate DHB. The resulting 26-fold switch in substrate specificity was achieved by the replacement of a Ser residue in the active site of EntE with a Cys toward the nonribosomal codes of Sal-activating enzymes. Bringing a laboratory ELISA technique and adenylating enzymes together using a combination of active site-directed probes for the A domains in NRPSs should accelerate both the functional characterization and manipulation of the A domains in NRPSs.

Separation of 'Uncharged' Oligodeoxynucleotide Analogs by Anion-Exchange Chromatography at High pH

NASA Technical Reports Server (NTRS)

Schmidt, Jurgen G.; Orgel, Leslie E.; Nielsen, Peter E.

1996-01-01

Ion-exchange chromatography is a well-established method for the analysis and purification of phosphodiester-linked oligonucleotides. If elution is carried out under alkaline conditions, the secondary structure of G- and C-rich oligomers is disrupted. Furthermore, elution times become more sensitive to the G and T content of the oligomer, because G and T are deprotonated at pH 10. In recent work on peptide-nucleic acids (PNAs) we noted that mixtures of PNA oligomers G(sub 4), G(sub 6), G(sub 8), and G9(sub 10) are readily separated by elution at pH 12 on an RPC-5 column. Here we show that this separation method is more generally applicable.

Cleavage of an amide bond by a ribozyme

NASA Technical Reports Server (NTRS)

Dai, X.; De Mesmaeker, A.; Joyce, G. F.; Miller, S. L. (Principal Investigator)

1995-01-01

A variant form of a group I ribozyme, optimized by in vitro evolution for its ability to catalyze magnesium-dependent phosphoester transfer reactions involving DNA substrates, also catalyzes the cleavage of an unactivated alkyl amide when that linkage is presented in the context of an oligodeoxynucleotide analog. Substrates containing an amide bond that joins either two DNA oligos, or a DNA oligo and a short peptide, are cleaved in a magnesium-dependent fashion to generate the expected products. The first-order rate constant, kcat, is 0.1 x 10(-5) min-1 to 1 x 10(-5) min-1 for the DNA-flanked substrates, which corresponds to a rate acceleration of more than 10(3) as compared with the uncatalyzed reaction.

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

Chenna, Ahmed; Gupta, Ramesh C.; Bonala, Radha R.

N2-(4-Hydroxyphenyl)-2'-deoxyguanosine-5'-O-DMT-3'-phosphoramidite has been synthesized and used to incorporate the N2-(4-hydroxyphenyl)-2'-dG (N2-4-HOPh-dG) into DNA, using solid-state synthesis technology. The key step to obtaining the xenonucleoside is a palladium (Xantphos-chelated) catalyzed N2-arylation (Buchwald-Hartwig reaction) of a fully protected 2'-deoxyguanosine derivative by 4-isobutyryloxybromobenzene. The reaction proceeded in good yield and the adduct was converted to the required 5'-O-DMT-3'-O-phosphoramidite by standard methods. The latter was used to synthesize oligodeoxynucleotides in which the N2-4-HOPh-dG adduct was incorporated site-specifically. The oligomers were purified by reverse-phase HPLC. Enzymatic hydrolysis and HPLC analysis confirmed the presence of this adduct in the oligomers.

Application of activity-based protein profiling to study enzyme function in adipocytes.

PubMed

Galmozzi, Andrea; Dominguez, Eduardo; Cravatt, Benjamin F; Saez, Enrique

2014-01-01

Activity-based protein profiling (ABPP) is a chemical proteomics approach that utilizes small-molecule probes to determine the functional state of enzymes directly in native systems. ABPP probes selectively label active enzymes, but not their inactive forms, facilitating the characterization of changes in enzyme activity that occur without alterations in protein levels. ABPP can be a tool superior to conventional gene expression and proteomic profiling methods to discover new enzymes active in adipocytes and to detect differences in the activity of characterized enzymes that may be associated with disorders of adipose tissue function. ABPP probes have been developed that react selectively with most members of specific enzyme classes. Here, using as an example the serine hydrolase family that includes many enzymes with critical roles in adipocyte physiology, we describe methods to apply ABPP analysis to the study of adipocyte enzymatic pathways. © 2014 Elsevier Inc. All rights reserved.

Detection of single-copy functional genes in prokaryotic cells by two-pass TSA-FISH with polynucleotide probes.

PubMed

Kawakami, Shuji; Hasegawa, Takuya; Imachi, Hiroyuki; Yamaguchi, Takashi; Harada, Hideki; Ohashi, Akiyoshi; Kubota, Kengo

2012-02-01

In situ detection of functional genes with single-cell resolution is currently of interest to microbiologists. Here, we developed a two-pass tyramide signal amplification (TSA)-fluorescence in situ hybridization (FISH) protocol with PCR-derived polynucleotide probes for the detection of single-copy genes in prokaryotic cells. The mcrA gene and the apsA gene in methanogens and sulfate-reducing bacteria, respectively, were targeted. The protocol showed bright fluorescence with a good signal-to-noise ratio and achieved a high efficiency of detection (>98%). The discrimination threshold was approximately 82-89% sequence identity. Microorganisms possessing the mcrA or apsA gene in anaerobic sludge samples were successfully detected by two-pass TSA-FISH with polynucleotide probes. The developed protocol is useful for identifying single microbial cells based on functional gene sequences. Copyright © 2011 Elsevier B.V. All rights reserved.

Assessment of right ventricular function with nonimaging first pass ventriculography and comparison of results with gamma camera studies.

PubMed

Zhang, Z; Liu, X J; Liu, Y Z; Lu, P; Crawley, J C; Lahiri, A

1990-08-01

A new technique has been developed for measuring right ventricular function by nonimaging first pass ventriculography. The right ventricular ejection fraction (RVEF) obtained by non-imaging first pass ventriculography was compared with that obtained by gamma camera first pass and equilibrium ventriculography. The data has demonstrated that the correlation of RVEFs obtained by the nonimaging nuclear cardiac probe and by gamma camera first pass ventriculography in 15 subjects was comparable (r = 0.93). There was also a good correlation between RVEFs obtained by the nonimaging nuclear probe and by equilibrium gated blood pool studies in 33 subjects (r = 0.89). RVEF was significantly reduced in 15 patients with right ventricular and/or inferior myocardial infarction compared to normal subjects (28 +/- 9% v. 45 +/- 9%). The data suggests that nonimaging probes may be used for assessing right ventricular function accurately.

Are you mind-wandering, or is your mind on task? The effect of probe framing on mind-wandering reports.

PubMed

Weinstein, Yana; De Lima, Henry J; van der Zee, Tim

2018-04-01

The last decade has seen a dramatic rise in the number of studies that utilize the probe-caught method of collecting mind-wandering reports. This method involves stopping participants during a task, presenting them with a thought probe, and asking them to choose the appropriate report option to describe their thought-state. In this experiment we manipulated the framing of this probe, and demonstrated a substantial difference in mind-wandering reports as a function of whether the probe was presented in a mind-wandering frame compared with an on-task frame. This framing effect has implications both for interpretations of existing data and for methodological choices made by researchers who use the probe-caught mind-wandering paradigm.

Circumferential pressure probe

NASA Technical Reports Server (NTRS)

Holmes, Harlan K. (Inventor); Moore, Thomas C. (Inventor); Fantl, Andrew J. (Inventor)

1989-01-01

A probe for measuring circumferential pressure inside a body cavity is disclosed. In the preferred embodiment, a urodynamic pressure measurement probe for evaluating human urinary sphincter function is disclosed. Along the length of the probe are disposed a multiplicity of deformable wall sensors which typically comprise support tube sections with flexible side wall areas. These are arranged along the length of the probe in two areas, one just proximal to the tip for the sensing of fluid pressure inside the bladder, and five in the sensing section which is positioned within the urethra at the point at which the urinary sphincter constricts to control the flow of urine. The remainder of the length of the probe comprises multiple rigid support tube sections interspersed with flexible support tube sections in the form of bellows to provide flexibility.

The contributions of cerebro-cerebellar circuitry to executive verbal working memory.

PubMed

Marvel, Cherie L; Desmond, John E

2010-01-01

Contributions of cerebro-cerebellar function to executive verbal working memory were examined using event-related functional magnetic resonance imaging (fMRI) while 16 subjects completed two versions of the Sternberg task. In both versions subjects were presented with two or six target letters during the encoding phase, which were held in memory during the maintenance phase. A single probe letter was presented during the retrieval phase. In the "match condition", subjects decided whether the probe matched the target letters. In the "executive condition", subjects created a new probe by counting two alphabetical letters forward (e.g., f-->h) and decided whether the new probe matched the target letters. Neural activity during the match and executive conditions was compared during each phase of the task. There were four main findings. First, cerebro-cerebellar activity increased as a function of executive load. Second, the dorsal cerebellar dentate co-activated with the supplementary motor area (SMA) during encoding. This likely represented the formation of an articulatory (motor) trajectory. Third, the ventral cerebellar dentate co-activated with anterior prefrontal regions Brodmann Area (BA) 9/46 and the pre-SMA during retrieval. This likely represented the manipulation of information and formation of a response. A functional dissociation between the dorsal "motor" dentate and "cognitive" ventral dentate agrees with neuroanatomical tract tracing studies that have demonstrated separate neural pathways involving each region of the dentate: the dorsal dentate projects to frontal motor areas (including the SMA), and the ventral dentate projects to frontal cognitive areas (including BA 9/46 and the pre-SMA). Finally, activity during the maintenance phase in BA 9, anterior insula, pre-SMA and ventral dentate predicted subsequent accuracy of response to the probe during the retrieval phase. This finding underscored the significant contribution of the pre-SMA/ventral dentate pathway--observed several seconds prior to any motor response to the probe--to executive verbal working memory. Copyright (c) 2009 Elsevier Srl. All rights reserved.

The Contributions of Cerebro-Cerebellar Circuitry to Executive Verbal Working Memory

PubMed Central

Marvel, Cherie L.; Desmond, John E.

2009-01-01

Contributions of cerebro-cerebellar function to executive verbal working memory were examined using event-related functional magnetic resonance imaging (fMRI) while 16 subjects completed two versions of the Sternberg task. In both versions subjects were presented with two or six target letters during the encoding phase, which were held in memory during the maintenance phase. A single probe letter was presented during the retrieval phase. In the “match condition”, subjects decided whether the probe matched the target letters. In the “executive condition”, subjects created a new probe by counting two alphabetical letters forward (e.g., f → h) and decided whether the new probe matched the target letters. Neural activity during the match and executive conditions was compared during each phase of the task. There were four main findings. First, cerebro-cerebellar activity increased as a function of executive load. Second, the dorsal cerebellar dentate co-activated with the supplementary motor area (SMA) during encoding. This likely represented the formation of an articulatory (motor) trajectory. Third, the ventral cerebellar dentate co-activated with anterior prefrontal regions BA 9/46 and the pre-SMA during retrieval. This likely represented the manipulation of information and formation of a response. A functional dissociation between the dorsal “motor” dentate and “cognitive” ventral dentate agrees with neuroanatomical tract tracing studies that have demonstrated separate neural pathways involving each region of the dentate: the dorsal dentate projects to frontal motor areas (including the SMA), and the ventral dentate projects to frontal cognitive areas (including BA 9/46 and the pre-SMA). Finally, activity during the maintenance phase in BA 9, anterior insula, pre-SMA and ventral dentate predicted subsequent accuracy of response to the probe during the retrieval phase. This finding underscored the significant contribution of the pre-SMA/ventral dentate pathway – observed several seconds prior to any motor response to the probe -- to executive verbal working memory. PMID:19811779

Advances in development of fluorescent probes for detecting amyloid-β aggregates.

PubMed

Xu, Ming-Ming; Ren, Wen-Ming; Tang, Xi-Can; Hu, You-Hong; Zhang, Hai-Yan

2016-06-01

With accumulating evidence suggesting that amyloid-β (Aβ) deposition is a good diagnostic biomarker for Alzheimer's disease (AD), the discovery of active Aβ probes has become an active area of research. Among the existing imaging methods, optical imaging targeting Aβ aggregates (fibrils or oligomers), especially using near-infrared (NIR) fluorescent probes, is increasingly recognized as a promising approach for the early diagnosis of AD due to its real time detection, low cost, lack of radioactive exposure and high-resolution. In the past decade, a variety of fluorescent probes have been developed and tested for efficiency in vitro, and several probes have shown efficacy in AD transgenic mice. This review classifies these representative probes based on their chemical structures and functional modes (dominant solvent-dependent mode and a novel solvent-independent mode). Moreover, the pharmaceutical characteristics of these representative probes are summarized and discussed. This review provides important perspectives for the future development of novel NIR Aβ diagnostic probes.

Advances in development of fluorescent probes for detecting amyloid-β aggregates

PubMed Central

Xu, Ming-ming; Ren, Wen-ming; Tang, Xi-can; Hu, You-hong; Zhang, Hai-yan

2016-01-01

With accumulating evidence suggesting that amyloid-β (Aβ) deposition is a good diagnostic biomarker for Alzheimer's disease (AD), the discovery of active Aβ probes has become an active area of research. Among the existing imaging methods, optical imaging targeting Aβ aggregates (fibrils or oligomers), especially using near-infrared (NIR) fluorescent probes, is increasingly recognized as a promising approach for the early diagnosis of AD due to its real time detection, low cost, lack of radioactive exposure and high-resolution. In the past decade, a variety of fluorescent probes have been developed and tested for efficiency in vitro, and several probes have shown efficacy in AD transgenic mice. This review classifies these representative probes based on their chemical structures and functional modes (dominant solvent-dependent mode and a novel solvent-independent mode). Moreover, the pharmaceutical characteristics of these representative probes are summarized and discussed. This review provides important perspectives for the future development of novel NIR Aβ diagnostic probes. PMID:26997567

Development of Si neural probe with piezoresistive force sensor for minimally invasive and precise monitoring of insertion forces

NASA Astrophysics Data System (ADS)

Harashima, Takuya; Morikawa, Takumi; Kino, Hisashi; Fukushima, Takafumi; Tanaka, Tetsu

2017-04-01

A Si neural probe is one of the most important tools for neurophysiology and brain science because of its various functions such as optical stimulation and drug delivery. However, the Si neural probe is not robust compared with a metal tetrode, and could be broken by mechanical stress caused by insertion to the brain. Therefore, the Si neural probe becomes more useful if it has a stress sensor that can measure mechanical forces applied to the probe so as not to be broken. In this paper, we proposed and fabricated the Si neural probe with a piezoresistive force sensor for minimally invasive and precise monitoring of insertion forces. The fabricated piezoresistive force sensor accurately measured forces and successfully detected insertion events without buckling or bending in the shank of the Si neural probe. This Si neural probe with a piezoresistive force sensor has become one of the most versatile tools for neurophysiology and brain science.

Measurement and analysis of electron-neutral collision frequency in the calibrated cutoff probe

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

You, K. H.; Seo, B. H.; Kim, J. H.

2016-03-15

As collisions between electrons and neutral particles constitute one of the most representative physical phenomena in weakly ionized plasma, the electron-neutral (e-n) collision frequency is a very important plasma parameter as regards understanding the physics of this material. In this paper, we measured the e-n collision frequency in the plasma using a calibrated cutoff-probe. A highly accurate reactance spectrum of the plasma/cutoff-probe system, which is expected based on previous cutoff-probe circuit simulations [Kim et al., Appl. Phys. Lett. 99, 131502 (2011)], is obtained using the calibrated cutoff-probe method, and the e-n collision frequency is calculated based on the cutoff-probe circuitmore » model together with the high-frequency conductance model. The measured e-n collision frequency (by the calibrated cutoff-probe method) is compared and analyzed with that obtained using a Langmuir probe, with the latter being calculated from the measured electron-energy distribution functions, in wide range of gas pressure.« less

A Redox-Nucleophilic Dual-Reactable Probe for Highly Selective and Sensitive Detection of H2S: Synthesis, Spectra and Bioimaging

NASA Astrophysics Data System (ADS)

Zhang, Changyu; Wang, Runyu; Cheng, Longhuai; Li, Bingjie; Xi, Zhen; Yi, Long

2016-07-01

Hydrogen sulfide (H2S) is an important signalling molecule with multiple biological functions. The reported H2S fluorescent probes are majorly based on redox or nucleophilic reactions. The combination usage of both redox and nucleophilic reactions could improve the probe’s selectivity, sensitivity and stability. Herein we report a new dual-reactable probe with yellow turn-on fluorescence for H2S detection. The sensing mechanism of the dual-reactable probe was based on thiolysis of NBD (7-nitro-1,2,3-benzoxadiazole) amine (a nucleophilic reaction) and reduction of azide to amine (a redox reaction). Compared with its corresponding single-reactable probes, the dual-reactable probe has higher selectivity and fluorescence turn-on fold with magnitude of multiplication from that of each single-reactable probe. The highly selective and sensitive properties enabled the dual-reactable probe as a useful tool for efficiently sensing H2S in aqueous buffer and in living cells.

Measurements With a Split-Fiber Probe in Complex Unsteady Flows

NASA Technical Reports Server (NTRS)

Lepicovsky, Jan

2004-01-01

A split-fiber probe was used to acquire unsteady data in a research compressor. A calibration method was devised for a split-fiber probe, and a new algorithm was developed to decompose split-fiber probe signals into velocity magnitude and direction. The algorithm is based on the minimum value of a merit function that is built over the entire range of flow velocities for which the probe was calibrated. The split-fiber probe performance and signal decomposition was first verified in a free-jet facility by comparing the data from three thermo-anemometric probes, namely a single-wire, a single-fiber, and the split-fiber probe. All three probes performed extremely well as far as the velocity magnitude was concerned. However, there are differences in the peak values of measured velocity unsteadiness in the jet shear layer. The single-wire probe indicates the highest unsteadiness level, followed closely by the split-fiber probe. The single-fiber probe indicates a noticeably lower level of velocity unsteadiness. Experiments in the NASA Low Speed Axial Compressor facility revealed similar results. The mean velocities agreed well, and differences in the velocity unsteadiness are similar to the case of a free jet. A reason for these discrepancies is in the different frequency response characteristics of probes used. It follows that the single-fiber probe has the slowest frequency response. In summary, the split-fiber probe worked reliably during the entire program. The acquired data averaged in time followed closely data acquired by conventional pneumatic probes.

Redox-Responsive Fluorescent Probes with Different Design Strategies.

PubMed

Lou, Zhangrong; Li, Peng; Han, Keli

2015-05-19

In an aerobic organism, reactive oxygen species (ROS) are an inevitable metabolic byproduct. Endogenously produced ROS have a significant role in physiological processes, but excess ROS can cause oxidative stress and can damage tissue. Cells possess elaborate mechanisms to regulate their internal redox status. The intracellular redox homeostasis plays an essential role in maintaining cellular function. However, moderate alterations in redox balance can accompany major transitions in a cell's life cycle. Because of the role of ROS in physiology and in pathology, researchers need new tools to study redox chemistry in biological systems.In recent years, researchers have made remarkable progress in developing new, highly sensitive and selective fluorescent probes that respond to redox changes, and in this Account we highlight related research, primarily from our own group. We present an overview of the design, photophysical properties, and fluorescence transduction mechanisms of reported molecules that probe redox changes. We have designed and synthesized a series of fluorescent probes for redox cycles in biological systems relying on the active center of glutathione peroxidase (GPx). We have also constructed probes based on the oxidation and reduction of hydroquinone and of 2,2,6,6-tetramethylpiperidinooxy (TEMPO). Most of these probes exhibit high sensitivity and good selectivity, absorb in the near-infrared, and respond rapidly. Such probes are useful for confocal fluorescence microscopy, a dynamic imaging technique that could allow researchers to observe biologically important ROS and antioxidants in real time. This technique and these probes provide potentially useful tools for exploring the generation, transport, physiological function, and pathogenic mechanisms of ROS and antioxidants.We also describe features that could improve the properties of redox-responsive fluorescent probes: greater photostability; rapid, dynamic, cyclic and ratiometric responses; and broader absorption in the near-IR region. In addition, fluorescent probes that include organochalcogens such as selenium and tellurium show promise for a new class of fluorescent redox probes that are both chemically stable and robustly reversible. However, further investigations of the chemical and fluorescence transduction mechanisms of selenium-based probes in response to ROS are needed.

In Situ Live-Cell Nucleus Fluorescence Labeling with Bioinspired Fluorescent Probes.

PubMed

Ding, Pan; Wang, Houyu; Song, Bin; Ji, Xiaoyuan; Su, Yuanyuan; He, Yao

2017-08-01

Fluorescent imaging techniques for visualization of nuclear structure and function in live cells are fundamentally important for exploring major cellular events. The ideal cellular labeling method is capable of realizing label-free, in situ, real-time, and long-term nucleus labeling in live cells, which can fully obtain the nucleus-relative information and effectively alleviate negative effects of alien probes on cellular metabolism. However, current established fluorescent probes-based strategies (e.g., fluorescent proteins-, organic dyes-, fluorescent organic/inorganic nanoparticles-based imaging techniques) are unable to simultaneously realize label-free, in situ, long-term, and real-time nucleus labeling, resulting in inevitable difficulties in fully visualizing nuclear structure and function in live cells. To this end, we present a type of bioinspired fluorescent probes, which are highly efficacious for in situ and label-free tracking of nucleus in long-term and real-time manners. Typically, the bioinspired polydopamine (PDA) nanoparticles, served as fluorescent probes, can be readily synthesized in situ within live cell nucleus without any further modifications under physiological conditions (37 °C, pH ∼7.4). Compared with other conventional nuclear dyes (e.g., propidium iodide (PI), Hoechst), superior spectroscopic properties (e.g., quantum yield of ∼35.8% and high photostability) and low cytotoxicity of PDA-based probes enable long-term (e.g., 3 h) fluorescence tracking of nucleus. We also demonstrate the generality of this type of bioinspired fluorescent probes in different cell lines and complex biological samples.

Surface-functionalized nanoparticles for biosensing and imaging-guided therapeutics

NASA Astrophysics Data System (ADS)

Jiang, Shan; Win, Khin Yin; Liu, Shuhua; Teng, Choon Peng; Zheng, Yuangang; Han, Ming-Yong

2013-03-01

In this article, the very recent progress of various functional inorganic nanomaterials is reviewed including their unique properties, surface functionalization strategies, and applications in biosensing and imaging-guided therapeutics. The proper surface functionalization renders them with stability, biocompatibility and functionality in physiological environments, and further enables their targeted use in bioapplications after bioconjugation via selective and specific recognition. The surface-functionalized nanoprobes using the most actively studied nanoparticles (i.e., gold nanoparticles, quantum dots, upconversion nanoparticles, and magnetic nanoparticles) make them an excellent platform for a wide range of bioapplications. With more efforts in recent years, they have been widely developed as labeling probes to detect various biological species such as proteins, nucleic acids and ions, and extensively employed as imaging probes to guide therapeutics such as drug/gene delivery and photothermal/photodynamic therapy.

Functional imaging of muscle oxygenation using a 200-channel cw NIRS system

NASA Astrophysics Data System (ADS)

Yamamoto, Katsuyuki; Niwayama, Masatsugu; Kohata, Daisuke; Kudo, Nobuki; Hamaoka, Takatumi; Kime, Ryotaro; Katsumura, Toshihito

2001-06-01

Functional imaging of muscle oxygenation using NIRS is a promising technique for evaluation of the heterogeneity of muscle function and diagnosis of peripheral vascular disease or muscle injury. We have developed a 200-channel imaging system that can measure the changes in oxygenation and blood volume of muscles and that covers wider area than previously reported systems. Our system consisted of 40 probes, a multiplexer for switching signals to and from the probes, and a personal computer for obtaining images. In each probe, one two-wavelength LED (770 and 830 nm) and five photodiodes were mounted on a flexible substrate. In order to eliminate the influence of a subcutaneous fat layer, a correction method, which we previously developed, was also used in imaging. Thus, quantitative changes in concentrations of oxy- and deoxy-hemoglobin were obtained. Temporal resolution was 1.5 s and spatial resolution was about 20 mm, depending on probe separations. Exercise tests (isometric contraction of 50% MVC) on the thigh with and without arterial occlusion were conducted, and changes in muscle oxygenation were imaged using the developed system. Results showed that the heterogeneity of deoxygenation and reoxygenation during exercise and recovery periods, respectively, were clearly observed. These results suggest that optical imaging of dynamic change in muscle oxygenation using NIRS would be useful not only for basic physiological studies but also for clinical applications with respect to muscle functions.

Toward reliable retrieval of functional information of papillary dermis using spatially resolved diffuse reflectance spectroscopy

PubMed Central

Chen, Yu-Wen; Guo, Jun-Yen; Tzeng, Shih-Yu; Chou, Ting-Chun; Lin, Ming-Jen; Huang, Lynn Ling-Huei; Yang, Chao-Chun; Hsu, Chao-Kai; Tseng, Sheng-Hao

2016-01-01

Spatially resolved diffuse reflectance spectroscopy (SRDRS) has been employed to quantify tissue optical properties and its interrogation volume is majorly controlled by the source-to-detector separations (SDSs). To noninvasively quantify properties of dermis, a SRDRS setup that includes SDS shorter than 1 mm is required. It will be demonstrated in this study that Monte Carlo simulations employing the Henyey-Greenstein phase function cannot always precisely predict experimentally measured diffuse reflectance at such short SDSs, and we speculated this could be caused by the non-negligible backward light scattering at short SDSs that cannot be properly modeled by the Henyey-Greenstein phase function. To accurately recover the optical properties and functional information of dermis using SRDRS, we proposed the use of the modified two-layer (MTL) geometry. Monte Carlo simulations and phantom experiment results revealed that the MTL probing geometry was capable of faithfully recovering the optical properties of upper dermis. The capability of the MTL geometry in probing the upper dermis properties was further verified through a swine study, and it was found that the measurement results were reasonably linked to histological findings. Finally, the MTL probe was utilized to study psoriatic lesions. Our results showed that the MTL probe was sensitive to the physiological condition of tissue volumes within the papillary dermis and could be used in studying the physiology of psoriasis. PMID:26977361

Toward reliable retrieval of functional information of papillary dermis using spatially resolved diffuse reflectance spectroscopy.

PubMed

Chen, Yu-Wen; Guo, Jun-Yen; Tzeng, Shih-Yu; Chou, Ting-Chun; Lin, Ming-Jen; Huang, Lynn Ling-Huei; Yang, Chao-Chun; Hsu, Chao-Kai; Tseng, Sheng-Hao

2016-02-01

Spatially resolved diffuse reflectance spectroscopy (SRDRS) has been employed to quantify tissue optical properties and its interrogation volume is majorly controlled by the source-to-detector separations (SDSs). To noninvasively quantify properties of dermis, a SRDRS setup that includes SDS shorter than 1 mm is required. It will be demonstrated in this study that Monte Carlo simulations employing the Henyey-Greenstein phase function cannot always precisely predict experimentally measured diffuse reflectance at such short SDSs, and we speculated this could be caused by the non-negligible backward light scattering at short SDSs that cannot be properly modeled by the Henyey-Greenstein phase function. To accurately recover the optical properties and functional information of dermis using SRDRS, we proposed the use of the modified two-layer (MTL) geometry. Monte Carlo simulations and phantom experiment results revealed that the MTL probing geometry was capable of faithfully recovering the optical properties of upper dermis. The capability of the MTL geometry in probing the upper dermis properties was further verified through a swine study, and it was found that the measurement results were reasonably linked to histological findings. Finally, the MTL probe was utilized to study psoriatic lesions. Our results showed that the MTL probe was sensitive to the physiological condition of tissue volumes within the papillary dermis and could be used in studying the physiology of psoriasis.

In situ intracellular spectroscopy with surface enhanced Raman spectroscopy (SERS)-enabled nanopipettes.

PubMed

Vitol, Elina A; Orynbayeva, Zulfiya; Bouchard, Michael J; Azizkhan-Clifford, Jane; Friedman, Gary; Gogotsi, Yury

2009-11-24

We report on a new analytical approach to intracellular chemical sensing that utilizes a surface-enhanced Raman spectroscopy (SERS)-enabled nanopipette. The probe is comprised of a glass capillary with a 100-500 nm tip coated with gold nanoparticles. The fixed geometry of the gold nanoparticles allows us to overcome the limitations of the traditional approach for intracellular SERS using metal colloids. We demonstrate that the SERS-enabled nanopipettes can be used for in situ analysis of living cell function in real time. In addition, SERS functionality of these probes allows tracking of their localization in a cell. The developed probes can also be applied for highly sensitive chemical analysis of nanoliter volumes of chemicals in a variety of environmental and analytical applications.

The development and evaluation of head probes for optical imaging of the infant head

NASA Astrophysics Data System (ADS)

Branco, Gilberto

The objective of this thesis was to develop and evaluate optical imaging probes for mapping oxygenation and haemodynamic changes in the newborn infant brain. Two imaging approaches are being developed at University College London (UCL): optical topography (surface mapping of the cortex) and optical tomography (volume imaging). Both have the potential to provide information about the function of the normal brain and about a variety of neurophysiologies! abnormalities. Both techniques require an array of optical fibres/fibre bundles to be held in contact with the head, for periods of time from tens of seconds to an hour or more. The design of suitable probes must ensure the comfort and safety of the subject, and provide measurements minimally sensitive to external sources of light and patient motion. A series of prototype adaptable helmets were developed for optical tomography of the premature infant brain using the UCL 32-channel time-resolved system. They were required to attach 32 optical fibre bundles over the infant scalp, and were designed to accommodate infants with a variety of head shapes and sizes, aged between 24-weeks gestational age and term. Continual improvements to the helmet design were introduced following the evaluation of each prototype on infants in the hospital. Data were acquired to generate images revealing the concentration and oxygenation of blood in the brain, and the response of the brain to sensory stimulation. This part of the project also involved designing and testing new methods of acquiring calibration data using reference phantoms. The second focus of the project was the development of probes for use with the UCL frequency-multiplexed near-infrared topography system. This is being used to image functional activation in the infant cortex. A series of probes were developed and experiments were conducted to evaluate their sensitivity to patient motion and to compression of the probe. The probes have been used for a variety of functional activation studies.

KiDS+GAMA: cosmology constraints from a joint analysis of cosmic shear, galaxy-galaxy lensing, and angular clustering

NASA Astrophysics Data System (ADS)

van Uitert, Edo; Joachimi, Benjamin; Joudaki, Shahab; Amon, Alexandra; Heymans, Catherine; Köhlinger, Fabian; Asgari, Marika; Blake, Chris; Choi, Ami; Erben, Thomas; Farrow, Daniel J.; Harnois-Déraps, Joachim; Hildebrandt, Hendrik; Hoekstra, Henk; Kitching, Thomas D.; Klaes, Dominik; Kuijken, Konrad; Merten, Julian; Miller, Lance; Nakajima, Reiko; Schneider, Peter; Valentijn, Edwin; Viola, Massimo

2018-06-01

We present cosmological parameter constraints from a joint analysis of three cosmological probes: the tomographic cosmic shear signal in ˜450 deg2 of data from the Kilo Degree Survey (KiDS), the galaxy-matter cross-correlation signal of galaxies from the Galaxies And Mass Assembly (GAMA) survey determined with KiDS weak lensing, and the angular correlation function of the same GAMA galaxies. We use fast power spectrum estimators that are based on simple integrals over the real-space correlation functions, and show that they are practically unbiased over relevant angular frequency ranges. We test our full pipeline on numerical simulations that are tailored to KiDS and retrieve the input cosmology. By fitting different combinations of power spectra, we demonstrate that the three probes are internally consistent. For all probes combined, we obtain S_8≡ σ _8 √{Ω _m/0.3}=0.800_{-0.027}^{+0.029}, consistent with Planck and the fiducial KiDS-450 cosmic shear correlation function results. Marginalizing over wide priors on the mean of the tomographic redshift distributions yields consistent results for S8 with an increase of 28 {per cent} in the error. The combination of probes results in a 26 per cent reduction in uncertainties of S8 over using the cosmic shear power spectra alone. The main gain from these additional probes comes through their constraining power on nuisance parameters, such as the galaxy intrinsic alignment amplitude or potential shifts in the redshift distributions, which are up to a factor of 2 better constrained compared to using cosmic shear alone, demonstrating the value of large-scale structure probe combination.

Apertureless scanning microscope probe as a detector of semiconductor laser emission

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

Dunaevskiy, Mikhail, E-mail: Mike.Dunaeffsky@mail.ioffe.ru; National Research University of Information Technologies, Mechanics and Optics; Dontsov, Anton

2015-04-27

An operating semiconductor laser has been studied using a scanning probe microscope. A shift of the resonance frequency of probe that is due to its heating by laser radiation has been analyzed. The observed shift is proportional to the absorbed radiation and can be used to measure the laser near field or its output power. A periodical dependence of the measured signal has been observed as a function of distance between the probe and the surface of the laser due to the interference of the outgoing and cantilever-reflected waves. Due to the multiple reflections resulting in the interference, the lightmore » absorption by the probe cantilever is greatly enhanced compared with a single pass case. Interaction of infrared emission of a diode laser with different probes has been studied.« less

Rational chemical design of the next generation of molecular imaging probes based on physics and biology: mixing modalities, colors and signals

PubMed Central

Longmire, Michelle R.; Ogawa, Mikako; Choyke, Peter L.

2012-01-01

In recent years, numerous in vivo molecular imaging probes have been developed. As a consequence, much has been published on the design and synthesis of molecular imaging probes focusing on each modality, each type of material, or each target disease. More recently, second generation molecular imaging probes with unique, multi-functional, or multiplexed characteristics have been designed. This critical review focuses on (i) molecular imaging using combinations of modalities and signals that employ the full range of the electromagnetic spectra, (ii) optimized chemical design of molecular imaging probes for in vivo kinetics based on biology and physiology across a range of physical sizes, (iii) practical examples of second generation molecular imaging probes designed to extract complementary data from targets using multiple modalities, color, and comprehensive signals (277 references). PMID:21607237

Affective priming with pictures of emotional scenes: the role of perceptual similarity and category relatedness.

PubMed

Avero, Pedro; Calvo, Manuel G

2006-05-01

Prime pictures portraying pleasant or unpleasant scenes were briefly presented (150-ms display; SOAs of 300 or 800 ms), followed by probe pictures either congruent or incongruent in emotional valence. In an evaluative decision task, participants responded whether the probe was emotionally positive or negative. Affective priming was reflected in shorter response latencies for congruent than for incongruent prime-probe pairs. Although this effect was enhanced by perceptual similarity between the prime and the probe, it also occurred for probes that were physically different, and the effect generalized across semantic categories (animals vs. people). It is concluded that affective priming is a genuine phenomenon, in that it occurs as a function of stimulus emotional content, in the absence of both perceptual similarity and semantic category relatedness between the prime and the probe.

Functional Scanning Probe Imaging of Nanostructured Solar Energy Materials

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

Giridharagopal, Rajiv; Cox, Phillip A.; Ginger, David S.

From hybrid perovskites to semiconducting polymer/fullerene blends for organic photovoltaics, many new materials being explored for energy harvesting and storage exhibit performance characteristics that depend sensitively on their nanoscale morphology. At the same time, rapid advances in the capability and accessibility of scanning probe microscopy methods over the past decade have made it possible to study processing/structure/function relationships ranging from photocurrent collection to photocarrier lifetimes with resolutions on the scale of tens of nanometers or better. Importantly, such scanning probe methods offer the potential to combine measurements of local structure with local function, and they can be implemented to studymore » materials in situ or devices in operando to better understand how materials evolve in time in response to an external stimulus or environmental perturbation. This Account highlights recent advances in the development and application of scanning probe microscopy methods that can help address such questions while filling key gaps between the capabilities of conventional electron microscopy and newer super-resolution optical methods. Focusing on semiconductor materials for solar energy applications, we highlight a range of electrical and optoelectronic scanning probe microscopy methods that exploit the local dynamics of an atomic force microscope tip to probe key properties of the solar cell material or device structure. We discuss how it is possible to extract relevant device properties using noncontact scanning probe methods as well as how these properties guide materials development. Specifically, we discuss intensity-modulated scanning Kelvin probe microscopy (IM-SKPM), time-resolved electrostatic force microscopy (trEFM), frequency-modulated electrostatic force microscopy (FM-EFM), and cantilever ringdown imaging. We explain these developments in the context of classic atomic force microscopy (AFM) methods that exploit the physics of cantilever motion and photocarrier generation to provide robust, nanoscale measurements of materials physics that are correlated with device operation. We predict that the multidimensional data sets made possible by these types of methods will become increasingly important as advances in data science expand capabilities and opportunities for image correlation and discovery.« less

Functional Scanning Probe Imaging of Nanostructured Solar Energy Materials

DOE PAGES

Giridharagopal, Rajiv; Cox, Phillip A.; Ginger, David S.

2016-08-30

From hybrid perovskites to semiconducting polymer/fullerene blends for organic photovoltaics, many new materials being explored for energy harvesting and storage exhibit performance characteristics that depend sensitively on their nanoscale morphology. At the same time, rapid advances in the capability and accessibility of scanning probe microscopy methods over the past decade have made it possible to study processing/structure/function relationships ranging from photocurrent collection to photocarrier lifetimes with resolutions on the scale of tens of nanometers or better. Importantly, such scanning probe methods offer the potential to combine measurements of local structure with local function, and they can be implemented to studymore » materials in situ or devices in operando to better understand how materials evolve in time in response to an external stimulus or environmental perturbation. This Account highlights recent advances in the development and application of scanning probe microscopy methods that can help address such questions while filling key gaps between the capabilities of conventional electron microscopy and newer super-resolution optical methods. Focusing on semiconductor materials for solar energy applications, we highlight a range of electrical and optoelectronic scanning probe microscopy methods that exploit the local dynamics of an atomic force microscope tip to probe key properties of the solar cell material or device structure. We discuss how it is possible to extract relevant device properties using noncontact scanning probe methods as well as how these properties guide materials development. Specifically, we discuss intensity-modulated scanning Kelvin probe microscopy (IM-SKPM), time-resolved electrostatic force microscopy (trEFM), frequency-modulated electrostatic force microscopy (FM-EFM), and cantilever ringdown imaging. We explain these developments in the context of classic atomic force microscopy (AFM) methods that exploit the physics of cantilever motion and photocarrier generation to provide robust, nanoscale measurements of materials physics that are correlated with device operation. We predict that the multidimensional data sets made possible by these types of methods will become increasingly important as advances in data science expand capabilities and opportunities for image correlation and discovery.« less

Detection of the CLOCK/BMAL1 heterodimer using a nucleic acid probe with cycling probe technology.

PubMed

Nakagawa, Kazuhiro; Yamamoto, Takuro; Yasuda, Akio

2010-09-15

An isothermal signal amplification technique for specific DNA sequences, known as cycling probe technology (CPT), has enabled rapid acquisition of genomic information. Here we report an analogous technique for the detection of an activated transcription factor, a transcription element-binding assay with fluorescent amplification by apurinic/apyrimidinic (AP) site lysis cycle (TEFAL). This simple amplification assay can detect activated transcription factors by using a unique nucleic acid probe containing a consensus binding sequence and an AP site, which enables the CPT reaction with AP endonuclease. In this article, we demonstrate that this method detects the functional CLOCK/BMAL1 heterodimer via the TEFAL probe containing the E-box consensus sequence to which the CLOCK/BMAL1 heterodimer binds. Using TEFAL combined with immunoassays, we measured oscillations in the amount of CLOCK/BMAL1 heterodimer in serum-stimulated HeLa cells. Furthermore, we succeeded in measuring the circadian accumulation of the functional CLOCK/BMAL1 heterodimer in human buccal mucosa cells. TEFAL contributes greatly to the study of transcription factor activation in mammalian tissues and cell extracts and is a powerful tool for less invasive investigation of human circadian rhythms. 2010 Elsevier Inc. All rights reserved.

A PCR-Based Method for RNA Probes and Applications in Neuroscience.

PubMed

Hua, Ruifang; Yu, Shanshan; Liu, Mugen; Li, Haohong

2018-01-01

In situ hybridization (ISH) is a powerful technique that is used to detect the localization of specific nucleic acid sequences for understanding the organization, regulation, and function of genes. However, in most cases, RNA probes are obtained by in vitro transcription from plasmids containing specific promoter elements and mRNA-specific cDNA. Probes originating from plasmid vectors are time-consuming and not suitable for the rapid gene mapping. Here, we introduce a simplified method to prepare digoxigenin (DIG)-labeled non-radioactive RNA probes based on polymerase chain reaction (PCR) amplification and applications in free-floating mouse brain sections. Employing a transgenic reporter line, we investigate the expression of the somatostatin (SST) mRNA in the adult mouse brain. The method can be applied to identify the colocalization of SST mRNA and proteins including corticotrophin-releasing hormone (CRH) and protein kinase C delta type (PKC-δ) using double immunofluorescence, which is useful for understanding the organization of complex brain nuclei. Moreover, the method can also be incorporated with retrograde tracing to visualize the functional connection in the neural circuitry. Briefly, the PCR-based method for non-radioactive RNA probes is a useful tool that can be substantially utilized in neuroscience studies.

Reaction-based small-molecule fluorescent probes for dynamic detection of ROS and transient redox changes in living cells and small animals.

PubMed

Lü, Rui

2017-09-01

Dynamic detection of transient redox changes in living cells and animals has broad implications for human health and disease diagnosis, because intracellular redox homeostasis regulated by reactive oxygen species (ROS) plays important role in cell functions, normal physiological functions and some serious human diseases (e.g., cancer, Alzheimer's disease, diabetes, etc.) usually have close relationship with the intracellular redox status. Small-molecule ROS-responsive fluorescent probes can act as powerful tools for dynamic detection of ROS and redox changes in living cells and animals through fluorescence imaging techniques; and great advances have been achieved recently in the design and synthesis of small-molecule ROS-responsive fluorescent probes. This article highlights up-to-date achievements in designing and using the reaction-based small-molecule fluorescent probes (with high sensitivity and selectivity to ROS and redox cycles) in the dynamic detection of ROS and transient redox changes in living cells and animals through fluorescence imaging. Copyright © 2017. Published by Elsevier Ltd.

Optimizing the specificity of nucleic acid hybridization

PubMed Central

Zhang, David Yu; Chen, Sherry Xi; Yin, Peng

2014-01-01

The specific hybridization of complementary sequences is an essential property of nucleic acids, enabling diverse biological and biotechnological reactions and functions. However, the specificity of nucleic acid hybridization is compromised for long strands, except near the melting temperature. Here, we analytically derived the thermodynamic properties of a hybridization probe that would enable near-optimal single-base discrimination and perform robustly across diverse temperature, salt and concentration conditions. We rationally designed ‘toehold exchange’ probes that approximate these properties, and comprehensively tested them against five different DNA targets and 55 spurious analogues with energetically representative single-base changes (replacements, deletions and insertions). These probes produced discrimination factors between 3 and 100+ (median, 26). Without retuning, our probes function robustly from 10 °C to 37 °C, from 1 mM Mg2+ to 47 mM Mg2+, and with nucleic acid concentrations from 1 nM to 5 μM. Experiments with RNA also showed effective single-base change discrimination. PMID:22354435

Near-infrared fluorescence probes for enzymes based on binding affinity modulation of squarylium dye scaffold.

PubMed

Oushiki, Daihi; Kojima, Hirotatsu; Takahashi, Yuki; Komatsu, Toru; Terai, Takuya; Hanaoka, Kenjiro; Nishikawa, Makiya; Takakura, Yoshinobu; Nagano, Tetsuo

2012-05-15

We present a novel design strategy for near-infrared (NIR) fluorescence probes utilizing dye-protein interaction as a trigger for fluorescence enhancement. The design principle involves modification of a polymethine dye with cleavable functional groups that reduce the dye's protein-binding affinity. When these functional groups are removed by specific interaction with the target enzymes, the dye's protein affinity is restored, protein binding occurs, and the dye's fluorescence is strongly enhanced. To validate this strategy, we first designed and synthesized an alkaline phosphatase (ALP) sensor by introducing phosphate into the squarylium dye scaffold; this sensor was able to detect ALP-labeled secondary antibodies in Western blotting analysis. Second, we synthesized a probe for β-galactosidase (widely used as a reporter of gene expression) by means of β-galactosyl substitution of the squarylium scaffold; this sensor was able to visualize β-galactosidase activity both in vitro and in vivo. Our strategy should be applicable to obtain NIR fluorescence probes for a wide range of target enzymes.

Electron density and electron temperature measurement in a bi-Maxwellian electron distribution using a derivative method of Langmuir probes

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

Choi, Ikjin; Chung, ChinWook; Youn Moon, Se

2013-08-15

In plasma diagnostics with a single Langmuir probe, the electron temperature T{sub e} is usually obtained from the slope of the logarithm of the electron current or from the electron energy probability functions of current (I)-voltage (V) curve. Recently, Chen [F. F. Chen, Phys. Plasmas 8, 3029 (2001)] suggested a derivative analysis method to obtain T{sub e} by the ratio between the probe current and the derivative of the probe current at a plasma potential where the ion current becomes zero. Based on this method, electron temperatures and electron densities were measured and compared with those from the electron energymore » distribution function (EEDF) measurement in Maxwellian and bi-Maxwellian electron distribution conditions. In a bi-Maxwellian electron distribution, we found the electron temperature T{sub e} obtained from the method is always lower than the effective temperatures T{sub eff} derived from EEDFs. The theoretical analysis for this is presented.« less

Kinetic damping in the spectra of the spherical impedance probe

NASA Astrophysics Data System (ADS)

Oberrath, J.

2018-04-01

The impedance probe is a measurement device to measure plasma parameters, such as electron density. It consists of one electrode connected to a network analyzer via a coaxial cable and is immersed into a plasma. A bias potential superposed with an alternating potential is applied to the electrode and the response of the plasma is measured. Its dynamical interaction with the plasma in an electrostatic, kinetic description can be modeled in an abstract notation based on functional analytic methods. These methods provide the opportunity to derive a general solution, which is given as the response function of the probe–plasma system. It is defined by the matrix elements of the resolvent of an appropriate dynamical operator. Based on the general solution, a residual damping for vanishing pressure can be predicted and can only be explained by kinetic effects. In this paper, an explicit response function of the spherical impedance probe is derived. Therefore, the resolvent is determined by its algebraic representation based on an expansion in orthogonal basis functions. This allows one to compute an approximated response function and its corresponding spectra. These spectra show additional damping due to kinetic effects and are in good agreement with former kinetically determined spectra.

Ultrasensitive colorimetric immunoassay for hCG detection based on dual catalysis of Au@Pt core-shell nanoparticle functionalized by horseradish peroxidase

NASA Astrophysics Data System (ADS)

Wang, Weiguo; Zou, Yake; Yan, Jinwu; Liu, Jing; Chen, Huixiong; Li, Shan; Zhang, Lei

2018-03-01

In this paper, an ultrasensitive colorimetric biosensor for human chorionic gonadotrophin (hCG) detection was designed from bottom-up method based on the dual catalysis of the horseradish peroxidase (HRP) and Au@Pt nanoparticles (NPs) relative to H2O2-TEM system. HRP and monoclonal mouse anti-hCG antibody (β-submit, mAb1) were co-immobilized onto the Au@Pt NP surface to improve catalytic efficiency and specificity, which formed a dual functionalized Au@Pt-HRP probe with the mean size of 42.8 nm (D50). The colorimetric immunoassay was developed for the hCG detection, and the Au@Pt-HRP probe featured a higher sensitivity in the concentration range of 0.4-12.8 IU L- 1 with a low limit of detection (LOD) of 0.1 IU L- 1 compared with the LODs of 0.8 IU L- 1 for BA-ELISA and of 2.0 IU L- 1 for Au@Pt, which indicated that the Au@Pt-HRP probe possessed higher catalytic efficiency with 2.8-fold increase over Au@Pt and 33.8-fold increase over HRP. Also, the Au@Pt-HRP probe exhibited good precision and reproducibility, high specificity and acceptable accuracy with CV being less than 15%. The dual functionalized Au@Pt-HRP probe as a type of signal amplified method was firstly applied in the colorimetric immunoassay for the hCG detection.

Nanoscale laminin coating modulates cortical scarring response around implanted silicon microelectrode arrays

NASA Astrophysics Data System (ADS)

He, Wei; McConnell, George C.; Bellamkonda, Ravi V.

2006-12-01

Neural electrodes could significantly enhance the quality of life for patients with sensory and/or motor deficits as well as improve our understanding of brain functions. However, long-term electrical connectivity between neural tissue and recording sites is compromised by the development of astroglial scar around the recording probes. In this study we investigate the effect of a nanoscale laminin (LN) coating on Si-based neural probes on chronic cortical tissue reaction in a rat model. Tissue reaction was evaluated after 1 day, 1 week, and 4 weeks post-implant for coated and uncoated probes using immunohistochemical techniques to evaluate activated microglia/macrophages (ED-1), astrocytes (GFAP) and neurons (NeuN). The coating did not have an observable effect on neuronal density or proximity to the electrode surface. However, the response of microglia/macrophages and astrocytes was altered by the coating. One day post-implant, we observed an ~60% increase in ED-1 expression near LN-coated probe sites compared with control uncoated probe sites. Four weeks post-implant, we observed an ~20% reduction in ED-1 expression along with an ~50% reduction in GFAP expression at coated relative to uncoated probe sites. These results suggest that LN has a stimulatory effect on early microglia activation, accelerating the phagocytic function of these cells. This hypothesis is further supported by the increased mRNA expression of several pro-inflammatory cytokines (TNF-α, IL-1 and IL-6) in cultured microglia on LN-bound Si substrates. LN immunostaining of coated probes immediately after insertion and retrieval demonstrates that the coating integrity is not compromised by the shear force during insertion. We speculate, based on these encouraging results, that LN coating of Si neural probes could potentially improve chronic neural recordings through dispersion of the astroglial scar.

The Sheath-less Planar Langmuir Probe

NASA Astrophysics Data System (ADS)

Cooke, D. L.

2017-12-01

The Langmuir probe is one of the oldest plasma diagnostics, provided the plasma density and species temperature from analysis of a current-voltage curve as the voltage is swept over a practically chosen range. The analysis depends on a knowledge or theory of the many factors that influence the current-voltage curve including, probe shape, size, nearby perturbations, and the voltage reference. For applications in Low Earth Orbit, the Planar Langmuir Probe, PLP, is an attractive geometry because the ram ion current is very constant over many Volts of a sweep, allowing the ion density and electron temperature to be determined independently with the same instrument, at different points on the sweep. However, when the physical voltage reference is itself small and electrically floating as with a small spacecraft, the spacecraft and probe system become a double probe where the current collection theory depends on the interaction of the spacecraft with the plasma which is generally not as simple as the probe itself. The Sheath-less PLP, SPLP, interlaces on a single ram facing surface, two variably biased probe elements, broken into many small and intertwined segments on a scale smaller than the plasma Debye length. The SPLP is electrically isolated from the rest of the spacecraft. For relative bias potentials of a few volts, the ion current to all segments of each element will be constant, while the electron currents will vary as a function of the element potential and the electron temperature. Because the segments are small, intertwined, and floating, the assembly will always present the same floating potential to the plasma, with minimal growth as a function of voltage, thus sheath-less and still planar. This concept has been modelled with Nascap, and tested with a physical model inserted into a Low Earth Orbit-like chamber plasma. Results will be presented.

Validating a new methodology for optical probe design and image registration in fNIRS studies

PubMed Central

Wijeakumar, Sobanawartiny; Spencer, John P.; Bohache, Kevin; Boas, David A.; Magnotta, Vincent A.

2015-01-01

Functional near-infrared spectroscopy (fNIRS) is an imaging technique that relies on the principle of shining near-infrared light through tissue to detect changes in hemodynamic activation. An important methodological issue encountered is the creation of optimized probe geometry for fNIRS recordings. Here, across three experiments, we describe and validate a processing pipeline designed to create an optimized, yet scalable probe geometry based on selected regions of interest (ROIs) from the functional magnetic resonance imaging (fMRI) literature. In experiment 1, we created a probe geometry optimized to record changes in activation from target ROIs important for visual working memory. Positions of the sources and detectors of the probe geometry on an adult head were digitized using a motion sensor and projected onto a generic adult atlas and a segmented head obtained from the subject's MRI scan. In experiment 2, the same probe geometry was scaled down to fit a child's head and later digitized and projected onto the generic adult atlas and a segmented volume obtained from the child's MRI scan. Using visualization tools and by quantifying the amount of intersection between target ROIs and channels, we show that out of 21 ROIs, 17 and 19 ROIs intersected with fNIRS channels from the adult and child probe geometries, respectively. Further, both the adult atlas and adult subject-specific MRI approaches yielded similar results and can be used interchangeably. However, results suggest that segmented heads obtained from MRI scans be used for registering children's data. Finally, in experiment 3, we further validated our processing pipeline by creating a different probe geometry designed to record from target ROIs involved in language and motor processing. PMID:25705757

A theoretical investigation of two typical two-photon pH fluorescent probes.

PubMed

Xu, Zhong; Ren, Ai-Min; Guo, Jing-Fu; Liu, Xiao-Ting; Huang, Shuang; Feng, Ji-Kang

2013-01-01

Intracellular pH plays an important role in many cellular events, such as cell growth, endocytosis, cell adhesion and so on. Some pH fluorescent probes have been reported, but most of them are one-photon fluorescent probes, studies about two-photon fluorescent probes are very rare. In this work, the geometrical structure, electronic structure and one-photon properties of a series of two-photon pH fluorescent probes have been theoretically studied by using density functional theory (DFT) method. Their two-photon absorption (TPA) properties are calculated using the method of ZINDO/sum-over-states method. Two types of two-photon pH fluorescent probes have been investigated by theoretical methods. The mechanisms of the Photoinduced Charge Transfer (PCT) probes and the Photoinduced Electron Transfer (PET) probes are verified specifically. Some designed strategies of good two-photon pH fluorescent probes are suggested on the basis of the investigated results of two mechanisms. For the PCT probes, substituting a stronger electron-donating group for the terminal methoxyl group is an advisable choice to increase the TPA cross section. For the PET probes, the TPA cross sections increase upon protonation. © 2012 Wiley Periodicals, Inc. Photochemistry and Photobiology © 2012 The American Society of Photobiology.

A new visible-light-excitable ICT-CHEF-mediated fluorescence 'turn-on' probe for the selective detection of Cd(2+) in a mixed aqueous system with live-cell imaging.

PubMed

Goswami, Shyamaprosad; Aich, Krishnendu; Das, Sangita; Das Mukhopadhyay, Chitrangada; Sarkar, Deblina; Mondal, Tapan Kumar

2015-03-28

A new quinoline based sensor was developed and applied for the selective detection of Cd(2+) both in vitro and in vivo. The designed probe displays a straightforward approach for the selective detection of Cd(2+) with a prominent fluorescence enhancement along with a large red shift (∼38 nm), which may be because of the CHEF (chelation-enhanced fluorescence) and ICT (internal charge transfer) processes after interaction with Cd(2+). The interference from other biologically important competing metal ions, particularly Zn(2+), has not been observed. The visible-light excitability of the probe merits in the viewpoint of its biological application. The probe enables the detection of intracellular Cd(2+) with non-cytotoxic effects, which was demonstrated with the live RAW cells. The experimentally observed change in the structure and electronic properties of the sensor after the addition of Cd(2+) were modelled by the density functional theory (DFT) and time-dependent density functional theory (TDDFT) computational calculations, respectively. Moreover, the test strip experiment with this sensor exhibits both absorption and fluorescence color changes when exposed to Cd(2+) in a mixed aqueous solution, which also makes the probe more useful. The minimum limit of detection of Cd(2+) by the probe was in the range of 9.9 × 10(-8) M level.

Fluorometric determination of Vibrio parahaemolyticus using an F0F1-ATPase-based aptamer and labeled chromatophores.

PubMed

Duan, Nuo; Wu, Shijia; Zhang, Huiling; Zou, Ying; Wang, Zhouping

2018-05-18

An F 0 F 1 -ATPase-based aptasensor is described for the fluorometric determination of Vibrio parahaemolyticus. Chromatophores containing F 0 F 1 -ATPases were first prepared from Rhodospirillum rubrum cells. Then, an aptamer-functionalized chromatophore acts as the capture probe, and a chromatophore labeled with the pH probe fluorescein acts as the signalling probe. In the presence of V. parahaemolyticus, the rotation rate of F 0 F 1 -ATPase is decreased due to the formation of the aptamer-chromatophore complex. This leads to a retarded proton flux out of the chromatophores. As a result, the pH value inside the chromatophores is reduced, and the fluorescence of the pH probe F1300 is accordingly decreased. The relative fluorescence varies linearly over the 15 to 1.5 × 10 6  cfu·mL -1 Vibrio parahaemolyticus concentration range, and the limit of detection is 15 cfu·mL -1 . The method was applied to analyze artificially contaminated salmon samples where it showed excellent perfomance. Graphical abstract In this assay, aptamer functionalized chromatophores act as a capture probe, and the fluoresce in labeled chromatophores as signalling probe. The formation of aptamer-chromatophore complex leads to a retarded proton flux out of the chromatophores. As a result, the pH value inside the chromatophores is reduced, and fluorescence intensity is accordingly decreased.

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.

Intravital FRET: Probing Cellular and Tissue Function in Vivo

PubMed Central

Radbruch, Helena; Bremer, Daniel; Mothes, Ronja; Günther, Robert; Rinnenthal, Jan Leo; Pohlan, Julian; Ulbricht, Carolin; Hauser, Anja E.; Niesner, Raluca

2015-01-01

The development of intravital Förster Resonance Energy Transfer (FRET) is required to probe cellular and tissue function in the natural context: the living organism. Only in this way can biomedicine truly comprehend pathogenesis and develop effective therapeutic strategies. Here we demonstrate and discuss the advantages and pitfalls of two strategies to quantify FRET in vivo—ratiometrically and time-resolved by fluorescence lifetime imaging—and show their concrete application in the context of neuroinflammation in adult mice. PMID:26006244

Application of Time-Resolved Spectroscopies to the Study of Energetic Materials - 1982

DTIC Science & Technology

1983-05-24

fluores- cence intensity as a function of UV pulse energy, for individual laser shots. The lower curve shows the UV + probe induced fluorescence... intensity as a function of UV pulse energy, for individual laser shots. The lower curve shows the UV + probe Induced fluorescence, at 1 ns delay...locked Nd:YAG Laser Pulse ", Appl. Phys. Lett 26, 501-503 (1975). 97 43. A. J. Campillo, V. H. Kollman and S. L. Shapiro, " Intensity Dependence of

Comparison of magnetic probe calibration at nano and millitesla magnitudes

NASA Astrophysics Data System (ADS)

Pahl, Ryan A.; Rovey, Joshua L.; Pommerenke, David J.

2014-01-01

Magnetic field probes are invaluable diagnostics for pulsed inductive plasma devices where field magnitudes on the order of tenths of tesla or larger are common. Typical methods of providing a broadband calibration of dot{{B}} probes involve either a Helmholtz coil driven by a function generator or a network analyzer. Both calibration methods typically produce field magnitudes of tens of microtesla or less, at least three and as many as six orders of magnitude lower than their intended use. This calibration factor is then assumed constant regardless of magnetic field magnitude and the effects of experimental setup are ignored. This work quantifies the variation in calibration factor observed when calibrating magnetic field probes in low field magnitudes. Calibration of two dot{{B}} probe designs as functions of frequency and field magnitude are presented. The first dot{{B}} probe design is the most commonly used design and is constructed from two hand-wound inductors in a differential configuration. The second probe uses surface mounted inductors in a differential configuration with balanced shielding to further reduce common mode noise. Calibration factors are determined experimentally using an 80.4 mm radius Helmholtz coil in two separate configurations over a frequency range of 100-1000 kHz. A conventional low magnitude calibration using a vector network analyzer produced a field magnitude of 158 nT and yielded calibration factors of 15 663 ± 1.7% and 4920 ± 0.6% {T}/{V {s}} at 457 kHz for the surface mounted and hand-wound probes, respectively. A relevant magnitude calibration using a pulsed-power setup with field magnitudes of 8.7-354 mT yielded calibration factors of 14 615 ± 0.3% and 4507 ± 0.4% {T}/{V {s}} at 457 kHz for the surface mounted inductor and hand-wound probe, respectively. Low-magnitude calibration resulted in a larger calibration factor, with an average difference of 9.7% for the surface mounted probe and 12.0% for the hand-wound probe. The maximum difference between relevant and low magnitude tests was 21.5%.

Pressure-Mediated Oligonucleotide Transfection of Rat and Human Cardiovascular Tissues

NASA Astrophysics Data System (ADS)

Mann, Michael J.; Gibbons, Gary H.; Hutchinson, Howard; Poston, Robert S.; Hoyt, E. Grant; Robbins, Robert C.; Dzau, Victor J.

1999-05-01

The application of gene therapy to human disease is currently restricted by the relatively low efficiency and potential hazards of methods of oligonucleotide or gene delivery. Antisense or transcription factor decoy oligonucleotides have been shown to be effective at altering gene expression in cell culture expreriments, but their in vivo application is limited by the efficiency of cellular delivery, the intracellular stability of the compounds, and their duration of activity. We report herein the development of a highly efficient method for naked oligodeoxynucleotide (ODN) transfection into cardiovascular tissues by using controlled, nondistending pressure without the use of viral vectors, lipid formulations, or exposure to other adjunctive, potentially hazardous substances. In this study, we have documented the ability of ex vivo, pressure-mediated transfection to achieve nuclear localization of fluorescent (FITC)-labeled ODN in approximately 90% and 50% of cells in intact human saphenous vein and rat myocardium, respectively. We have further documented that pressure-mediated delivery of antisense ODN can functionally inhibited target gene expression in both of these tissues in a sequence-specific manner at the mRNA and protein levels. This oligonucleotide transfection system may represent a safe means of achieving the intraoperative genetic engineering of failure-resistant human bypass grafts and may provide an avenue for the genetic manipulation of cardiac allograft rejection, allograft vasculopathy, or other transplant diseases.

Increased expression of CaV3.2 T-type calcium channels in damaged DRG neurons contributes to neuropathic pain in rats with spared nerve injury.

PubMed

Kang, Xue-Jing; Chi, Ye-Nan; Chen, Wen; Liu, Feng-Yu; Cui, Shuang; Liao, Fei-Fei; Cai, Jie; Wan, You

2018-01-01

Ion channels are very important in the peripheral sensitization in neuropathic pain. Our present study aims to investigate the possible contribution of Ca V 3.2 T-type calcium channels in damaged dorsal root ganglion neurons in neuropathic pain. We established a neuropathic pain model of rats with spared nerve injury. In these model rats, it was easy to distinguish damaged dorsal root ganglion neurons (of tibial nerve and common peroneal nerve) from intact dorsal root ganglion neurons (of sural nerves). Our results showed that Ca V 3.2 protein expression increased in medium-sized neurons from the damaged dorsal root ganglions but not in the intact ones. With whole cell patch clamp recording technique, it was found that after-depolarizing amplitudes of the damaged medium-sized dorsal root ganglion neurons increased significantly at membrane potentials of -85 mV and -95 mV. These results indicate a functional up-regulation of Ca V 3.2 T-type calcium channels in the damaged medium-sized neurons after spared nerve injury. Behaviorally, blockade of Ca V 3.2 with antisense oligodeoxynucleotides could significantly reverse mechanical allodynia. These results suggest that Ca V 3.2 T-type calcium channels in damaged medium-sized dorsal root ganglion neurons might contribute to neuropathic pain after peripheral nerve injury.

Static micromixer-coaxial electrospray synthesis of theranostic lipoplexes.

PubMed

Wu, Yun; Li, Lei; Mao, Yicheng; Lee, Ly James

2012-03-27

Theranostic lipoplexes are an integrated nanotherapeutic system with diagnostic imaging capability and therapeutic functions. They hold great promise to improve current cancer treatments; however, producing uniform theranostic lipoplexes with multiple components in a reproducible manner is a highly challenging task. Conventional methods, such as bulk mixing, are not able to achieve this goal because of their macroscale and random nature. Here we report a novel technique, called the static micromixer-coaxial electrospray (MCE), to synthesize theranostic lipoplexes in a single step with high reproducibility. In this work, quantum dots (QD605) and Cy5-labeled antisense oligodeoxynucleotides (Cy5-G3139) were chosen as the model imaging reagent and therapeutic drug, respectively. Compared with bulk mixing, QD605/Cy5-G3139-loaded lipoplexes produced by MCE were highly uniform with polydispersity of 0.024 ± 0.006 and mean diameter by volume of 194 ± 15 nm. MCE also showed higher encapsulation efficiency of QD605 and Cy5-G3139. QD605 and Cy5 also formed the Förster resonance energy transfer pair, and thus the cellular uptake and intracellular fate of theranostic lipoplexes could be visualized by flow cytometry and confocal microscopy. The lipoplexes were efficiently delivered to A549 cells (non-small cell lung cancer cell line) and down-regulated the Bcl-2 gene expression by 48 ± 6%. © 2012 American Chemical Society

Carbon nanotubes enhance CpG uptake and potentiate antiglioma immunity.

PubMed

Zhao, Dongchang; Alizadeh, Darya; Zhang, Leying; Liu, Wei; Farrukh, Omar; Manuel, Edwin; Diamond, Don J; Badie, Behnam

2011-02-15

Stimulation of toll-like receptor-9 (TLR9) by CpG oligodeoxynucleotides (CpG) has been shown to counteract the immunosuppressive microenvironment and to inhibit tumor growth in glioma models. Because TLR9 is located intracellularly, we hypothesized that methods that enhance its internalization may also potentiate its immunostimulatory response. The goal of this study was to evaluate carbon nanotubes (CNT) as a CpG delivery vehicle in brain tumor models. Functionalized single-walled CNTs were conjugated with CpG (CNT-CpG) and evaluated in vitro and in mice bearing intracranial GL261 gliomas. Flow cytometry was used to assess CNT-CpG uptake and antiglioma immune response. Tumor growth was measured by bioluminescent imaging, histology, and animal survival. CNT-CpG was nontoxic and enhanced CpG uptake both in vitro and intracranial gliomas. CNT-mediated CpG delivery also potentiated proinflammatory cytokine production by primary monocytes. Interestingly, a single intracranial injection of low-dose CNT-CpG (but not free CpG or blank CNT) eradicated intracranial GL261 gliomas in half of tumor-bearing mice. Moreover, surviving animals exhibited durable tumor-free remission (>3 months), and were protected from intracranial tumor rechallenge, demonstrating induction of long-term antitumor immunity. These findings suggest that CNTs can potentiate CpG immunopotency by enhancing its delivery into tumor-associated inflammatory cells. ©2010 AACR.

New Surface-Enhanced Raman Sensing Chip Designed for On-Site Detection of Active Ricin in Complex Matrices Based on Specific Depurination.

PubMed

Tang, Ji-Jun; Sun, Jie-Fang; Lui, Rui; Zhang, Zong-Mian; Liu, Jing-Fu; Xie, Jian-Wei

2016-01-27

Quick and accurate on-site detection of active ricin has very important realistic significance in view of national security and defense. In this paper, optimized single-stranded oligodeoxynucleotides named poly(21dA), which function as a depurination substrate of active ricin, were screened and chemically attached on gold nanoparticles (AuNPs, ∼100 nm) via the Au-S bond [poly(21dA)-AuNPs]. Subsequently, poly(21dA)-AuNPs were assembled on a dihydrogen lipoic-acid-modified Si wafer (SH-Si), thus forming the specific surface-enhanced Raman spectroscopy (SERS) chip [poly(21dA)-AuNPs@SH-Si] for depurination of active ricin. Under optimized conditions, active ricin could specifically hydrolyze multiple adenines from poly(21dA) on the chip. This depurination-induced composition change could be conveniently monitored by measuring the distinct attenuation of the SERS signature corresponding to adenine. To improve sensitivity of this method, a silver nanoshell was deposited on post-reacted poly(21dA)-AuNPs, which lowered the limit of detection to 8.9 ng mL(-1). The utility of this well-controlled SERS chip was successfully demonstrated in food and biological matrices spiked with different concentrations of active ricin, thus showing to be very promising assay for reliable and rapid on-site detection of active ricin.

Highly Efficient Targeted Mutagenesis in Mice Using TALENs

PubMed Central

Panda, Sudeepta Kumar; Wefers, Benedikt; Ortiz, Oskar; Floss, Thomas; Schmid, Bettina; Haass, Christian; Wurst, Wolfgang; Kühn, Ralf

2013-01-01

Targeted mouse mutants are instrumental for the analysis of gene function in health and disease. We recently provided proof-of-principle for the fast-track mutagenesis of the mouse genome, using transcription activator-like effector nucleases (TALENs) in one-cell embryos. Here we report a routine procedure for the efficient production of disease-related knockin and knockout mutants, using improved TALEN mRNAs that include a plasmid-coded poly(A) tail (TALEN-95A), circumventing the problematic in vitro polyadenylation step. To knock out the C9orf72 gene as a model of frontotemporal lobar degeneration, TALEN-95A mutagenesis induced sequence deletions in 41% of pups derived from microinjected embryos. Using TALENs together with mutagenic oligodeoxynucleotides, we introduced amyotrophic lateral sclerosis patient-derived missense mutations in the fused in sarcoma (Fus) gene at a rate of 6.8%. For the simple identification of TALEN-induced mutants and their progeny we validate high-resolution melt analysis (HRMA) of PCR products as a sensitive and universal genotyping tool. Furthermore, HRMA of off-target sites in mutant founder mice revealed no evidence for undesired TALEN-mediated processing of related genomic sequences. The combination of TALEN-95A mRNAs for enhanced mutagenesis and of HRMA for simplified genotyping enables the accelerated, routine production of new mouse models for the study of genetic disease mechanisms. PMID:23979585

Hippocampal Arc (Arg3.1) expression is induced by memory recall and required for memory reconsolidation in trace fear conditioning.

PubMed

Chia, Chester; Otto, Tim

2013-11-01

Mounting evidence suggests that long-lasting, protein synthesis-dependent changes in synaptic strength accompany both the initial acquisition and subsequent recall of specific memories. Within brain areas thought to be important for learning and memory, including the hippocampus, learning-related plasticity is likely mediated in part by NMDA receptor activation and experience-dependent changes in gene expression. In the present study, we examined the role of activity-regulated cytoskeletal-associated protein (Arc/Arg3.1) expression in the acquisition, recall, and reconsolidation of memory in a trace fear conditioning paradigm. First, we show that the expression of Arc protein in ventral hippocampus (VH) is dramatically enhanced by memory recall 24h after the acquisition of trace fear conditioning, and that both memory recall and the associated recall-induced enhancement of Arc expression are blocked by pre-training administration of 2-amino-5-phosphonovaleric acid (APV). Next, we show that while infusion of Arc antisense oligodeoxynucleotides (ODNs) into VH prior to testing had little effect on memory recall, it significantly reduced both Arc protein expression and freezing behavior during subsequent testing sessions. Collectively, these results suggest that Arc/Arg3.1 protein plays an important functional role in both the initial acquisition of hippocampal-dependent memory and the reconsolidation of these memories after recall. Copyright © 2013 Elsevier Inc. All rights reserved.

Carbon Nanotubes Enhance CpG Uptake and Potentiate Anti-Glioma Immunity

PubMed Central

Zhao, Dongchang; Alizadeh, Darya; Zhang, Leying; Liu, Wei; Farrukh, Omar; Manuel, Edwin; Diamond, Don J.; Badie, Behnam

2010-01-01

Purpose Stimulation of toll-like receptor-9 (TLR9) by CpG oligodeoxynucleotides (CpG) has been shown to counteract the immunosuppressive microenvironment and to inhibit tumor growth in glioma models. Since TLR9 is located intracellularly, we hypothesized that methods that enhance its internalization may also potentiate its immunostimulatory response. The goal of this study was to evaluate carbon nanotubes (CNTs) as a CpG delivery vehicle in brain tumor models. Experimental Design Functionalized single-walled CNTs were conjugated with CpG (CNT-CpG) and evaluated in vitro and in mice bearing intracranial GL261 gliomas. Flow cytometry was used to assess CNT-CpG uptake and anti-glioma immune response. Tumor growth was measured by bioluminescent imaging, histology, and animal survival. Results CNT-CpG was nontoxic and enhanced CpG uptake both in vitro and intracranial gliomas. CNT-mediated CpG delivery also potentiated pro-inflammatory cytokine production by primary monocytes. Interestingly, a single intracranial injection of low-dose CNT-CpG (but not free CpG or blank CNT) eradicated intracranial GL261 gliomas in half of tumor-bearing mice. Moreover, surviving animals exhibited durable tumor-free remission (> 3 months), and were protected from intracranial tumor rechallenge, demonstrating induction of long-term anti-tumor immunity. Conclusions These findings suggest that CNTs can potentiate CpG immunopotency by enhancing its delivery into tumor-associated inflammatory cells. PMID:21088258

Differentiation and Distributions of DNA/Cisplatin Crosslinks by Liquid Chromatography-Electrospray Ionization-Infrared Multiphoton Dissociation Mass Spectrometry

PubMed Central

Xu, Zhe; Brodbelt, Jennifer S.

2013-01-01

Liquid chromatography-electrospray ionization-infrared multiphoton dissociation (IRMPD) mass spectrometry was developed to investigate the distributions of intrastrand crosslinks formed between cisplatin and two oligodeoxynucleotides (ODNs), d(A1T2G3G4G5T6A7C8C9C10A11T12) (G3-D) and its analog d(A1T2G3G4G5T6T7C8C9C10A11T12) (G3-H), that have been reported to adopt different secondary structures in solution. Based on the formation of site-specific fragment ions upon IRMPD, two isobaric crosslink products were differentiated for each ODN. The preferential formation of G3G4 and G4G5 crosslinks was determined as a function of reaction conditions, including incubation temperature and presence of metal ions. G3-D consistently exhibited a greater preference for formation of the G4G5 crosslink compared to the G3-H ODN. The ratio of G3G4:G4G5 crosslinks increased for both G3-D and G3-H at higher incubation temperatures or when metal salts were added. Comparison of the IRMPD fragmentation patterns of the unmodified ODNs and the intramolecular platinated crosslinks indicated that backbone cleavage was significantly suppressed near the crosslink. PMID:24135806

Generation and Characterization of a Transgenic Mouse Carrying a Functional Human β-Globin Gene with the IVSI-6 Thalassemia Mutation

PubMed Central

Mancini, Irene; Lampronti, Ilaria; Salvatori, Francesca; Fabbri, Enrica; Zuccato, Cristina; Cosenza, Lucia C.; Montagner, Giulia; Borgatti, Monica; Altruda, Fiorella; Fagoonee, Sharmila; Carandina, Gianni; Aiello, Vincenzo; Breda, Laura; Rivella, Stefano; Gambari, Roberto

2015-01-01

Mouse models that carry mutations causing thalassemia represent a suitable tool to test in vivo new mutation-specific therapeutic approaches. Transgenic mice carrying the β-globin IVSI-6 mutation (the most frequent in Middle-Eastern regions and recurrent in Italy and Greece) are, at present, not available. We report the production and characterization of a transgenic mouse line (TG-β-IVSI-6) carrying the IVSI-6 thalassemia point mutation within the human β-globin gene. In the TG-β-IVSI-6 mouse (a) the transgenic integration region is located in mouse chromosome 7; (b) the expression of the transgene is tissue specific; (c) as expected, normally spliced human β-globin mRNA is produced, giving rise to β-globin production and formation of a human-mouse tetrameric chimeric hemoglobin mu α-globin2/hu β-globin2 and, more importantly, (d) the aberrant β-globin-IVSI-6 RNAs are present in blood cells. The TG-β-IVSI-6 mouse reproduces the molecular features of IVSI-6 β-thalassemia and might be used as an in vivo model to characterize the effects of antisense oligodeoxynucleotides targeting the cryptic sites responsible for the generation of aberrantly spliced β-globin RNA sequences, caused by the IVSI-6 mutation. These experiments are expected to be crucial for the development of a personalized therapy for β-thalassemia. PMID:26097845

The hairpin resonator: A plasma density measuring technique revisited

NASA Astrophysics Data System (ADS)

Piejak, R. B.; Godyak, V. A.; Garner, R.; Alexandrovich, B. M.; Sternberg, N.

2004-04-01

A microwave resonator probe is a resonant structure from which the relative permittivity of the surrounding medium can be determined. Two types of microwave resonator probes (referred to here as hairpin probes) have been designed and built to determine the electron density in a low-pressure gas discharge. One type, a transmission probe, is a functional equivalent of the original microwave resonator probe introduced by R. L. Stenzel [Rev. Sci. Instrum. 47, 603 (1976)], modified to increase coupling to the hairpin structure and to minimize plasma perturbation. The second type, a reflection probe, differs from the transmission probe in that it requires only one coaxial feeder cable. A sheath correction, based on the fluid equations for collisionless ions in a cylindrical electron-free sheath, is presented here to account for the sheath that naturally forms about the hairpin structure immersed in plasma. The sheath correction extends the range of electron density that can be accurately measured with a particular wire separation of the hairpin structure. Experimental measurements using the hairpin probe appear to be highly reproducible. Comparisons with Langmuir probes show that the Langmuir probe determines an electron density that is 20-30% lower than the hairpin. Further comparisons, with both an interferometer and a Langmuir probe, show hairpin measurements to be in good agreement with the interferometer while Langmuir probe measurements again result in a lower electron density.

Development of background-free tame fluorescent probes for intracellular live cell imaging

PubMed Central

Alamudi, Samira Husen; Satapathy, Rudrakanta; Kim, Jihyo; Su, Dongdong; Ren, Haiyan; Das, Rajkumar; Hu, Lingna; Alvarado-Martínez, Enrique; Lee, Jung Yeol; Hoppmann, Christian; Peña-Cabrera, Eduardo; Ha, Hyung-Ho; Park, Hee-Sung; Wang, Lei; Chang, Young-Tae

2016-01-01

Fluorescence labelling of an intracellular biomolecule in native living cells is a powerful strategy to achieve in-depth understanding of the biomolecule's roles and functions. Besides being nontoxic and specific, desirable labelling probes should be highly cell permeable without nonspecific interactions with other cellular components to warrant high signal-to-noise ratio. While it is critical, rational design for such probes is tricky. Here we report the first predictive model for cell permeable background-free probe development through optimized lipophilicity, water solubility and charged van der Waals surface area. The model was developed by utilizing high-throughput screening in combination with cheminformatics. We demonstrate its reliability by developing CO-1 and AzG-1, a cyclooctyne- and azide-containing BODIPY probe, respectively, which specifically label intracellular target organelles and engineered proteins with minimum background. The results provide an efficient strategy for development of background-free probes, referred to as ‘tame' probes, and novel tools for live cell intracellular imaging. PMID:27321135

A quinoline-based Cu2 + ion complex fluorescence probe for selective detection of inorganic phosphate anion in aqueous solution and its application to living cells

NASA Astrophysics Data System (ADS)

Dai, Yanpeng; Wang, Peng; Fu, Jiaxin; Yao, Kun; Xu, Kuoxi; Pang, Xiaobin

2017-08-01

A quinaldine functionalized probe QP has been designed and synthesized. It exhibited selective turn-off fluorescence response toward Cu2 + ion over most of the biologically important ions at physiological pH. The binding ratio of the probe QP and Cu2 + ion was determined to be 1:1 through fluorescence titration, Job's plot and ESI-MS. The binding constant (K) of Cu2 + to probe QP was found to be 2.12 × 104 M- 1. Further, the Cu2 + ensemble of probe QP was found to respond H2PO4- and HPO42 - among other important biological anions via fluorescence turn-on response at physiological pH. Fluorescence microscopy imaging using living Hela cells showed that probe QP could be used as an effective fluorescent probe for detecting Cu2 + cation and H2PO4- and HPO42 - anions in living cells.

A quinoline-based Cu2+ ion complex fluorescence probe for selective detection of inorganic phosphate anion in aqueous solution and its application to living cells.

PubMed

Dai, Yanpeng; Wang, Peng; Fu, Jiaxin; Yao, Kun; Xu, Kuoxi; Pang, Xiaobin

2017-08-05

A quinaldine functionalized probe QP has been designed and synthesized. It exhibited selective turn-off fluorescence response toward Cu 2+ ion over most of the biologically important ions at physiological pH. The binding ratio of the probe QP and Cu 2+ ion was determined to be 1:1 through fluorescence titration, Job's plot and ESI-MS. The binding constant (K) of Cu 2+ to probe QP was found to be 2.12×10 4 M -1 . Further, the Cu 2+ ensemble of probe QP was found to respond H 2 PO 4 - and HPO 4 2- among other important biological anions via fluorescence turn-on response at physiological pH. Fluorescence microscopy imaging using living Hela cells showed that probe QP could be used as an effective fluorescent probe for detecting Cu 2+ cation and H 2 PO 4 - and HPO 4 2- anions in living cells. Copyright © 2017 Elsevier B.V. All rights reserved.

Design and Realization of 3D Printed AFM Probes.

PubMed

Alsharif, Nourin; Burkatovsky, Anna; Lissandrello, Charles; Jones, Keith M; White, Alice E; Brown, Keith A

2018-05-01

Atomic force microscope (AFM) probes and AFM imaging by extension are the product of exceptionally refined silicon micromachining, but are also restricted by the limitations of these fabrication techniques. Here, the nanoscale additive manufacturing technique direct laser writing is explored as a method to print monolithic cantilevered probes for AFM. Not only are 3D printed probes found to function effectively for AFM, but they also confer several advantages, most notably the ability to image in intermittent contact mode with a bandwidth approximately ten times larger than analogous silicon probes. In addition, the arbitrary structural control afforded by 3D printing is found to enable programming the modal structure of the probe, a capability that can be useful in the context of resonantly amplifying nonlinear tip-sample interactions. Collectively, these results show that 3D printed probes complement those produced using conventional silicon micromachining and open the door to new imaging techniques. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Class of Multiresponsive Colorimetric and Fluorescent pH Probes via Three Different Reaction Mechanisms of Salen Complexes: A Selective and Accurate pH Measurement.

PubMed

Cheng, Jinghui; Gou, Fei; Zhang, Xiaohong; Shen, Guangyu; Zhou, Xiangge; Xiang, Haifeng

2016-09-19

We report a class of multiresponsive colorimetric and fluorescent pH probes based on three different reaction mechanisms including cation exchange, protonation, and hydrolysis reaction of K(I), Ca(II), Zn(II), Cu(II), Al(III), and Pd(II) Salen complexes. Compared with traditional pure organic pH probes, these complex-based pH probes exhibited a much better selectivity due to the shielding function of the filled-in metal ion in the complex. Their pH sensing performances were affected by the ligand structure and the central metal ion. This work is the first report of "off-on-on'-off" colorimetric and fluorescent pH probes that possess three different reaction mechanisms and should inspire the design of multiple-responsive probes for important analytes in biological systems.

Donated chemical probes for open science

PubMed Central

Ackloo, Suzanne; Arrowsmith, Cheryl H; Bauser, Marcus; Baryza, Jeremy L; Blagg, Julian; Böttcher, Jark; Bountra, Chas; Brown, Peter J; Bunnage, Mark E; Carter, Adrian J; Damerell, David; Dötsch, Volker; Drewry, David H; Edwards, Aled M; Edwards, James; Elkins, Jon M; Fischer, Christian; Frye, Stephen V; Gollner, Andreas; Grimshaw, Charles E; IJzerman, Adriaan; Hanke, Thomas; Hartung, Ingo V; Hitchcock, Steve; Howe, Trevor; Hughes, Terry V; Laufer, Stefan; Li, Volkhart MJ; Liras, Spiros; Marsden, Brian D; Matsui, Hisanori; Mathias, John; O'Hagan, Ronan C; Owen, Dafydd R; Pande, Vineet; Rauh, Daniel; Rosenberg, Saul H; Roth, Bryan L; Schneider, Natalie S; Scholten, Cora; Singh Saikatendu, Kumar; Simeonov, Anton; Takizawa, Masayuki; Tse, Chris; Thompson, Paul R; Treiber, Daniel K; Viana, Amélia YI; Wells, Carrow I; Willson, Timothy M; Zuercher, William J; Knapp, Stefan

2018-01-01

Potent, selective and broadly characterized small molecule modulators of protein function (chemical probes) are powerful research reagents. The pharmaceutical industry has generated many high-quality chemical probes and several of these have been made available to academia. However, probe-associated data and control compounds, such as inactive structurally related molecules and their associated data, are generally not accessible. The lack of data and guidance makes it difficult for researchers to decide which chemical tools to choose. Several pharmaceutical companies (AbbVie, Bayer, Boehringer Ingelheim, Janssen, MSD, Pfizer, and Takeda) have therefore entered into a pre-competitive collaboration to make available a large number of innovative high-quality probes, including all probe-associated data, control compounds and recommendations on use (https://openscienceprobes.sgc-frankfurt.de/). Here we describe the chemical tools and target-related knowledge that have been made available, and encourage others to join the project. PMID:29676732

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.

Fast-Response Turn-on Fluorescent Probes Based on Thiolysis of NBD Amine for H2 S Bioimaging.

PubMed

Wang, Runyu; Li, Zhifei; Zhang, Changyu; Li, Yanyan; Xu, Guoce; Zhang, Qiang-Zhe; Li, Lu-Yuan; Yi, Long; Xi, Zhen

2016-05-17

Hydrogen sulfide (H2 S) is an important endogenous signaling molecule with multiple biological functions. New selective fluorescent turn-on probes based on fast thiolyling of NBD (7-nitro-1,2,3-benzoxadiazole) amine were explored for sensing H2 S in aqueous buffer and in living cells. The syntheses of both probes are simple and quite straightforward. The probes are highly sensitive and selective toward H2 S over other biologically relevant species. The fluorescein-NBD-based probe showed 65-fold green fluorescent increase upon H2 S activation. The rhodamine-NBD-based probe reacted rapidly with H2 S (t1/2 ≈1 min) to give a 4.5-fold increase in red fluorescence. Moreover, both probes were successfully used for monitoring H2 S in living cells and in mice. Based on such probe-based tools, we could observe H2 O2 -induced H2 S biogenesis in a concentration-dependent and time-dependent fashion in living cells. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Theoretical Design of a Two-Photon Fluorescent Probe for Nitric Oxide with Enhanced Emission Induced by Photoninduced Electron Transfer.

PubMed

Zhang, Yujin; Leng, Jiancai; Hu, Wei

2018-04-25

In the present work, we systematically investigate the sensing abilities of two recently literature-reported two-photon fluorescent NO probes, i.e., the o-phenylenediamine derivative of Nile Red and the p-phenylenediamine derivative of coumarin. The recognition mechanisms of these probes are studied by using the molecular orbital classifying method, which demonstrates the photoinduced electron transfer process. In addition, we have designed two new probes by swapping receptor units present on fluorophores, i.e., the p-phenylenediamine derivative of Nile Red and the o-phenylenediamine derivative of coumarin. However, it illustrates that only the latter has ability to function as off-on typed fluorescent probe for NO. More importantly, calculations on the two-photon absorption properties of the probes demonstrate that both receptor derivatives of coumarin possess larger TPA cross-sections than Nile Red derivatives, which makes a better two photon fluorescent probe. Our theoretical investigations reveal that the underlying mechanism satisfactorily explain the experimental results, providing a theoretical basis on the structure-property relationships which is beneficial to developing new two-photon fluorescent probes for NO.

Reaction-Based Off-On Near-infrared Fluorescent Probe for Imaging Alkaline Phosphatase Activity in Living Cells and Mice.

PubMed

Tan, Yi; Zhang, Ling; Man, Ka Ho; Peltier, Raoul; Chen, Ganchao; Zhang, Huatang; Zhou, Liyi; Wang, Feng; Ho, Derek; Yao, Shao Q; Hu, Yi; Sun, Hongyan

2017-03-01

Alkaline phosphatases are a group of enzymes that play important roles in regulating diverse cellular functions and disease pathogenesis. Hence, developing fluorescent probes for in vivo detection of alkaline phosphatase activity is highly desirable for studying the dynamic phosphorylation in living organisms. Here, we developed the very first reaction-based near-infrared (NIR) probe (DHXP) for sensitive detection of alkaline phosphatase activity both in vitro and in vivo. Our studies demonstrated that the probe displayed an up to 66-fold fluorescence increment upon incubation with alkaline phosphatases, and the detection limit of our probe was determined to be 0.07 U/L, which is lower than that of most of alkaline phosphatase probes reported in literature. Furthermore, we demonstrated that the probe can be applied to detecting alkaline phosphatase activity in cells and mice. In addition, our probe possesses excellent biocompatibility and rapid cell-internalization ability. In light of these prominent properties, we envision that DHXP will add useful tools for investigating alkaline phosphatase activity in biomedical research.

Orientational Dynamics of a Functionalized Alkyl Planar Monolayer Probed by Polarization-Selective Angle-Resolved Infrared Pump-Probe Spectroscopy.

PubMed

Nishida, Jun; Yan, Chang; Fayer, Michael D

2016-10-12

Polarization-selective angle-resolved infrared pump-probe spectroscopy was developed and used to study the orientational dynamics of a planar alkylsiloxane monolayer functionalized with a rhenium metal carbonyl headgroup on an SiO 2 surface. The technique, together with a time-averaged infrared linear dichroism measurement, characterized picosecond orientational relaxation of the headgroup occurring at the monolayer-air interface by employing several sets of incident angles of the infrared pulses relative to the sample surface. By application of this method and using a recently developed theory, it was possible to extract both the out-of-plane and "mainly"-in-plane orientational correlation functions in a model-independent manner. The observed correlation functions were compared with theoretically derived correlation functions based on several dynamical models. The out-of-plane correlation function reveals the highly restricted out-of-plane motions of the head groups and also suggests that the angular distribution of the transition dipole moments is bimodal. The mainly-in-plane correlation function, for the sample studied here with the strongly restricted out-of-plane motions, essentially arises from the purely in-plane dynamics. In contrast to the out-of-plane dynamics, significant in-plane motions occurring over various time scales were observed including an inertial motion, a restricted wobbling motion of ∼3 ps, and complete randomization occurring in ∼25 ps.

Label-free biosensing with functionalized nanopipette probes.

PubMed

Umehara, Senkei; Karhanek, Miloslav; Davis, Ronald W; Pourmand, Nader

2009-03-24

Nanopipette technology can uniquely identify biomolecules such as proteins based on differences in size, shape, and electrical charge. These differences are determined by the detection of changes in ionic current as the proteins interact with the nanopipette tip coated with probe molecules. Here we show that electrostatic, biotin-streptavidin, and antibody-antigen interactions on the nanopipette tip surface affect ionic current flowing through a 50-nm pore. Highly charged polymers interacting with the glass surface modulated the rectification property of the nanopipette electrode. Affinity-based binding between the probes tethered to the surface and their target proteins caused a change in the ionic current due to a partial blockade or an altered surface charge. These findings suggest that nanopipettes functionalized with appropriate molecular recognition elements can be used as nanosensors in biomedical and biological research.

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.

Thin Cu film resistivity using four probe techniques: Effect of film thickness and geometrical shapes

NASA Astrophysics Data System (ADS)

Choudhary, Sumita; Narula, Rahul; Gangopadhyay, Subhashis

2018-05-01

Precise measurement of electrical sheet resistance and resistivity of metallic thin Cu films may play a significant role in temperature sensing by means of resistivity changes which can further act as a safety measure of various electronic devices during their operation. Four point probes resistivity measurement is a useful approach as it successfully excludes the contact resistance between the probes and film surface of the sample. Although, the resistivity of bulk samples at a particular temperature mostly depends on its materialistic property, however, it may significantly differ in the case of thin films, where the shape and thickness of the sample can significantly influence on it. Depending on the ratio of the film thickness to probe spacing, samples are usually classified in two segments such as (i) thick films or (ii) thin films. Accordingly, the geometric correction factors G can be related to the sample resistivity r, which has been calculated here for thin Cu films of thickness up to few 100 nm. In this study, various rectangular shapes of thin Cu films have been used to determine the shape induced geometric correction factors G. An expressions for G have been obtained as a function of film thickness t versus the probe spacing s. Using these expressions, the correction factors have been plotted separately for each cases as a function of (a) film thickness for fixed linear probe spacing and (b) probe distance from the edge of the film surface for particular thickness. Finally, we compare the experimental results of thin Cu films of various rectangular geometries with the theoretical reported results.

Design and fabrication of a polyimide-based microelectrode array: application in neural recording and repeatable electrolytic lesion in rat brain.

PubMed

Chen, You-Yin; Lai, Hsin-Yi; Lin, Sheng-Huang; Cho, Chien-Wen; Chao, Wen-Hung; Liao, Chia-Hsin; Tsang, Siny; Chen, Yi-Fan; Lin, Si-Yue

2009-08-30

The design and testing of a new microelectrode array, the NCTU (National Chiao Tung University) probe, was presented. Evaluation results showed it has good biocompatibility, high signal-to-noise ratio (SNR: the root mean square of background noise to the average peak-to-peak amplitude of spikes) during chronic neural recordings, and high reusability for electrolytic lesions. The probe was a flexible, polyimide-based microelectrode array with a long shaft (14.9 mm in length) and 16 electrodes (5 microm-thick and 16 microm in radius); its performance in chronic in vivo recordings was examined in rodents. To improve the precision of implantation, a metallic, impact-resistant layer was sandwiched between the polyimide layers to strengthen the probe. The three-dimensional (3D) structure of electrodes fabricated by electroplating produced rough textures that increased the effective surface area. The in vitro impedance of electrodes on the NCTU probe was 2.4+/-0.52 MOmega at 1 kHz. In addition, post-surgical neural recordings of implanted NCTU probes were conducted for up to 40 days in awake, normally behaving rats. The electrodes on the NCTU probe functioned well and had a high SNR (range: 4-5) with reliable in vivo impedance (<0.7 MOmega). The electrodes were also robust enough to functionally record events, even after the anodal current (30 microA, 10s) was repeatedly applied for 60 times. With good biocompatibility, high and stable SNR for chronic recording, and high tolerance for electrolytic lesion, the NCTU probe would serve as a useful device in future neuroscience research.

Enhancement of infectious disease vaccines through TLR9-dependent recognition of CpG DNA.

PubMed

McCluskie, M J; Krieg, A M

2006-01-01

The adaptive immune system-with its remarkable ability to generate antigen-specific antibodies and T lymphocytes against pathogens never before "seen" by an organism-is one of the marvels of evolution. However, to generate these responses, the adaptive immune system requires activation by the innate immune system. Toll-like receptors (TLRs) are perhaps the best-understood family of innate immune receptors for detecting infections and stimulating adaptive immune responses. TLR9 appears to have evolved to recognize infections by a subtle structural difference between eukaryotic and prokaryotic/viral DNA; only the former frequently methylates CpG dinucleotides. Used as vaccine adjuvants, synthetic oligodeoxynucleotide (ODN) ligands for TLR9--CpG ODN--greatly enhance the speed and strength of the immune responses to vaccination.

Dendritic cell-targeting DNA-based mucosal adjuvants for the development of mucosal vaccines

PubMed Central

Kataoka, Kosuke; Fujihashi, Kohtaro

2009-01-01

In order to establish effective mucosal immunity against various mucosal pathogens, vaccines must be delivered via the mucosal route and contain effective adjuvant(s). Since mucosal adjuvants can simply mix with the antigen, it is relatively easy to adapt them for different types of vaccine development. Even in simple admixture vaccines, the adjuvant itself must be prepared without any complications. Thus, CpG oligodeoxynucleotides or plasmids encoding certain cDNA(s) would be potent mucosal adjuvant candidates when compared with other substances that can be used as mucosal adjuvants. The strategy of a DNA-based mucosal adjuvant facilitates the targeting of mucosal dendritic cells, and thus is an effective and safe approach. It would also provide great flexibility for the development of effective vaccines for various mucosal pathogens. PMID:19722892

Formulation of vaccines containing CpG oligonucleotides and alum

PubMed Central

Aebig, Joan A.; Mullen, Gregory E. D.; Dobrescu, Gelu; Rausch, Kelly; Lambert, Lynn; Ajose-Popoola, Olubunmi; Long, Carole A.; Saul, Allan; Miles, Aaron P.

2007-01-01

CpG oligodeoxynucleotides are potent immunostimulants. For parenterally delivered alum based vaccines, the immunostimulatory effect of CpG depends on the association of the CpG and antigen to the alum. We describe effects of buffer components on the binding of CPG 7909 to aluminum hydroxide (Alhydrogel), assays for measuring binding of CPG 7909 to alum and CPG 7909 induced dissociation of antigen from the alum. Free CPG 7909 is a potent inducer of IP-10 in mice. However the lack of IP-10 production from formulations containing bound CPG 7909 suggested that CPG 7909 does not rapidly dissociate from the alum after injection. It also suggests that IP-10 assays are not a good basis for potency assays for alum based vaccines containing CPG 7909. PMID:17512533

Expanding the potential of G-quadruplex structures: formation of a heterochiral TBA analogue.

PubMed

Virgilio, Antonella; Varra, Michela; Scuotto, Maria; Capuozzo, Antonella; Irace, Carlo; Mayol, Luciano; Esposito, Veronica; Galeone, Aldo

2014-03-21

In order to expand the potential applications of G-quadruplex structures, we explored the ability of heterochiral oligodeoxynucleotides based on the thrombin-binding aptamer (TBA) sequence to fold into similar complexes, with particular focus on their resistance in biological environments. A combination of CD and NMR techniques was used. Similarly to TBA, the ODN ggTTggtgtggTTgg (lower case letters indicate L residues) is able to fold into a chair-like antiparallel G-quadruplex structure, but has a slightly higher thermal stability. The discovery that heterochiral ODNs are able to form stable G-quadruplex structures opens up new possibilities for their development in several fields, as aptamers, sensors and, as recently shown, as catalysts for enantioselective reactions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optimized knock-in of point mutations in zebrafish using CRISPR/Cas9.

PubMed

Prykhozhij, Sergey V; Fuller, Charlotte; Steele, Shelby L; Veinotte, Chansey J; Razaghi, Babak; Robitaille, Johane M; McMaster, Christopher R; Shlien, Adam; Malkin, David; Berman, Jason N

2018-06-14

We have optimized point mutation knock-ins into zebrafish genomic sites using clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 reagents and single-stranded oligodeoxynucleotides. The efficiency of knock-ins was assessed by a novel application of allele-specific polymerase chain reaction and confirmed by high-throughput sequencing. Anti-sense asymmetric oligo design was found to be the most successful optimization strategy. However, cut site proximity to the mutation and phosphorothioate oligo modifications also greatly improved knock-in efficiency. A previously unrecognized risk of off-target trans knock-ins was identified that we obviated through the development of a workflow for correct knock-in detection. Together these strategies greatly facilitate the study of human genetic diseases in zebrafish, with additional applicability to enhance CRISPR-based approaches in other animal model systems.

Covalent Incorporation of Selenium into Oligonucleotides for X-ray Crystal Structure Determination via MAD: Proof of Principle

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

Teplova, M.; Wilds, C.J.; Wawrzak, Z.

2010-03-08

Selenium was incorporated into an oligodeoxynucleotide in the form of 2'-methylseleno-uridine (U{sub Se}). The X-ray crystal structure of the duplex d(GCGTA)U{sub Se}d(ACGC){sub 2} was determined by the multiwavelength anomalous dispersion (MAD) technique and refined to a resolution of 1.3 {angstrom}, demonstrating that selenium can selectively substitute oxygen in DNA and that the resulting compounds are chemically stable. Since derivatization at the 2'-{alpha}-position with selenium does not affect the preference of the sugar for the C3'-endo conformation, this strategy is suitable for incorporating selenium into RNA. The availability of selenium-containing nucleic acids for crystallographic phasing offers an attractive alternative to themore » commonly used halogenated pyrimidines.« less

Nano-optical functionality based on local photoisomerization in photochromic single crystal

NASA Astrophysics Data System (ADS)

Nakagomi, Ryo; Uchiyama, Kazuharu; Kubota, Satoru; Hatano, Eri; Uchida, Kingo; Naruse, Makoto; Hori, Hirokazu

2018-01-01

Towards the construction of functional devices and systems using optical near-field processes, we demonstrate the multivalent features in the path-branching phenomena in a photochromic single crystal observed in optical phase change between colorless (1o) and blue-colored (1c) phases that transmits in subwavelength scale over a macroscopic spatial range associated with local mechanical distortions induced. To observe the near-field optical processes of transmission path branching, we have developed a top-to-bottom double-probe scanning near-field optical microscope capable of nanometer-scale correlation measurements by two individually position-controlled probes that face each other sandwiching the photochromic material. We have experimentally confirmed that a local near-field optical excitation applied to one side of the photochromic crystal by a probe tip resulted in characteristic structures of subwavelength scale around 100 nm or less that are observed by the other probe tip located on the opposite side. The structures are different from those resulting from far-field excitations that are quantitively evaluated by autocorrelations. The results suggest that the mechanical distortion caused by the local phase change in the photochromic crystal suppresses the phase change of the neighboring molecules. This new type of optical-near-field-induced local photoisomerization has the potential to allow the construction of functional devices with multivalent properties for natural intelligence.

The Evaluation of Bioelectrical Activity of Pelvic Floor Muscles Depending on Probe Location: A Pilot Study

PubMed Central

Słupska, Lucyna

2013-01-01

Objectives. The main objective was to determine how the depth of probe placement affects functional and resting bioelectrical activity of the PFM and whether the recorded signal might be dependent on the direction in which the probe is rotated. Participants. The study comprised of healthy, nulliparous women between the ages of 21 and 25. Outcome Measures. Bioelectric activity of the PFM was recorded from four locations of the vagina by surface EMG and vaginal probe. Results. There were no statistically significant differences between the results during functional sEMG activity. During resting sEMG activity, the highest bioelectrical activity of the PFM was observed in the L1 and the lowest in the L4 and a statistically significant difference between the highest and the lowest results of resting sEMG activity was observed (P = 0.0043). Conclusion. Different electrodes placement during functional contraction of PFM does not affect the obtained results in sEMG evaluation. In order to diagnose the highest resting activity of PFM the recording plates should be placed toward the anterior vaginal wall and distally from the introitus. However, all of the PFM have similar bioelectrical activity and it seems that these muscles could be treated as a single muscle. PMID:24392449

Small-molecule-based protein-labeling technology in live cell studies: probe-design concepts and applications.

PubMed

Mizukami, Shin; Hori, Yuichiro; Kikuchi, Kazuya

2014-01-21

The use of genetic engineering techniques allows researchers to combine functional proteins with fluorescent proteins (FPs) to produce fusion proteins that can be visualized in living cells, tissues, and animals. However, several limitations of FPs, such as slow maturation kinetics or issues with photostability under laser illumination, have led researchers to examine new technologies beyond FP-based imaging. Recently, new protein-labeling technologies using protein/peptide tags and tag-specific probes have attracted increasing attention. Although several protein-labeling systems are com mercially available, researchers continue to work on addressing some of the limitations of this technology. To reduce the level of background fluorescence from unlabeled probes, researchers have pursued fluorogenic labeling, in which the labeling probes do not fluoresce until the target proteins are labeled. In this Account, we review two different fluorogenic protein-labeling systems that we have recently developed. First we give a brief history of protein labeling technologies and describe the challenges involved in protein labeling. In the second section, we discuss a fluorogenic labeling system based on a noncatalytic mutant of β-lactamase, which forms specific covalent bonds with β-lactam antibiotics such as ampicillin or cephalosporin. Based on fluorescence (or Förster) resonance energy transfer and other physicochemical principles, we have developed several types of fluorogenic labeling probes. To extend the utility of this labeling system, we took advantage of a hydrophobic β-lactam prodrug structure to achieve intracellular protein labeling. We also describe a small protein tag, photoactive yellow protein (PYP)-tag, and its probes. By utilizing a quenching mechanism based on close intramolecular contact, we incorporated a turn-on switch into the probes for fluorogenic protein labeling. One of these probes allowed us to rapidly image a protein while avoiding washout. In the future, we expect that protein-labeling systems with finely designed probes will lead to novel methodologies that allow researchers to image biomolecules and to perturb protein functions.

Morpholine Derivative-Functionalized Carbon Dots-Based Fluorescent Probe for Highly Selective Lysosomal Imaging in Living Cells.

PubMed

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

2017-08-30

The development of a suitable fluorescent probe for the specific labeling and imaging of lysosomes through the direct visual fluorescent signal is extremely important for understanding the dysfunction of lysosomes, which might induce various pathologies, including neurodegenerative diseases, cancer, and Alzheimer's disease. Herein, a new carbon dot-based fluorescent probe (CDs-PEI-ML) was designed and synthesized for highly selective imaging of lysosomes in live cells. In this probe, PEI (polyethylenimine) is introduced to improve water solubility and provide abundant amine groups for the as-prepared CDs-PEI, and the morpholine group (ML) serves as a targeting unit for lysosomes. More importantly, passivation with PEI could dramatically increase the fluorescence quantum yield of CDs-PEI-ML as well as their stability in fluorescence emission under different excitation wavelength. Consequently, experimental data demonstrated that the target probe CDs-PEI-ML has low cytotoxicity and excellent photostability. Additionally, further live cell imaging experiment indicated that CDs-PEI-ML is a highly selective fluorescent probe for lysosomes. We speculate the mechanism for selective staining of lysosomes that CDs-PEI-ML was initially taken up by lysosomes through the endocytic pathway and then accumulated in acidic lysosomes. It is notable that there was less diffusion of CDs-PEI-ML into cytoplasm, which could be ascribed to the presence of lysosome target group morpholine on surface of CDs-PEI-ML. The blue emission wavelength combined with the high photo stability and ability of long-lasting cell imaging makes CDs-PEI-ML become an alternative fluorescent probe for multicolor labeling and long-term tracking of lysosomes in live cells and the potential application in super-resolution imaging. To best of our knowledge, there are still limited carbon dots-based fluorescent probes that have been studied for specific lysosomal imaging in live cells. The concept of surface functionality of carbon dots will also pave a new avenue for developing carbon dots-based fluorescent probes for subcellular labeling.

probeBase—an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016

PubMed Central

Greuter, Daniel; Loy, Alexander; Horn, Matthias; Rattei, Thomas

2016-01-01

probeBase http://www.probebase.net is a manually maintained and curated database of rRNA-targeted oligonucleotide probes and primers. Contextual information and multiple options for evaluating in silico hybridization performance against the most recent rRNA sequence databases are provided for each oligonucleotide entry, which makes probeBase an important and frequently used resource for microbiology research and diagnostics. Here we present a major update of probeBase, which was last featured in the NAR Database Issue 2007. This update describes a complete remodeling of the database architecture and environment to accommodate computationally efficient access. Improved search functions, sequence match tools and data output now extend the opportunities for finding suitable hierarchical probe sets that target an organism or taxon at different taxonomic levels. To facilitate the identification of complementary probe sets for organisms represented by short rRNA sequence reads generated by amplicon sequencing or metagenomic analysis with next generation sequencing technologies such as Illumina and IonTorrent, we introduce a novel tool that recovers surrogate near full-length rRNA sequences for short query sequences and finds matching oligonucleotides in probeBase. PMID:26586809

Probe for high resolution NMR with sample reorientation

DOEpatents

Pines, Alexander; Samoson, Ago

1990-01-01

An improved NMR probe and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise orientationally disordered samples. The apparatus mechanically varies the orientation of the sample such that the time average of two or more sets of spherical harmonic functions are zero.

A Probe Intermix Procedure for Fading Response Prompts.

ERIC Educational Resources Information Center

Billingsley, Felix F.

1987-01-01

A prompt fading method was employed to teach an eight-year-old student with severe behavior disorders the self-paced use of a functional behavior (requesting rather than grabbing food items). Initial pairing of prompts and natural cues was followed by a mix of prompted and probe (unprompted) trials. (Author/JW)

Some Options for a Minimum Solar Probe Mission

NASA Technical Reports Server (NTRS)

Randolph, J. E.; Tsurutani, B. T.; Turner, P. R.; Miyake, R. M.; Ayon, J. A.

1996-01-01

Smaller and lower cost options of NASA's Solar Probe mission have recently been studied. The difference between these options and the results of earlier studies is dramatic. The motivation for low cost has encouraged the JPL design team to accomodate a smaller scientific payload using innovative multi-functional subsystems.

Novel Optical Methods for Identification, Imaging, and Preservation of the Cavernous Nerves Responsible for Penile Erections during Prostate Cancer Surgery

DTIC Science & Technology

2009-03-01

wavelength, pulse energy, and pulse rate) to produce strongest and most rapid erectile response as measured by intracavernosal pressure in the penis ...PC Fiber Rod Housing Optics 5-mm-ID Port Probe Handle Probe Stem Enlarged View of Probe Tip Oscilloscope FunctionGenerator Thulium Fiber Laser Shutter...rapid erectile response as measured by intracavernosal pressure (ICP) in the penis . ICP values were increased from an initial range of 30-40 mmHg

Use of a pitot probe for determining wing section drag in flight

NASA Technical Reports Server (NTRS)

Saltzman, E. J.

1975-01-01

A wake traversing probe was used to obtain section drag and wake profile data from the wing of a sailplane. The transducer sensed total pressure defect in the wake as well as freestream total pressure on both sides of the sensing element when the probe moved beyond the wake. Profiles of wake total pressure defects plotted as a function of distance above and below the trailing edge plane were averaged for calculating section drag coefficients for flights at low dynamic pressures.

Outer planet atmospheric entry probes - An overview of technology readiness

NASA Technical Reports Server (NTRS)

Vojvodich, N. S.; Reynolds, R. T.; Grant, T. L.; Nachtsheim, P. R.

1975-01-01

Entry probe systems for characterizing, by in situ measurements, the atmospheric properties, chemical composition, and cloud structure of the planets Saturn, Uranus, and Jupiter are examined from the standpoint of unique mission requirements, associated subsystem performance, and degree of commonality of design. Past earth entry vehicles (PAET) and current planetary spacecraft (Pioneer Venus probes and Viking lander) are assessed to identify the extent of potential subsystem inheritance, as well as to establish the significant differences, in both form and function, relative to outer planet requirements. Recent research results are presented and reviewed for the most critical probe technology areas, including: science accommodation, telecommunication, and entry heating and thermal protection. Finally presented is a brief discussion of the use of decision analysis techniques for quantifying various probe heat-shield test alternatives and performance risk.

SCANNING VOLTA POTENTIALS MEASUREMENTS OF METALS IN IRRADIATED AIR.

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

ISAACS, H.S.; ADZIC, G.; AND ENERGY SCIENCES AND TECHNOLOGY DEPARTMENT

2000-10-22

A method for direct dc measurement of the Volta potential is presented. High intensity synchrotron x-ray beams were used to locally irradiate the atmosphere adjacent to the metal surface and produce a conducting path between a sample and a reference probe. The direct measurements of potential in the ionized air could be made at probe heights of around 1 mm compared to less than 0.1 mm for the Kelvin probe. The measurements were similar to traditional Kelvin probe measurements, but had a poorer spatial resolution. In contrast to the Kelvin probe methods, the approach described allows observation of the currentmore » as a function of impressed voltage. Methods to improve the special resolution of the technique and applications to corrosion under coating will be presented.« less

Langmuir Probe Measurements in an Inductively Coupled GEC Reference Cell Plasma

NASA Technical Reports Server (NTRS)

Ji, J. S.; Kim, J. S.; Cappelli, M. A.; Sharma, S. P.; Arnold, J. O. (Technical Monitor)

1998-01-01

Measurements of electron number density, electron temperature, and electron energy distribution function (EEDF) using a compensated Langmuir probe have been performed on an inductively (transformer ) coupled Gaseous Electronics Conference (GEC) reference cell plasma. The plasma source is operated with CH4, CF4, or their mixtures with argon. The effect of independently driving the electrode supporting the wafer on the probe data is studied. In particular, we find that the plasma structure depends on the phase in addition to the magnitude of the power coupled to the electrode relative to that of the transformer coil. The Langmuir probe is translated in a plane parallel to the electrode to investigate the spatial structure of the plasma. The probe data is also compared with fluid model predictions.

Flow cytometric sorting of fecal bacteria after in situ hybridization with polynucleotide probes.

PubMed

Bruder, Lena M; Dörkes, Marcel; Fuchs, Bernhard M; Ludwig, Wolfgang; Liebl, Wolfgang

2016-10-01

The gut microbiome represents a key contributor to human physiology, metabolism, immune function, and nutrition. Elucidating the composition and genetics of the gut microbiota under various conditions is essential to understand how microbes function individually and as a community. Metagenomic analyses are increasingly used to study intestinal microbiota. However, for certain scientific questions it is sufficient to examine taxon-specific submetagenomes, covering selected bacterial genera in a targeted manner. Here we established a new variant of fluorescence in situ hybridization (FISH) combined with fluorescence-activated cell sorting (FACS), providing access to the genomes of specific taxa belonging to the complex community of the intestinal microbiota. In contrast to standard oligonucleotide probes, the RNA polynucleotide probe used here, which targets domain III of the 23S rRNA gene, extends the resolution power in environmental samples by increasing signal intensity. Furthermore, cells hybridized with the polynucleotide probe are not subjected to harsh pretreatments, and their genetic information remains intact. The protocol described here was tested on genus-specifically labeled cells in various samples, including complex fecal samples from different laboratory mouse types that harbor diverse intestinal microbiota. Specifically, as an example for the protocol described here, RNA polynucleotide probes could be used to label Enterococcus cells for subsequent sorting by flow cytometry. To detect and quantify enterococci in fecal samples prior to enrichment, taxon-specific PCR and qPCR detection systems have been developed. The accessibility of the genomes from taxon-specifically sorted cells for subsequent molecular analyses was demonstrated by amplification of functional genes. Copyright © 2016 Elsevier GmbH. All rights reserved.

Unusual Fluorescent Responses of Morpholine-functionalized Fluorescent Probes to pH via Manipulation of BODIPY’s HOMO and LUMO Energy Orbitals for Intracellular pH Detection

PubMed Central

Zhang, Jingtuo; Yang, Mu; Mazi, Wafa; Adhikari, Kapil; Fang, Mingxi; Xie, Fei; Valenzano, Loredana; Tiwari, Ashutosh; Luo, Fen-Tair; Liu, Haiying

2016-01-01

Three uncommon morpholine-based fluorescent probes (A, B and C) for pH were prepared by introducing morpholine residues to BODIPY dyes at 4,4’- and 2,6-positions, respectively. In contrast to morpholine-based fluorescent probes for pH reported in literature, these fluorescent probes display high fluorescence in a basic condition while they exhibit very weak fluorescence in an acidic condition. The theoretical calculation confirmed that morpholine is unable to function as either an electron donor or an electron acceptor to quench the BODIPY fluorescence in the neutral and basic condition via photo-induced electron transfer (PET) mechanism because the LUMO energy of morpholine is higher than those of the BODIPY dyes while its HOMO energy is lower than those of the BODIPY dyes. However, the protonation of tertiary amines of the morpholine residues in an acidic environment leads to fluorescence quenching of the BODIPY dyes via d-PET mechanism. The fluorescence quenching is because the protonation effectively decreases the LUMO energy which locates between the HOMO and LUMO energies of the BODIPY dyes. Fluorescent probe C with deep-red emission has been successfully used to detect pH changes in mammalian cells. PMID:27547822

Chloro-Functionalized Photo-crosslinking BODIPY for Glutathione Sensing and Subcellular Trafficking.

PubMed

Murale, Dhiraj P; Hong, Seong Cheol; Haque, Md Mamunul; Lee, Jun-Seok

2018-05-18

Glutathione (GSH) is one of major antioxidants inside cells that regulates oxidoreduction homeostasis. Recently, there have been extensive efforts to visualize GSH in live cells, but most of the probes available today are simple detection sensors and do not provide details of cellular localization. A new fluorescent probe (pcBD2-Cl), which is cell permeable and selectively reacts with GSH in situ, has been developed. The in situ GSH-labeled probe (pcBD2-GSH) exhibited quenches fluorescence, but subsequent binding to cellular abundant glutathione S-transferase (GST) recovers the fluorescence intensity, which makes it possible to image the GSH-GST complex in live cells. Interactions between probe and GST were confirmed by means of photo-crosslinking under intact live-cell conditions. Interestingly, isomers of chloro-functionalized 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) compounds behaved very distinctively inside the cells. Following co-staining imaging with MitoTracker and mitochondria fractionation upon lipopolysaccharide-mediated reactive oxygen species induction experiments showed that pcBD2-GSH accumulated in mitochondria. This is the first example of a live-cell imaging probe to visualize translocation of GSH from the cytosol to mitochondria. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Atom probe trajectory mapping using experimental tip shape measurements.

PubMed

Haley, D; Petersen, T; Ringer, S P; Smith, G D W

2011-11-01

Atom probe tomography is an accurate analytical and imaging technique which can reconstruct the complex structure and composition of a specimen in three dimensions. Despite providing locally high spatial resolution, atom probe tomography suffers from global distortions due to a complex projection function between the specimen and detector which is different for each experiment and can change during a single run. To aid characterization of this projection function, this work demonstrates a method for the reverse projection of ions from an arbitrary projection surface in 3D space back to an atom probe tomography specimen surface. Experimental data from transmission electron microscopy tilt tomography are combined with point cloud surface reconstruction algorithms and finite element modelling to generate a mapping back to the original tip surface in a physically and experimentally motivated manner. As a case study, aluminium tips are imaged using transmission electron microscopy before and after atom probe tomography, and the specimen profiles used as input in surface reconstruction methods. This reconstruction method is a general procedure that can be used to generate mappings between a selected surface and a known tip shape using numerical solutions to the electrostatic equation, with quantitative solutions to the projection problem readily achievable in tens of minutes on a contemporary workstation. © 2011 The Authors Journal of Microscopy © 2011 Royal Microscopical Society.

Chemical methodology as a source of small-molecule checkpoint inhibitors and heat shock protein 70 (Hsp70) modulators.

PubMed

Huryn, Donna M; Brodsky, Jeffrey L; Brummond, Kay M; Chambers, Peter G; Eyer, Benjamin; Ireland, Alex W; Kawasumi, Masaoki; Laporte, Matthew G; Lloyd, Kayla; Manteau, Baptiste; Nghiem, Paul; Quade, Bettina; Seguin, Sandlin P; Wipf, Peter

2011-04-26

Unique chemical methodology enables the synthesis of innovative and diverse scaffolds and chemotypes and allows access to previously unexplored "chemical space." Compound collections based on such new synthetic methods can provide small-molecule probes of proteins and/or pathways whose functions are not fully understood. We describe the identification, characterization, and evolution of two such probes. In one example, a pathway-based screen for DNA damage checkpoint inhibitors identified a compound, MARPIN (ATM and ATR pathway inhibitor) that sensitizes p53-deficient cells to DNA-damaging agents. Modification of the small molecule and generation of an immobilized probe were used to selectively bind putative protein target(s) responsible for the observed activity. The second example describes a focused library approach that relied on tandem multicomponent reaction methodologies to afford a series of modulators of the heat shock protein 70 (Hsp70) molecular chaperone. The synthesis of libraries based on the structure of MAL3-101 generated a collection of chemotypes, each modulating Hsp70 function, but exhibiting divergent pharmacological activities. For example, probes that compromise the replication of a disease-associated polyomavirus were identified. These projects highlight the importance of chemical methodology development as a source of small-molecule probes and as a drug discovery starting point.

Chemical methodology as a source of small-molecule checkpoint inhibitors and heat shock protein 70 (Hsp70) modulators

PubMed Central

Huryn, Donna M.; Brodsky, Jeffrey L.; Brummond, Kay M.; Chambers, Peter G.; Eyer, Benjamin; Ireland, Alex W.; Kawasumi, Masaoki; LaPorte, Matthew G.; Lloyd, Kayla; Manteau, Baptiste; Nghiem, Paul; Quade, Bettina; Seguin, Sandlin P.; Wipf, Peter

2011-01-01

Unique chemical methodology enables the synthesis of innovative and diverse scaffolds and chemotypes and allows access to previously unexplored “chemical space.” Compound collections based on such new synthetic methods can provide small-molecule probes of proteins and/or pathways whose functions are not fully understood. We describe the identification, characterization, and evolution of two such probes. In one example, a pathway-based screen for DNA damage checkpoint inhibitors identified a compound, MARPIN (ATM and ATR pathway inhibitor) that sensitizes p53-deficient cells to DNA-damaging agents. Modification of the small molecule and generation of an immobilized probe were used to selectively bind putative protein target(s) responsible for the observed activity. The second example describes a focused library approach that relied on tandem multicomponent reaction methodologies to afford a series of modulators of the heat shock protein 70 (Hsp70) molecular chaperone. The synthesis of libraries based on the structure of MAL3-101 generated a collection of chemotypes, each modulating Hsp70 function, but exhibiting divergent pharmacological activities. For example, probes that compromise the replication of a disease-associated polyomavirus were identified. These projects highlight the importance of chemical methodology development as a source of small-molecule probes and as a drug discovery starting point. PMID:21502524

The conservation and function of RNA secondary structure in plants

PubMed Central

Vandivier, Lee E.; Anderson, Stephen J.; Foley, Shawn W.; Gregory, Brian D.

2016-01-01

RNA transcripts fold into secondary structures via intricate patterns of base pairing. These secondary structures impart catalytic, ligand binding, and scaffolding functions to a wide array of RNAs, forming a critical node of biological regulation. Among their many functions, RNA structural elements modulate epigenetic marks, alter mRNA stability and translation, regulate alternative splicing, transduce signals, and scaffold large macromolecular complexes. Thus, the study of RNA secondary structure is critical to understanding the function and regulation of RNA transcripts. Here, we review the origins, form, and function of RNA secondary structure, focusing on plants. We then provide an overview of methods for probing secondary structure, from physical methods such as X-ray crystallography and nuclear magnetic resonance imaging (NMR) to chemical and nuclease probing methods. Marriage with high-throughput sequencing has enabled these latter methods to scale across whole transcriptomes, yielding tremendous new insights into the form and function of RNA secondary structure. PMID:26865341

Prolonged, brain-wide expression of nuclear-localized GCaMP3 for functional circuit mapping

PubMed Central

Kim, Christina K.; Miri, Andrew; Leung, Louis C.; Berndt, Andre; Mourrain, Philippe; Tank, David W.; Burdine, Rebecca D.

2014-01-01

Larval zebrafish offer the potential for large-scale optical imaging of neural activity throughout the central nervous system; however, several barriers challenge their utility. First, ~panneuronal probe expression has to date only been demonstrated at early larval stages up to 7 days post-fertilization (dpf), precluding imaging at later time points when circuits are more mature. Second, nuclear exclusion of genetically-encoded calcium indicators (GECIs) limits the resolution of functional fluorescence signals collected during imaging. Here, we report the creation of transgenic zebrafish strains exhibiting robust, nuclearly targeted expression of GCaMP3 across the brain up to at least 14 dpf utilizing a previously described optimized Gal4-UAS system. We confirmed both nuclear targeting and functionality of the modified probe in vitro and measured its kinetics in response to action potentials (APs). We then demonstrated in vivo functionality of nuclear-localized GCaMP3 in transgenic zebrafish strains by identifying eye position-sensitive fluorescence fluctuations in caudal hindbrain neurons during spontaneous eye movements. Our methodological approach will facilitate studies of larval zebrafish circuitry by both improving resolution of functional Ca2+ signals and by allowing brain-wide expression of improved GECIs, or potentially any probe, further into development. PMID:25505384

Integrated RFA/OCT catheter for real-time guidance of cardiac RFA therapy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Fu, Xiaoyong; Blumenthal, Colin; Dosluoglu, Deniz; Wang, Yves T.; Jenkins, Michael W.; Souza, Rakesh; Snyder, Christopher; Arruda, Mauricio; Rollins, Andrew M.

2016-03-01

Currently, cardiac radiofrequency ablation is guided by indirect signals. We demonstrate an integrated radiofrequency ablation (RFA) and optical coherence tomography (OCT) probe for directly monitoring of the RFA procedure with OCT images in real time. The integrated RFA/OCT probe is modified from a standard commercial RFA catheter, and a newly designed and fabricated miniature forward-viewing cone-scanning OCT probe is integrated into the modified probe. The OCT system is verified with the human finger images, and the results show the integrated RFA/OCT probe can acquire high quality OCT images. The radiofrequency energy delivering function of the integrated probe is verified by comparing the RFA lesion sizes with standard commercial RFA probe. For the standard commercial probe, the average width and depth of the 10 lesions were 3.5 mm and 1.8 mm respectively. For the integrated RFA/OCT probe, the average width and depth of the 10 lesions were 3.6 mm and 1.7 mm respectively. The lesions created by the two probes are indistinguishable in size. This demonstrates that our glass window in the integrated probe has little effect on the RF energy delivery. And the integrated probe is used to monitoring the cardiac RFA procedure in real time. The results show that the RFA lesion formation can be confirmed by the loss of birefringence in the heart tissue. The system can potentially in vivo image of the cardiac wall to aid RFA therapy for cardiac arrhythmias.

[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.

Preliminary evaluation of several disinfection/sterilization techniques for use with microdialysis probes.

PubMed

Huff, Jacquelyn K; Bresnahan, James F; Davies, Malonne I

2003-06-06

This study evaluated the suitability of some disinfection and sterilization methods for use with microdialysis probes. Disinfection or sterilization should minimize the tissue inflammatory reaction and improve the long-term health of rats on study and ensure the quality of data obtained by microdialysis sampling. Furthermore, the treatment should not negatively impact probe integrity or sampling performance. The techniques chosen for evaluation included two disinfection methods (70% ethanol and a commercial contact lens solution) and two sterilization methods (hydrogen peroxide plasma, and e-beam radiation). Linear microdialysis probes treated by these processes were compared to untreated probes removed from the manufacturer's packaging as if sterile (the control group). The probes were aseptically implanted in the livers of rats and monitored for 72 hours. The parameters chosen to evaluate probe performance were relative sample mass recovery and the relative in vivo extraction efficiency of the probe for caffeine. Post mortem bacterial counts and histopathology examination of liver tissue were also conducted. The probes remained intact and functional for the entire study period. The methods tested did not acutely alter the probes although hydrogen peroxide plasma and contact lens solution groups showed reduced extraction efficiencies. Minimal tissue damage was observed surrounding the probes and acute inflammatory reaction was mild to moderate. Low numbers of bacterial colonies from the implantation sites indicates that the health of animals in this study was not impaired. This was also true for the control group (untreated probe).

Tissue-like Neural Probes for Understanding and Modulating the Brain.

PubMed

Hong, Guosong; Viveros, Robert D; Zwang, Theodore J; Yang, Xiao; Lieber, Charles M

2018-03-19

Electrophysiology tools have contributed substantially to understanding brain function, yet the capabilities of conventional electrophysiology probes have remained limited in key ways because of large structural and mechanical mismatches with respect to neural tissue. In this Perspective, we discuss how the general goal of probe design in biochemistry, that the probe or label have a minimal impact on the properties and function of the system being studied, can be realized by minimizing structural, mechanical, and topological differences between neural probes and brain tissue, thus leading to a new paradigm of tissue-like mesh electronics. The unique properties and capabilities of the tissue-like mesh electronics as well as future opportunities are summarized. First, we discuss the design of an ultraflexible and open mesh structure of electronics that is tissue-like and can be delivered in the brain via minimally invasive syringe injection like molecular and macromolecular pharmaceuticals. Second, we describe the unprecedented tissue healing without chronic immune response that leads to seamless three-dimensional integration with a natural distribution of neurons and other key cells through these tissue-like probes. These unique characteristics lead to unmatched stable long-term, multiplexed mapping and modulation of neural circuits at the single-neuron level on a year time scale. Last, we offer insights on several exciting future directions for the tissue-like electronics paradigm that capitalize on their unique properties to explore biochemical interactions and signaling in a "natural" brain environment.

Role of the external NH2 linker on the conformation of surface immobilized single strand DNA probes and their SERS detection

NASA Astrophysics Data System (ADS)

He, Lijie; Langlet, Michel; Stambouli, Valerie

2017-03-01

The conformation and topological properties of DNA single strand probe molecules attached on solid surfaces are important, notably for the performances of devices such as biosensors. Commonly, the DNA probes are tethered to the surface using external linkers such as NH2. In this study, the role and influence of this amino-linker on the immobilization way and conformation of DNA probes on Ag nanoparticle surface is emphasized using Surface Enhanced Raman Spectroscopy (SERS). We compare the SERS spectra and their reproducibility in the case of two groups of DNA polybase probes which are polyA, polyC, polyT, and polyG. In the first group, the polybases exhibit an external NH2 functional linker while in the second group the polybases are NH2-free. The results show that the reproducibility of SERS spectra is enhanced in the case of the first group. It leads us to propose two models of polybase conformation on Ag surface according to the presence or the absence of the external NH2 linker. In the presence of the NH2 external linker, the latter would act as a major anchoring point. As a result, the polybases are much ordered with a less random orientation than in the case of NH2-free polybases. Consequently, in view of further in situ hybridization for biosensing applications, it is strongly recommended to use NH2 linker functionalized DNA probes.

Characterization of power induced heating and damage in fiber optic probes for near-field scanning optical microscopy

NASA Astrophysics Data System (ADS)

Dickenson, Nicholas E.; Erickson, Elizabeth S.; Mooren, Olivia L.; Dunn, Robert C.

2007-05-01

Tip-induced sample heating in near-field scanning optical microscopy (NSOM) is studied for fiber optic probes fabricated using the chemical etching technique. To characterize sample heating from etched NSOM probes, the spectra of a thermochromic polymer sample are measured as a function of probe output power, as was previously reported for pulled NSOM probes. The results reveal that sample heating increases rapidly to ˜55-60°C as output powers reach ˜50nW. At higher output powers, the sample heating remains approximately constant up to the maximum power studied of ˜450nW. The sample heating profiles measured for etched NSOM probes are consistent with those previously measured for NSOM probes fabricated using the pulling method. At high powers, both pulled and etched NSOM probes fail as the aluminum coating is damaged. For probes fabricated in our laboratory we find failure occurring at input powers of 3.4±1.7 and 20.7±6.9mW for pulled and etched probes, respectively. The larger half-cone angle for etched probes (˜15° for etched and ˜6° for pulled probes) enables more light delivery and also apparently leads to a different failure mechanism. For pulled NSOM probes, high resolution images of NSOM probes as power is increased reveal the development of stress fractures in the coating at a taper diameter of ˜6μm. These stress fractures, arising from the differential heating expansion of the dielectric and the metal coating, eventually lead to coating removal and probe failure. For etched tips, the absence of clear stress fractures and the pooled morphology of the damaged aluminum coating following failure suggest that thermal damage may cause coating failure, although other mechanisms cannot be ruled out.

Characterization of power induced heating and damage in fiber optic probes for near-field scanning optical microscopy.

PubMed

Dickenson, Nicholas E; Erickson, Elizabeth S; Mooren, Olivia L; Dunn, Robert C

2007-05-01

Tip-induced sample heating in near-field scanning optical microscopy (NSOM) is studied for fiber optic probes fabricated using the chemical etching technique. To characterize sample heating from etched NSOM probes, the spectra of a thermochromic polymer sample are measured as a function of probe output power, as was previously reported for pulled NSOM probes. The results reveal that sample heating increases rapidly to approximately 55-60 degrees C as output powers reach approximately 50 nW. At higher output powers, the sample heating remains approximately constant up to the maximum power studied of approximately 450 nW. The sample heating profiles measured for etched NSOM probes are consistent with those previously measured for NSOM probes fabricated using the pulling method. At high powers, both pulled and etched NSOM probes fail as the aluminum coating is damaged. For probes fabricated in our laboratory we find failure occurring at input powers of 3.4+/-1.7 and 20.7+/-6.9 mW for pulled and etched probes, respectively. The larger half-cone angle for etched probes ( approximately 15 degrees for etched and approximately 6 degrees for pulled probes) enables more light delivery and also apparently leads to a different failure mechanism. For pulled NSOM probes, high resolution images of NSOM probes as power is increased reveal the development of stress fractures in the coating at a taper diameter of approximately 6 microm. These stress fractures, arising from the differential heating expansion of the dielectric and the metal coating, eventually lead to coating removal and probe failure. For etched tips, the absence of clear stress fractures and the pooled morphology of the damaged aluminum coating following failure suggest that thermal damage may cause coating failure, although other mechanisms cannot be ruled out.

Optically Driven Spin Based Quantum Dots for Quantum Computing

DTIC Science & Technology

2008-01-01

time . Figure 3. Demonstration of optical pumping. This shows the absorption as a function of bias voltage and laser energy. In region...319,076 319,079 0 2 0 2 0 2 0 2 0 2 R el at iv e ab so rp tio n (× 1 0– 4 ) Probe frequency (GHz) Time constant (ms) 1 1 3 10 30 c Figure 1 | Laser ...spectrum of the forward (or backward) scan. c, The probe absorption spectrum as a function of the laser scan rate, indicated by the lock-in time

Oligonucleotide probes functionalization of nanogap electrodes.

PubMed

Zaffino, Rosa Letizia; Mir, Mònica; Samitier, Josep

2017-11-01

Nanogap electrodes have attracted a lot of consideration as promising platform for molecular electronic and biomolecules detection. This is mainly for their higher aspect ratio, and because their electrical properties are easily accessed by current-voltage measurements. Nevertheless, application of standard current-voltages measurements used to characterize nanogap response, and/or to modify specific nanogap electrodes properties, represents an issue. Since the strength of electrical fields in nanoscaled devices can reach high values, even at low voltages. Here, we analyzed the effects induced by different methods of surface modification of nanogap electrodes, in test-voltage application, employed for the electrical detection of a desoxyribonucleic acid (DNA) target. Nanogap electrodes were functionalized with two antisymmetric oligo-probes designed to have 20 terminal bases complementary to the edges of the target, which after hybridization bridges the nanogap, closing the electrical circuit. Two methods of functionalization were studied for this purpose; a random self-assembling of a mixture of the two oligo-probes (OPs) used in the platform, and a selective method that controls the position of each OP at selected side of nanogap electrodes. We used for this aim, the electrophoretic effect induced on negatively charged probes by the application of an external direct current voltage. The results obtained with both functionalization methods where characterized and compared in terms of electrode surface covering, calculated by using voltammetry analysis. Moreover, we contrasted the electrical detection of a DNA target in the nanogap platform either in site-selective and in randomly assembled nanogap. According to our results, a denser, although not selective surface functionalization, is advantageous for such kind of applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Label-free biosensing with functionalized nanopipette probes

PubMed Central

Umehara, Senkei; Karhanek, Miloslav; Davis, Ronald W.; Pourmand, Nader

2009-01-01

Nanopipette technology can uniquely identify biomolecules such as proteins based on differences in size, shape, and electrical charge. These differences are determined by the detection of changes in ionic current as the proteins interact with the nanopipette tip coated with probe molecules. Here we show that electrostatic, biotin-streptavidin, and antibody-antigen interactions on the nanopipette tip surface affect ionic current flowing through a 50-nm pore. Highly charged polymers interacting with the glass surface modulated the rectification property of the nanopipette electrode. Affinity-based binding between the probes tethered to the surface and their target proteins caused a change in the ionic current due to a partial blockade or an altered surface charge. These findings suggest that nanopipettes functionalized with appropriate molecular recognition elements can be used as nanosensors in biomedical and biological research. PMID:19264962

Small Molecule Chemical Probes of MicroRNA Function

PubMed Central

Velagapudi, Sai Pradeep; Vummidi, Balayeshwanth R.; Disney, Matthew D.

2015-01-01

MicroRNAs (miRNAs) are small, non-coding RNAs that control protein expression. Aberrant miRNA expression has been linked to various human diseases, and thus miRNAs have been explored as diagnostic markers and therapeutic targets. Although it is challenging to target RNA with small molecules in general, there have been successful campaigns that have identified small molecule modulators of miRNA function by targeting various pathways. For example, small molecules that modulate transcription and target nuclease processing sites in miRNA precursors have been identified. Herein, we describe challenges in developing chemical probes that target miRNAs and highlight aspects of miRNA cellular biology elucidated by using small molecule chemical probes. We expect that this area will expand dramatically in the near future as strides are made to understand small molecule recognition of RNA from a fundamental perspective. PMID:25500006

Means and methods for cytometric therapies

DOEpatents

Gillies, George T.; Fillmore, Helen; Broaddus, William C.; Evans, III, Boyd M.; Allison, Stephen W.

2013-03-26

A functionalized tip is incorporated into catheters for the cytometric delivery of cells into the brain and other body parts. For use in the brain, the tip forms part of a neurosurgical probe having a proximal end and a distal end. In addition to the functionalized tip, the probe has at least one cell slurry delivery lumen and a plurality of optical fibers configured along the probe, terminating in the tip to provide the photo-optical capability needed to monitor the viability and physiological behavior of the grafted cells as well as certain characteristics of the cellular environment. Details are also presented of the use of a neurocatheter having a cytometric tip of the type disclosed in the invention, as employed within the context of a feedback and control system for regulating the number of cells delivered to the brain of a patient.

Studying Electrical Conductivity Using a 3D Printed Four-Point Probe Station

ERIC Educational Resources Information Center

Lu, Yang; Santino, Luciano M.; Acharya, Shinjita; Anandarajah, Hari; D'Arcy, Julio M.

2017-01-01

The design and fabrication of functional scientific instrumentation allows students to forge a link between commonly reported numbers and physical material properties. Here, a two-point and four-point probe station for measuring electrical properties of solid materials is fabricated via 3D printing utilizing an inexpensive benchtop…

Probe for high resolution NMR with sample reorientation

DOEpatents

Pines, A.; Samoson, A.

1990-02-06

An improved NMR probe and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise orientationally disordered samples. The apparatus mechanically varies the orientation of the sample such that the time average of two or more sets of spherical harmonic functions are zero. 8 figs.

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.

A Wirelessly Powered Micro-Spectrometer for Neural Probe-Pin Device

NASA Technical Reports Server (NTRS)

Choi, Sang H.; Kim, Min Hyuck; Song, Kyo D.; Yoon, Hargsoon; Lee, Uhn

2015-01-01

Treatment of neurological anomalies, places stringent demands on device functionality and size. A micro-spectrometer has been developed for use as an implantable neural probe to monitor neuro-chemistry in synapses. The microspectrometer, based on a NASA-invented miniature Fresnel grating, is capable of differentiating the emission spectra from various brain tissues. The micro-spectrometer meets the size requirements, and is able to probe the neuro-chemistry and suppression voltage typically associated with a neural anomaly. This neural probe-pin device (PPD) is equipped with wireless power technology (WPT) enabling operation in a continuous manner without requiring an implanted battery. The implanted neural PPD, together with a neural electronics interface and WPT, allow real-time measurement and control/feedback for remediation of neural anomalies. The design and performance of the combined PPD/WPT device for monitoring dopamine in a rat brain will be presented to demonstrate the current level of development. Future work on this device will involve the addition of an embedded expert system capable of performing semi-autonomous management of neural functions through a routine of sensing, processing, and control.

NHS-Esters As Versatile Reactivity-Based Probes for Mapping Proteome-Wide Ligandable Hotspots.

PubMed

Ward, Carl C; Kleinman, Jordan I; Nomura, Daniel K

2017-06-16

Most of the proteome is considered undruggable, oftentimes hindering translational efforts for drug discovery. Identifying previously unknown druggable hotspots in proteins would enable strategies for pharmacologically interrogating these sites with small molecules. Activity-based protein profiling (ABPP) has arisen as a powerful chemoproteomic strategy that uses reactivity-based chemical probes to map reactive, functional, and ligandable hotspots in complex proteomes, which has enabled inhibitor discovery against various therapeutic protein targets. Here, we report an alkyne-functionalized N-hydroxysuccinimide-ester (NHS-ester) as a versatile reactivity-based probe for mapping the reactivity of a wide range of nucleophilic ligandable hotspots, including lysines, serines, threonines, and tyrosines, encompassing active sites, allosteric sites, post-translational modification sites, protein interaction sites, and previously uncharacterized potential binding sites. Surprisingly, we also show that fragment-based NHS-ester ligands can be made to confer selectivity for specific lysine hotspots on specific targets including Dpyd, Aldh2, and Gstt1. We thus put forth NHS-esters as promising reactivity-based probes and chemical scaffolds for covalent ligand discovery.

A wirelessly powered microspectrometer for neural probe-pin device

NASA Astrophysics Data System (ADS)

Choi, Sang H.; Kim, Min H.; Song, Kyo D.; Yoon, Hargsoon; Lee, Uhn

2015-12-01

Treatment of neurological anomalies, whether done invasively or not, places stringent demands on device functionality and size. We have developed a micro-spectrometer for use as an implantable neural probe to monitor neuro-chemistry in synapses. The micro-spectrometer, based on a NASA-invented miniature Fresnel grating, is capable of differentiating the emission spectra from various brain tissues. The micro-spectrometer meets the size requirements, and is able to probe the neuro-chemistry and suppression voltage typically associated with a neural anomaly. This neural probe-pin device (PPD) is equipped with wireless power technology (WPT) to enable operation in a continuous manner without requiring an implanted battery. The implanted neural PPD, together with a neural electronics interface and WPT, enable real-time measurement and control/feedback for remediation of neural anomalies. The design and performance of the combined PPD/WPT device for monitoring dopamine in a rat brain will be presented to demonstrate the current level of development. Future work on this device will involve the addition of an embedded expert system capable of performing semi-autonomous management of neural functions through a routine of sensing, processing, and control.

Improving stochastic estimates with inference methods: calculating matrix diagonals.

PubMed

Selig, Marco; Oppermann, Niels; Ensslin, Torsten A

2012-02-01

Estimating the diagonal entries of a matrix, that is not directly accessible but only available as a linear operator in the form of a computer routine, is a common necessity in many computational applications, especially in image reconstruction and statistical inference. Here, methods of statistical inference are used to improve the accuracy or the computational costs of matrix probing methods to estimate matrix diagonals. In particular, the generalized Wiener filter methodology, as developed within information field theory, is shown to significantly improve estimates based on only a few sampling probes, in cases in which some form of continuity of the solution can be assumed. The strength, length scale, and precise functional form of the exploited autocorrelation function of the matrix diagonal is determined from the probes themselves. The developed algorithm is successfully applied to mock and real world problems. These performance tests show that, in situations where a matrix diagonal has to be calculated from only a small number of computationally expensive probes, a speedup by a factor of 2 to 10 is possible with the proposed method. © 2012 American Physical Society

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

Holdaway, David I. H., E-mail: d.holdaway@ucl.ac.uk; Olaya-Castro, Alexandra, E-mail: a.olaya@ucl.ac.uk; Collini, Elisabetta, E-mail: elisabetta.collini@unipd.it

We examine transient circular dichroism (TRCD) spectroscopy as a technique to investigate signatures of exciton coherence dynamics under the influence of structured vibrational environments. We consider a pump-probe configuration with a linearly polarized pump and a circularly polarized probe, with a variable angle θ between the two directions of propagation. In our theoretical formalism the signal is decomposed in chiral and achiral doorway and window functions. Using this formalism, we show that the chiral doorway component, which beats during the population time, can be isolated by comparing signals with different values of θ. As in the majority of time-resolved pump-probemore » spectroscopy, the overall TRCD response shows signatures of both excited and ground state dynamics. However, we demonstrate that the chiral doorway function has only a weak ground state contribution, which can generally be neglected if an impulsive pump pulse is used. These findings suggest that the pump-probe configuration of optical TRCD in the impulsive limit has the potential to unambiguously probe quantum coherence beating in the excited state. We present numerical results for theoretical signals in an example dimer system.« less

Cell-free production of a functional oligomeric form of a Chlamydia major outer-membrane protein (MOMP) for vaccine development

DOE PAGES

He, Wei; Felderman, Martina; Evans, Angela C.; ...

2017-07-24

Chlamydia is a prevalent sexually transmitted disease that infects more than 100 million people worldwide. Although most individuals infected with Chlamydia trachomatis are initially asymptomatic, symptoms can arise if left undiagnosed. Long-term infection can result in debilitating conditions such as pelvic inflammatory disease, infertility, and blindness. Chlamydia infection, therefore, constitutes a significant public health threat, underscoring the need for a Chlamydia-specific vaccine. Chlamydia strains express a major outer-membrane protein (MOMP) that has been shown to be an effective vaccine antigen. However, approaches to produce a functional recombinant MOMP protein for vaccine development are limited by poor solubility, low yield, andmore » protein misfolding. For this study, we used an Escherichia coli-based cell-free system to express a MOMP protein from the mouse-specific species Chlamydia muridarum (MoPn-MOMP or mMOMP). The codon-optimized mMOMP gene was co-translated with Δ49apolipoprotein A1 (Δ49ApoA1), a truncated version of mouse ApoA1 in which the N-terminal 49 amino acids were removed. This co-translation process produced mMOMP supported within a telodendrimer nanolipoprotein particle (mMOMP–tNLP). The cell-free expressed mMOMP–tNLPs contain mMOMP multimers similar to the native MOMP protein. This cell-free process produced on average 1.5 mg of purified, water-soluble mMOMP–tNLP complex in a 1-ml cell-free reaction. The mMOMP–tNLP particle also accommodated the co-localization of CpG oligodeoxynucleotide 1826, a single-stranded synthetic DNA adjuvant, eliciting an enhanced humoral immune response in vaccinated mice. Using our mMOMP–tNLP formulation, we demonstrate a unique approach to solubilizing and administering membrane-bound proteins for future vaccine development. This method can be applied to other previously difficult-to-obtain antigens while maintaining full functionality and immunogenicity.« less

Cell-free production of a functional oligomeric form of a Chlamydia major outer-membrane protein (MOMP) for vaccine development

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

He, Wei; Felderman, Martina; Evans, Angela C.

Chlamydia is a prevalent sexually transmitted disease that infects more than 100 million people worldwide. Although most individuals infected with Chlamydia trachomatis are initially asymptomatic, symptoms can arise if left undiagnosed. Long-term infection can result in debilitating conditions such as pelvic inflammatory disease, infertility, and blindness. Chlamydia infection, therefore, constitutes a significant public health threat, underscoring the need for a Chlamydia-specific vaccine. Chlamydia strains express a major outer-membrane protein (MOMP) that has been shown to be an effective vaccine antigen. However, approaches to produce a functional recombinant MOMP protein for vaccine development are limited by poor solubility, low yield, andmore » protein misfolding. For this study, we used an Escherichia coli-based cell-free system to express a MOMP protein from the mouse-specific species Chlamydia muridarum (MoPn-MOMP or mMOMP). The codon-optimized mMOMP gene was co-translated with Δ49apolipoprotein A1 (Δ49ApoA1), a truncated version of mouse ApoA1 in which the N-terminal 49 amino acids were removed. This co-translation process produced mMOMP supported within a telodendrimer nanolipoprotein particle (mMOMP–tNLP). The cell-free expressed mMOMP–tNLPs contain mMOMP multimers similar to the native MOMP protein. This cell-free process produced on average 1.5 mg of purified, water-soluble mMOMP–tNLP complex in a 1-ml cell-free reaction. The mMOMP–tNLP particle also accommodated the co-localization of CpG oligodeoxynucleotide 1826, a single-stranded synthetic DNA adjuvant, eliciting an enhanced humoral immune response in vaccinated mice. Using our mMOMP–tNLP formulation, we demonstrate a unique approach to solubilizing and administering membrane-bound proteins for future vaccine development. This method can be applied to other previously difficult-to-obtain antigens while maintaining full functionality and immunogenicity.« less

Possibility to Probe Negative Values of a Wigner Function in Scattering of a Coherent Superposition of Electronic Wave Packets by Atoms.

PubMed

Karlovets, Dmitry V; Serbo, Valeriy G

2017-10-27

Within a plane-wave approximation in scattering, an incoming wave packet's Wigner function stays positive everywhere, which obscures such purely quantum phenomena as nonlocality and entanglement. With the advent of the electron microscopes with subnanometer-sized beams, one can enter a genuinely quantum regime where the latter effects become only moderately attenuated. Here we show how to probe negative values of the Wigner function in scattering of a coherent superposition of two Gaussian packets with a nonvanishing impact parameter between them (a Schrödinger's cat state) by atomic targets. For hydrogen in the ground 1s state, a small parameter of the problem, a ratio a/σ_{⊥} of the Bohr radius a to the beam width σ_{⊥}, is no longer vanishing. We predict an azimuthal asymmetry of the scattered electrons, which is found to be up to 10%, and argue that it can be reliably detected. The production of beams with the not-everywhere-positive Wigner functions and the probing of such quantum effects can open new perspectives for noninvasive electron microscopy, quantum tomography, particle physics, and so forth.

Inhibition of G protein-coupled P2Y2 receptor induced analgesia in a rat model of trigeminal neuropathic pain.

PubMed

Li, Na; Lu, Zhan-ying; Yu, Li-hua; Burnstock, Geoffrey; Deng, Xiao-ming; Ma, Bei

2014-03-18

ATP and P2X receptors play important roles in the modulation of trigeminal neuropathic pain, while the role of G protein-coupled P2Y₂ receptors and the underlying mechanisms are less clear. The threshold and frequency of action potentials, fast inactivating transient K+ channels (IA) are important regulators of membrane excitability in sensory neurons because of its vital role in the control of the spike onset. In this study, pain behavior tests, QT-RT-PCR, immunohistochemical staining, and patch-clamp recording, were used to investigate the role of P2Y₂ receptors in pain behaviour. In control rats: 1) UTP, an agonist of P2Y₂/P2Y₄ receptors, caused a significant decrease in the mean threshold intensities for evoking action potentials and a striking increase in the mean number of spikes evoked by TG neurons. 2) UTP significantly inhibited IA and the expression of Kv1.4, Kv3.4 and Kv4.2 subunits in TG neurons, which could be reversed by the P2 receptor antagonist suramin and the ERK antagonist U0126. In ION-CCI (chronic constriction injury of infraorbital nerve) rats: 1) mRNA levels of Kv1.4, Kv3.4 and Kv4.2 subunits were significantly decreased, while the protein level of phosphorylated ERK was significantly increased. 2) When blocking P2Y₂ receptors by suramin or injection of P2Y2R antisense oligodeoxynucleotides both led to a time- and dose-dependent reverse of allodynia in ION-CCI rats. 3) Injection of P2Y₂ receptor antisense oligodeoxynucleotides induced a pronounced decrease in phosphorylated ERK expression and a significant increase in Kv1.4, Kv3.4 and Kv4.2 subunit expression in trigeminal ganglia. Our data suggest that inhibition of P2Y₂ receptors leads to down-regulation of ERK-mediated phosphorylation and increase of the expression of I(A)-related Kv channels in trigeminal ganglion neurons, which might contribute to the clinical treatment of trigeminal neuropathic pain.

Effect of injection of antisense oligodeoxynucleotides of GAD isozymes into rat ventromedial hypothalamus on food intake and locomotor activity.

PubMed

Bannai, M; Ichikawa, M; Nishihara, M; Takahashi, M

1998-02-16

In the ventromedial hypothalamus (VMH), gamma-aminobutyric acid (GABA) plays a role in regulating feeding and running behaviors. The GABA synthetic enzyme, glutamic acid decarboxylase (GAD), consists of two isozymes, GAD65 and GAD67. In the present study, the phosphorothioated antisense oligodeoxynucleotides (ODNs) of each GAD isozyme were injected bilaterally into the VMH of male rats, and food intake, body weight and locomotor activity were monitored. ODNs were incorporated in the water-absorbent polymer (WAP, 0.2 nmol/microliter) so that ODNs were retained at the injection site. Each antisense ODN of GAD65 or GAD67 tended to reduce food intake on day 1 (day of injection=day 0) though not significantly. An injection combining both antisense ODNs significantly decreased food intake only on day 1, but body weight remained significantly lower than the control for 5 days. This suppression of body weight gain could be attributed to a significant increase in locomotor activity between days 3 and 5. Individual treatment with either ODNs did not change locomotor activity. The increase in daily locomotor activity in the group receiving the combined antisense ODNs occurred mainly during the light phase. Neither vehicle (WAP) nor control ODN affected food intake, body weight and locomotor activity. Histological studies indicated that antisense ODN distributed within 800 micron from the edge of the area where WAP was located 24 h after the injection gradually disappeared within days, but still remained within 300 micron m distance even 7 days after the injection. Antisense ODN was effectively incorporated by all the cell types examined, i.e., neurons, astrocytes and microglias. Further, HPLC analysis revealed that antisense ODNs of GAD isozymes, either alone or combined, decreased the content of GABA by 50% in VMH 24 h after the injection. These results indicate that suppression of GABA synthesis by either of the GAD isozymes is synergistically involved in suppressing food intake and enhancing locomotor activity in rat VMH. Copyright 1998 Elsevier Science B.V.

In vitro and in vivo effects of CpG-Oligodeoxynucleotides (CpG-ODN) on murine transitional cell carcinoma and on the native murine urinary bladder wall.

PubMed

Olbert, Peter Jochen; Schrader, Andres Jan; Simon, Corinna; Dalpke, Alexander; Barth, Peter; Hofmann, Rainer; Hegele, Axel

2009-06-01

Intravesical BCG instillation is established and efficient in the prophylaxis of recurrent transitional cell carcinoma. A Th-1 biased immune response is postulated. Recent work has proven the efficacy of synthetic CpG-Oligodeoxynucleotides (ODN) as inducers and adjuvants for a strong Th1-response and there is evidence for a direct and/or adjuvant anti-neoplastic effect. The purpose of this study was to examine the local effects of CpG-ODN on the murine bladder wall after intravesical instillation and the effects on cytokine expression in an orthotopic murine bladder cancer model. Histopathology, immunohistochemistry and fluorescence microscopy were performed after different instillation schedules of stimulatory, non-stimulatory biotinylized and FITC-labelled CpG-ODN into the murine bladder. MB-49 murine bladder cancer cells were tested for TLR-9 expression to exclude a potential direct responsiveness to CpG-ODN. Furthermore induction of apoptosis was tested by annexin V staining and FACS analysis of CpG-ODN stimulated tumor cells. In an orthotopic C57/Bl6 murine bladder cancer model, the expressions of IL-12, IFNgamma, IL-10 and TGF-beta were evaluated after repeated CpG-ODN treatment. Single and repeated instillation of CpG-ODN induced subepithelial and urothelial lymphocytic infiltrations with consecutive apoptoses. PBS and non-stimulative ODN induced no visible reaction. Bladder submucosa stained positive for biotin. Controls showed no endogenic biotin staining. FITC-labelled ODN adhered to the bladder mucosa and penetration of the mucosal barrier was not detected. MB-49 TCC cells did not express TLR-9 and CpG-ODN did not induce apoptosis in these cells. Repeated intravesical instillations of CpG-ODN in orthotopic murine tumor bearing urinary bladders resulted in significant up-regulation of both Th-1 and Th-2 cytokines. CpG-ODNs have promising anti-neoplastic potential. They exert a pronounced immunological response both in the native murine urinary bladder and in murine TCC. The mechanisms of action appear to be mediated immunologically, There was no direct effect of CpG-ODN on the tumor cells in this model.

Antibody classes & subclasses induced by mucosal immunization of mice with Streptococcus pyogenes M6 protein & oligodeoxynucleotides containing CpG motifs.

PubMed

Teloni, R; von Hunolstein, C; Mariotti, S; Donati, S; Orefici, G; Nisini, R

2004-05-01

Type-specific antibodies against M protein are critical for human protection as they enhance phagocytosis and are protective. An ideal vaccine for the protection against Streptococcus pyogenes would warrant mucosal immunity, but mucosally administered M-protein has been shown to be poorly immunogenic in animals. We used a recombinant M type 6 protein to immunize mice in the presence of synthetic oligodeoxynucleotides containing CpG motifs (immunostimulatory sequences: ISS) or cholera toxin (CT) to explore its possible usage in a mucosal vaccine. Mice were immunized by intranasal (in) or intradermal (id) administration with four doses at weekly intervals of M6-protein (10 microg/mouse) with or without adjuvant (ISS, 10 microg/mouse or CT, 0,5 microg/mouse). M6 specific antibodies were measured by enzyme linked immunosorbent assay using class and subclass specific monoclonal antibodies. The use of ISS induced an impressive anti M-protein serum IgG response but when id administered was not detectable in the absence of adjuvant. When used in, M-protein in the presence of both ISS and CT induced anti M-protein IgA in the bronchoalveolar lavage, as well as specific IgG in the serum. IgG were able to react with serotype M6 strains of S. pyogenes. The level of antibodies obtained by immunizing mice in with M-protein and CT was higher in comparison to M-protein and ISS. The analysis of anti-M protein specific IgG subclasses showed high levels of IgG1, IgG2a and IgG2b, and low levels of IgG3 when ISS were used as adjuvant. Thus, in the presence of ISS, the ratio IgG2a/IgG1 and (IgG2a+IgG3)/IgG1 >1 indicated a type 1-like response obtained both in mucosally or systemically vaccinated mice. Our study offers a reproducible model of anti-M protein vaccination that could be applied to test new antigenic formulations to induce an anti-group A Streptococcus (GAS) vaccination suitable for protection against the different diseases caused by this bacterium.

CpG-B Oligodeoxynucleotides Inhibit TLR-Dependent and -Independent Induction of Type I IFN in Dendritic Cells

PubMed Central

Liu, Yi C.; Gray, Reginald C.; Hardy, Gareth A. D.; Kuchtey, John; Abbott, Derek W.; Emancipator, Steven N.; Harding, Clifford V.

2010-01-01

CpG oligodeoxynucleotides (ODNs) signal through TLR9 to induce type I IFN (IFN-αβ) in dendritic cells (DCs). CpG-A ODNs are more efficacious than CpG-B ODNs for induction of IFN-αβ. Because IFN-αβ may contribute to autoimmunity, it is important to identify mechanisms to inhibit induction of IFN-αβ. In our studies, CpG-B ODN inhibited induction of IFN-αβ by CpG-A ODN, whereas induction of TNF-α and IL-12p40 by CpG-A ODN was not affected. CpG-B inhibition of IFN-αβ was observed in FLT3 ligand-induced murine DCs, purified murine myeloid DCs, plasmacytoid DCs, and human PBMCs. CpG-B ODN inhibited induction of IFN-αβ by agonists of multiple receptors, including MyD88-dependent TLRs (CpG-AODN signaling via TLR9, or R837 or Sendai virus signaling via TLR7) and MyD88-independent receptors (polyinosinic:polycytidylic acid signaling via TLR3 or ds break-DNA signaling via a cytosolic pathway). CpG-B ODN did not inhibit the IFN-αβ positive feedback loop second-wave IFN-αβ, because IFN-αβ–induced expression of IFN-αβ was unaffected, and CpG-B inhibition of IFN-αβ was manifested in IFN-αβR−/− DCs, which lack the positive feedback mechanism. Rather, CpG-B ODN inhibited early TLR-induced first wave IFN-α4 and IFN-β. Chromatin immunoprecipitation revealed that association of IFN regulatory factor 1 with the IFN-α4 and IFN-β promoters was induced by CpG-A ODN but not CpG-B ODN. Moreover, CpG-A–induced association of IFN regulatory factor 1 with these promoters was inhibited by CpG-B ODN. Our studies demonstrate a novel mechanism of transcriptional regulation of first-wave IFN-αβ that selectively inhibits induction of IFN-αβ downstream of multiple receptors and may provide targets for future therapeutic inhibition of IFN-αβ expression in vivo. PMID:20181884

Instant live-cell super-resolution imaging of cellular structures by nanoinjection of fluorescent probes.

PubMed

Hennig, Simon; van de Linde, Sebastian; Lummer, Martina; Simonis, Matthias; Huser, Thomas; Sauer, Markus

2015-02-11

Labeling internal structures within living cells with standard fluorescent probes is a challenging problem. Here, we introduce a novel intracellular staining method that enables us to carefully control the labeling process and provides instant access to the inner structures of living cells. Using a hollow glass capillary with a diameter of <100 nm, we deliver functionalized fluorescent probes directly into the cells by (di)electrophoretic forces. The label density can be adjusted and traced directly during the staining process by fluorescence microscopy. We demonstrate the potential of this technique by delivering and imaging a range of commercially available cell-permeable and nonpermeable fluorescent probes to cells.

Thermodynamic correction of particle concentrations measured by underwing probes on fast flying aircraft

NASA Astrophysics Data System (ADS)

Weigel, R.; Spichtinger, P.; Mahnke, C.; Klingebiel, M.; Afchine, A.; Petzold, A.; Krämer, M.; Costa, A.; Molleker, S.; Jurkat, T.; Minikin, A.; Borrmann, S.

2015-12-01

Particle concentration measurements with underwing probes on aircraft are impacted by air compression upstream of the instrument body as a function of flight velocity. In particular for fast-flying aircraft the necessity arises to account for compression of the air sample volume. Hence, a correction procedure is needed to invert measured particle number concentrations to ambient conditions that is commonly applicable for different instruments to gain comparable results. In the compression region where the detection of particles occurs (i.e. under factual measurement conditions), pressure and temperature of the air sample are increased compared to ambient (undisturbed) conditions in certain distance away from the aircraft. Conventional procedures for scaling the measured number densities to ambient conditions presume that the particle penetration speed through the instruments' detection area equals the aircraft speed (True Air Speed, TAS). However, particle imaging instruments equipped with pitot-tubes measuring the Probe Air Speed (PAS) of each underwing probe reveal PAS values systematically below those of the TAS. We conclude that the deviation between PAS and TAS is mainly caused by the compression of the probed air sample. From measurements during two missions in 2014 with the German Gulfstream G-550 (HALO - High Altitude LOng range) research aircraft we develop a procedure to correct the measured particle concentration to ambient conditions using a thermodynamic approach. With the provided equation the corresponding concentration correction factor ξ is applicable to the high frequency measurements of each underwing probe which is equipped with its own air speed sensor (e.g. a pitot-tube). ξ-values of 1 to 0.85 are calculated for air speeds (i.e. TAS) between 60 and 260 m s-1. From HALO data it is found that ξ does not significantly vary between the different deployed instruments. Thus, for the current HALO underwing probe configuration a parameterisation of ξ as a function of TAS is provided for instances if PAS measurements are lacking. The ξ-correction yields higher ambient particle concentration by about 15-25 % compared to conventional procedures - an improvement which can be considered as significant for many research applications. The calculated ξ-values are specifically related to the considered HALO underwing probe arrangement and may differ for other aircraft or instrument geometries. Moreover, the ξ-correction may not cover all impacts originating from high flight velocities and from interferences between the instruments and, e.g., the aircraft wings and/or fuselage. Consequently, it is important that PAS (as a function of TAS) is individually measured by each probe deployed underneath the wings of a fast-flying aircraft.

Thermodynamic correction of particle concentrations measured by underwing probes on fast-flying aircraft

NASA Astrophysics Data System (ADS)

Weigel, Ralf; Spichtinger, Peter; Mahnke, Christoph; Klingebiel, Marcus; Afchine, Armin; Petzold, Andreas; Krämer, Martina; Costa, Anja; Molleker, Sergej; Reutter, Philipp; Szakáll, Miklós; Port, Max; Grulich, Lucas; Jurkat, Tina; Minikin, Andreas; Borrmann, Stephan

2016-10-01

Particle concentration measurements with underwing probes on aircraft are impacted by air compression upstream of the instrument body as a function of flight velocity. In particular, for fast-flying aircraft the necessity arises to account for compression of the air sample volume. Hence, a correction procedure is needed to invert measured particle number concentrations to ambient conditions that is commonly applicable to different instruments to gain comparable results. In the compression region where the detection of particles occurs (i.e. under factual measurement conditions), pressure and temperature of the air sample are increased compared to ambient (undisturbed) conditions in certain distance away from the aircraft. Conventional procedures for scaling the measured number densities to ambient conditions presume that the air volume probed per time interval is determined by the aircraft speed (true air speed, TAS). However, particle imaging instruments equipped with pitot tubes measuring the probe air speed (PAS) of each underwing probe reveal PAS values systematically below those of the TAS. We conclude that the deviation between PAS and TAS is mainly caused by the compression of the probed air sample. From measurements during two missions in 2014 with the German Gulfstream G-550 (HALO - High Altitude LOng range) research aircraft we develop a procedure to correct the measured particle concentration to ambient conditions using a thermodynamic approach. With the provided equation, the corresponding concentration correction factor ξ is applicable to the high-frequency measurements of the underwing probes, each of which is equipped with its own air speed sensor (e.g. a pitot tube). ξ values of 1 to 0.85 are calculated for air speeds (i.e. TAS) between 60 and 250 m s-1. For different instruments at individual wing position the calculated ξ values exhibit strong consistency, which allows for a parameterisation of ξ as a function of TAS for the current HALO underwing probe configuration. The ability of cloud particles to adopt changes of air speed between ambient and measurement conditions depends on the cloud particles' inertia as a function of particle size (diameter Dp). The suggested inertia correction factor μ (Dp) for liquid cloud drops ranges between 1 (for Dp < 70 µm) and 0.8 (for 100 µm < Dp < 225 µm) but it needs to be applied carefully with respect to the particles' phase and nature. The correction of measured concentration by both factors, ξ and μ (Dp), yields higher ambient particle concentration by about 10-25 % compared to conventional procedures - an improvement which can be considered as significant for many research applications. The calculated ξ values are specifically related to the considered HALO underwing probe arrangement and may differ for other aircraft. Moreover, suggested corrections may not cover all impacts originating from high flight velocities and from interferences between the instruments and e.g. the aircraft wings and/or fuselage. Consequently, it is important that PAS (as a function of TAS) is individually measured by each probe deployed underneath the wings of a fast-flying aircraft.

Atomic magnetometer

DOEpatents

Schwindt, Peter [Albuquerque, NM; Johnson, Cort N [Albuquerque, NM

2012-07-03

An atomic magnetometer is disclosed which uses a pump light beam at a D1 or D2 transition of an alkali metal vapor to magnetically polarize the vapor in a heated cell, and a probe light beam at a different D2 or D1 transition to sense the magnetic field via a polarization rotation of the probe light beam. The pump and probe light beams are both directed along substantially the same optical path through an optical waveplate and through the heated cell to an optical filter which blocks the pump light beam while transmitting the probe light beam to one or more photodetectors which generate electrical signals to sense the magnetic field. The optical waveplate functions as a quarter waveplate to circularly polarize the pump light beam, and as a half waveplate to maintain the probe light beam linearly polarized.

Misregulation of Stromelysin-1 in Mouse Mammary Tumor Cells Accompanies Acquisition of Stromelysin-1 dependent Invasive Properties

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

Lochter, A.; Srebrow, A.; Sympson, C.J.

1997-02-21

Stromelysin-1 is a member of the metalloproteinase family of extracellular matrix-degrading enzymes that regulates tissue remodeling. We previously established a transgenic mouse model in which rat stromelysin-1 targeted to the mammary gland augmented expression of endogenous stromelysin-1, disrupted functional differentiation, and induced mammary tumors. A cell line generated from an adenocarcinoma in one of these animals and a previously described mammary tumor cell line generated in culture readily invaded both a reconstituted basement membrane and type I collagen gels, whereas a nonmalignant, functionally normal epithelial cell line did not. Invasion of Matrigel by tumor cells was largely abolished by metalloproteinasemore » inhibitors, but not by inhibitors of other proteinase families. Inhibition experiments with antisense oligodeoxynucleotides revealed that Matrigel invasion of both cell lines was critically dependent on stromelysin-1 expression. Invasion of collagen, on the other hand, was reduced by only 40-50%. Stromelysin-1 was expressed in both malignant and nonmalignant cells grown on plastic substrata. Its expression was completely inhibited in nonmalignant cells, but up-regulated in tumor cells, in response to Matrigel. Thus misregulation of stromelysin-1 expression appears to be an important aspect of mammary tumor cell progression to an invasive phenotype. The matrix metalloproteinases (MMPs) are a family of extracellular matrix (ECM)-degrading enzymes that have been implicated in a variety of normal developmental and pathological processes, including tumorigenesis. The MMP family comprises at least 15 members with different, albeit overlapping, substrate specificities. During activation of latent MMPs, their propeptides are cleaved and they are converted to a lower molecular weight form by other enzymes, including serine proteinases, and by autocatalytic cleavage. Among the MMPs, stromelysin-1 (SL1) possesses the broadest substrate specificity. Despite increasing knowledge about its enzymatic properties and the regulation of its expression, little is known about its function. We have generated transgenic animals that express an autoactivating mutant of rat SL1 targeted to the epithelial compartment of the mammary gland. Phenotypically, SL1 transgenic mice display increased branching morphogenesis and lactogenic differentiation at prepubertal stages and premature involution during late pregnancy. Branching morphogenesis requires the invasion of epithelial cells into the adipose tissue, a process reminiscent of invasion of stromal compartments by tumor cells. Strikingly, a large number of SL1 transgenic animals also develop mammary tumors of various histotypes, including invasive adenocarcinomas. Because tumor development is a late response of SL1 transgenic mice to overexpression of the transgene, it remains unclear whether SL1 plays a direct role in tumor growth and/or invasion or whether the observed tumors are a consequence of other molecular alterations in the microenvironment of the mammary gland before the onset of tumor growth. Studies performed with synthetic inhibitors of MMP activity and tissue inhibitors of metalloproteinases (TIMPs) have shown that suppression of MMP activity also suppresses tumor growth and metastasis. In many cases, the level of SL1 expression in tumors of the mammary gland and other tissues is positively correlated with the degree of malignancy. However, the only direct evidence for the nature of the MMPs involved was provided by the demonstration that function-blocking antibodies against gelatinase A and antisense inhibition of matrilysin expression decreased the invasiveness of tumor cells in a reconstituted basement membrane assay. These studies encouraged us to investigate whether SL1 plays a direct role in invasion of ECM. We used two carcinoma cell lines, TCL1 and SCg6 that formed rapidly growing, invasive tumors in vivo and migrated through Matrigel and collagen gels in culture. Antisense oligodeoxynucleotides (ODNs) against SL1 inhibited Matrigel invasion by TCL1 and SCg6 cells by more than 80% and collagen invasion by about 50%. Comparison of the regulation of SL1 expression by ECM in TCL1 and SCg6 cells with the nonmalignant, functional cell line SCp2 revealed striking differences that could play a role in the acquisition of an invasive tumor phenotype.« less

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

Zhukov, A. A., E-mail: azhukov@issp.ac.ru; Chernysheva, M. V.; Eliseev, A. A.

We report the results on the measurements of the work function of single-walled carbon nanotubes encapsulated by Agl (AgI@SWCNT), AgCl (AgCl@SWCNT), and CuBr (CuBr@SWCNT) by the local Kelvin probe technique. We found the values of the work function of tubes encapsulated with AgI and AgCl (Φ(AgI@SWCNT) = 5.08 ± 0.02, Φ(AgCl@SWCNT) = 5.10 ± 0.02 eV) to exceed substantially that of pristine carbon nanotubes, and the value of the work function of carbon nanotubes encapsulated with CuBr is Φ(CuBr@SWCNT) = 4.89 ± 0.03 (eV). The measurements are carried out using different kinds of microscope probes including multi-walled carbon nanotube tips.

Characterizing the performance of an affordable, multichannel conductivity probe for density measurements in stratified flows

NASA Astrophysics Data System (ADS)

Subramanian, Balaji; Carminati, Marco; Luzzatto-Fegiz, Paolo

2017-11-01

In stratified flows, conductivity (combined with temperature) is often used to measure density. The conductivity probes typically used can resolve very fine spatial scales, but on the downside they are fragile, expensive, sensitive to environmental noise and have only single channel capability. Recently a low-cost, robust, arduino-based probe called Conduino was developed, which can be valuable in a wide range of applications where resolving extremely small spatial scales is not needed. This probe uses micro-USB connectors as actual conductivity sensors with a custom designed electronic board for simultaneous acquisition from multiple probes, with conductivity resolution comparable to commercially available PME conductivity probe. A detailed assessment of performance of this Conduino probe is described here. To establish time response and sensitivity as a function of electrode geometry, we build a variety of shapes for different kinds of applications, with tip spacing ranging from 0.5-2.5 mm, and with electrode length ranging from 2.3-6 mm. We set up a two-layer density profile and traverse it rapidly, yielding a time response comparable to PME. The Conduino's multi-channel capability is used to operate probe arrays, which helps to construct density fields in stratified flows.

HAADF-STEM atom counting in atom probe tomography specimens: Towards quantitative correlative microscopy.

PubMed

Lefebvre, W; Hernandez-Maldonado, D; Moyon, F; Cuvilly, F; Vaudolon, C; Shinde, D; Vurpillot, F

2015-12-01

The geometry of atom probe tomography tips strongly differs from standard scanning transmission electron microscopy foils. Whereas the later are rather flat and thin (<20 nm), tips display a curved surface and a significantly larger thickness. As far as a correlative approach aims at analysing the same specimen by both techniques, it is mandatory to explore the limits and advantages imposed by the particular geometry of atom probe tomography specimens. Based on simulations (electron probe propagation and image simulations), the possibility to apply quantitative high angle annular dark field scanning transmission electron microscopy to of atom probe tomography specimens has been tested. The influence of electron probe convergence and the benefice of deconvolution of electron probe point spread function electron have been established. Atom counting in atom probe tomography specimens is for the first time reported in this present work. It is demonstrated that, based on single projections of high angle annular dark field imaging, significant quantitative information can be used as additional input for refining the data obtained by correlative analysis of the specimen in APT, therefore opening new perspectives in the field of atomic scale tomography. Copyright © 2015 Elsevier B.V. All rights reserved.

Design of a dual-function peptide probe as a binder of angiotensin II and an inducer of silver nanoparticle aggregation for use in label-free colorimetric assays.

PubMed

Okochi, Mina; Kuboyama, Masashi; Tanaka, Masayoshi; Honda, Hiroyuki

2015-09-01

Label-free colorimetric assays using metallic nanoparticles have received much recent attention, for their application in simple and sensitive methods for detection of biomolecules. Short peptide probes that can bind to analyte biomolecules are attractive ligands in molecular nanotechnology; however, identification of biological recognition motifs is usually based on trial-and-error experiments. Herein, a peptide probe was screened for colorimetric detection of angiotensin II (Ang II) using a mechanism for non-crosslinking aggregation of silver nanoparticles (AgNPs). The dual-function peptides, which bind to the analyte and induce AgNP aggregation, were identified using a two-step strategy: (1) screening of an Ang II-binding peptide from an Ang II receptor sequence library, using SPOT technology, which enable peptides synthesis on cellulose membranes via an Fmoc method and (2) selection of peptide probes that effectively induce aggregation of AgNPs using a photolinker modified peptide array. Using the identified peptide probe, KGKNKRRR, aggregation of AgNPs was detected by observation of a pink color in the absence of Ang II, whereas AgNPs remained dispersed in the presence of Ang II (yellow). The color changes were not observed in the presence of other hormone molecules. Ang II could be detected within 15 min, with a detection limit of 10 µM, by measuring the ratio of absorbance at 400 nm and 568 nm; the signal could also be observed with the naked eye. These data suggest that the peptide identified here could be used as a probe for simple and rapid colorimetric detection of Ang II. This strategy for the identification of functional peptides shows promise for the development of colorimetric detection of various diagnostically important biomolecules. Copyright © 2015 Elsevier B.V. All rights reserved.

Dual immobilization and magnetic manipulation of magnetic nanoparticles

NASA Astrophysics Data System (ADS)

Yang, S. Y.; Jian, Z. F.; Horng, H. E.; Hong, Chin-Yih; Yang, H. C.; Wu, C. C.; Lee, Y. H.

By suitably bio-functionalizing the surfaces, magnetic nanoparticles are able to bind specific biomolecules, and may serve as vectors for delivering bio-entities to target tissues. In this work, the synthesis of bio-functionalized magnetic nanoparticles with two kinds of bio-probes is developed. Here, the stem cell is selected as a to-be-delivered bio-entity and infarcted myocardium is the target issue. Thus, cluster designation-34 (CD-34) on stem cell and creatine kinase-MB (CK-MB) (or troponin I) on infarcted myocardium are the specific biomolecules to be bound with bio-functionalized magnetic nanoparticles. In addition to demonstrating the co-coating of two kinds of bio-probes on a magnetic nanoparticle, the feasibility of manipulation on bio-functionalized magnetic nanoparticles by external magnetic fields is investigated.

Probing plasma fluorinated graphene via spectromicroscopy.

PubMed

Struzzi, C; Scardamaglia, M; Reckinger, N; Sezen, H; Amati, M; Gregoratti, L; Colomer, J-F; Ewels, C; Snyders, R; Bittencourt, C

2017-11-29

Plasma fluorination of graphene is studied using a combination of spectroscopy and microscopy techniques, giving insight into the yield and fluorination mechanism for functionalization of supported graphene with both CF 4 and SF 6 gas precursors. Ion acceleration during fluorination is used to probe the effect on grafting functionalities. Adatom clustering, which occurs with CF 4 plasma treatment, is suppressed when higher kinetic energy is supplied to the ions. During SF 6 plasma functionalization, the sulfur atoms tend to bond to bare copper areas instead of affecting the graphene chemistry, except when the kinetic energy of the ions is restricted. Using scanning photoelectron microscopy, with a 100 nm spatial resolution, the chemical bonding environment is evaluated in the fluorinated carbon network at selected regions and the functionalization homogeneity is controlled in individual graphene flakes.

A multifunctional fluorescence sensor for Cd2+, PO43- and Cr3+ in different system and the practical application.

PubMed

Wang, Qingming; Tan, Yingzi; Wang, Nianhua; Lu, Zhixiang; Wang, Wenling

2018-05-07

A fluorescence probe based on thiosemicarbazide has been synthesized and well characterized by 1 H NMR, 13 C NMR, Elemental analysis, Electrospray ionization mass spectra. The probe 1 functions as a multitarget ion sensor, detect biologically and ecologically important Cd 2+ , PO 4 3- and Cr 3+ . Meanwhile, probe 1 displays selectivity for Cd 2+ over other metal ions and anions in DMF by emission spectrum. Interestingly, probe 1 has been explored to recognize PO 4 3- in CH 3 OH-H 2 O (v:v = 1:9). The binding stoichiometry of probe 1 with Cd 2+ and PO 4 3- are 2:1 and 1:1, respectively, which are confirmed by Electrospray ionization mass spectra. Probe 1 is selective, sensitive and reversibility/reusability to Cd 2+ and PO 4 3- with the detection limit as low as 0.035 μM and 0.011 μM respectively. Besides, the designed probe 1 has shown potential applications in the area of photo-printing. Copyright © 2018. Published by Elsevier B.V.

Fiber-Optical Sensors: Basics and Applications in Multiphase Reactors

PubMed Central

Li, Xiangyang; Yang, Chao; Yang, Shifang; Li, Guozheng

2012-01-01

This work presents a brief introduction on the basics of fiber-optical sensors and an overview focused on the applications to measurements in multiphase reactors. The most commonly principle utilized is laser back scattering, which is also the foundation for almost all current probes used in multiphase reactors. The fiber-optical probe techniques in two-phase reactors are more developed than those in three-phase reactors. There are many studies on the measurement of gas holdup using fiber-optical probes in three-phase fluidized beds, but negative interference of particles on probe function was less studied. The interactions between solids and probe tips were less studied because glass beads etc. were always used as the solid phase. The vision probes may be the most promising for simultaneous measurements of gas dispersion and solids suspension in three-phase reactors. Thus, the following techniques of the fiber-optical probes in multiphase reactors should be developed further: (1) online measuring techniques under nearly industrial operating conditions; (2) corresponding signal data processing techniques; (3) joint application with other measuring techniques.

Utilizing Gold Nanoparticle Probes to Visually Detect DNA Methylation

NASA Astrophysics Data System (ADS)

Chen, Kui; Zhang, Mingyi; Chang, Ya-Nan; Xia, Lin; Gu, Weihong; Qin, Yanxia; Li, Juan; Cui, Suxia; Xing, Gengmei

2016-06-01

The surface plasmon resonance (SPR) effect endows gold nanoparticles (GNPs) with the ability to visualize biomolecules. In the present study, we designed and constructed a GNP probe to allow the semi-quantitative analysis of methylated tumor suppressor genes in cultured cells. To construct the probe, the GNP surfaces were coated with single-stranded DNA (ssDNA) by forming Au-S bonds. The ssDNA contains a thiolated 5'-end, a regulatory domain of 12 adenine nucleotides, and a functional domain with absolute pairing with methylated p16 sequence (Met- p16). The probe, paired with Met- p16, clearly changed the color of aggregating GNPs probe in 5 mol/L NaCl solution. Utilizing the probe, p16 gene methylation in HCT116 cells was semi-quantified. Further, the methylation of E-cadherin, p15, and p16 gene in Caco2, HepG2, and HCT116 cell lines were detected by the corresponding probes, constructed with three domains. This simple and cost-effective method was useful for the diagnosis of DNA methylation-related diseases.

What does the dot-probe task measure? A reverse correlation analysis of electrocortical activity.

PubMed

Thigpen, Nina N; Gruss, L Forest; Garcia, Steven; Herring, David R; Keil, Andreas

2018-06-01

The dot-probe task is considered a gold standard for assessing the intrinsic attentive selection of one of two lateralized visual cues, measured by the response time to a subsequent, lateralized response probe. However, this task has recently been associated with poor reliability and conflicting results. To resolve these discrepancies, we tested the underlying assumption of the dot-probe task-that fast probe responses index heightened cue selection-using an electrophysiological measure of selective attention. Specifically, we used a reverse correlation approach in combination with frequency-tagged steady-state visual potentials (ssVEPs). Twenty-one participants completed a modified dot-probe task in which each member of a pair of lateralized face cues, varying in emotional expression (angry-angry, neutral-angry, neutral-neutral), flickered at one of two frequencies (15 or 20 Hz), to evoke ssVEPs. One cue was then replaced by a response probe, and participants indicated the probe orientation (0° or 90°). We analyzed the ssVEP evoked by the cues as a function of response speed to the subsequent probe (i.e., a reverse correlation analysis). Electrophysiological measures of cue processing varied with probe hemifield location: Faster responses to left probes were associated with weak amplification of the preceding left cue, apparent only in a median split analysis. By contrast, faster responses to right probes were systematically and parametrically predicted by diminished visuocortical selection of the preceding right cue. Together, these findings highlight the poor validity of the dot-probe task, in terms of quantifying intrinsic, nondirected attentive selection irrespective of probe/cue location. © 2018 Society for Psychophysiological Research.

Chemical Probes of Histone Lysine Methyltransferases

PubMed Central

2015-01-01

Growing evidence suggests that histone methyltransferases (HMTs, also known as protein methyltransferases (PMTs)) play an important role in diverse biological processes and human diseases by regulating gene expression and the chromatin state. Therefore, HMTs have been increasingly recognized by the biomedical community as a class of potential therapeutic targets. High quality chemical probes of HMTs, as tools for deciphering their physiological functions and roles in human diseases and testing therapeutic hypotheses, are critical for advancing this promising field. In this review, we focus on the discovery, characterization, and biological applications of chemical probes for HMTs. PMID:25423077

Development, fabrication and testing of a magnetically connected plastic vacuum probe surface sampler

NASA Technical Reports Server (NTRS)

Phillips, G. B.; Pace, V. A., Jr.

1972-01-01

The sampler utilizes permanent magnets and soft metal pole pieces to connect the cone/filter assembly to the sampling head and vacuum supply. The cone/filter assembly is packaged in a plastic container and presterilized so that the need for any human contact during the sampling procedure is completely eliminated. Microbiological tests have demonstrated that the sampling efficiency is not affected by the magnetic coupling apparatus and that the probe appears to function as efficiently as the conventional plastic and Sandia vacuum probes.

Microwave resonances in dielectric samples probed in Corbino geometry: simulation and experiment.

PubMed

Felger, M Maximilian; Dressel, Martin; Scheffler, Marc

2013-11-01

The Corbino approach, where the sample of interest terminates a coaxial cable, is a well-established method for microwave spectroscopy. If the sample is dielectric and if the probe geometry basically forms a conductive cavity, this combination can sustain well-defined microwave resonances that are detrimental for broadband measurements. Here, we present detailed simulations and measurements to investigate the resonance frequencies as a function of sample and probe size and of sample permittivity. This allows a quantitative optimization to increase the frequency of the lowest-lying resonance.

Multi-Modal Nano-Probes for Radionuclide and 5-color Near Infrared Optical Lymphatic Imaging

PubMed Central

Kobayashi, Hisataka; Koyama, Yoshinori; Barrett, Tristan; Hama, Yukihiro; Regino, Celeste A. S.; Shin, In Soo; Jang, Beom-Su; Le, Nhat; Paik, Chang H.; Choyke, Peter L.; Urano, Yasuteru

2008-01-01

Current contrast agents generally have one function and can only be imaged in monochrome, therefore, the majority of imaging methods can only impart uniparametric information. A single nano-particle has the potential to be loaded with multiple payloads. Such multi-modality probes have the ability to be imaged by more than one imaging technique, which could compensate for the weakness or even combine the advantages of each individual modality. Furthermore, optical imaging using different optical probes enables us to achieve multi-color in vivo imaging, wherein multiple parameters can be read from a single image. To allow differentiation of multiple optical signals in vivo, each probe should have a close but different near infrared emission. To this end, we synthesized nano-probes with multi-modal and multi-color potential, which employed a polyamidoamine dendrimer platform linked to both radionuclides and optical probes, permitting dual-modality scintigraphic and 5-color near infrared optical lymphatic imaging using a multiple excitation spectrally-resolved fluorescence imaging technique. PMID:19079788

Some exact properties of the nonequilibrium response function for transient photoabsorption

NASA Astrophysics Data System (ADS)

Perfetto, E.; Stefanucci, G.

2015-03-01

The physical interpretation of time-resolved photoabsorption experiments is not as straightforward as for the more conventional photoabsorption experiments conducted on equilibrium systems. In fact, the relation between the transient photoabsorption spectrum and the properties of the examined sample can be rather intricate since the former is a complicated functional of both the driving pump and the feeble probe fields. In this work, we critically review the derivation of the time-resolved photoabsorption spectrum in terms of the nonequilibrium dipole response function χ and assess its domain of validity. We then analyze χ in detail and discuss a few exact properties useful to interpret the transient spectrum during (overlapping regime) and after (nonoverlapping regime) the action of the pump. The nonoverlapping regime is the simplest to address. The absorption energies are indeed independent of the delay between the pump and probe pulses and hence the transient spectrum can change only by a rearrangement of the spectral weights. We give a close expression of these spectral weights in two limiting cases (ultrashort and everlasting monochromatic probes) and highlight their strong dependence on coherence and probe envelope. In the overlapping regime, we obtain a Lehmann-type representation of χ in terms of light-dressed states and provide a unifying framework of various well-known effects in pump-driven systems. We also show the emergence of spectral substructures due to the finite duration of the pump pulse.

Fabrication of transferrin functionalized gold nanoclusters/graphene oxide nanocomposite for turn-on near-infrared fluorescent bioimaging of cancer cells and small animals.

PubMed

Wang, Yong; Chen, Jia-Tong; Yan, Xiu-Ping

2013-02-19

Transferrin (Tf)-functionalized gold nanoclusters (Tf-AuNCs)/graphene oxide (GO) nanocomposite (Tf-AuNCs/GO) was fabricated as a turn-on near-infrared (NIR) fluorescent probe for bioimaging cancer cells and small animals. A one-step approach was developed to prepare Tf-AuNCs via a biomineralization process with Tf as the template. Tf acted not only as a stabilizer and a reducer but also as a functional ligand for targeting the transferrin receptor (TfR). The prepared Tf-AuNCs gave intense NIR fluorescence that can avoid interference from biological media such as tissue autofluorescence and scattering light. The assembly of Tf-AuNCs and GO gave the Tf-AuNCs/GO nanocomposite, a turn-on NIR fluorescent probe with negligible background fluorescence due to the super fluorescence quenching property of GO. The NIR fluorescence of the Tf-AuNCs/GO nanocomposite was effectively restored in the presence of TfR, due to the specific interaction between Tf and TfR and the competition of TfR with the GO for the Tf in Tf-AuNCs/GO composite. The developed turn-on NIR fluorescence probe offered excellent water solubility, stability, and biocompatibility, and exhibited high specificity to TfR with negligible cytotoxicity. The probe was successfully applied for turn-on fluorescent bioimaging of cancer cells and small animals.

Simulation of Mach Probes in Non-Uniform Magnetized Plasmas: the Influence of a Background Density Gradient

NASA Astrophysics Data System (ADS)

Haakonsen, Christian Bernt; Hutchinson, Ian H.

2013-10-01

Mach probes can be used to measure transverse flow in magnetized plasmas, but what they actually measure in strongly non-uniform plasmas has not been definitively established. A fluid treatment in previous work has suggested that the diamagnetic drifts associated with background density and temperature gradients affect transverse flow measurements, but detailed computational study is required to validate and elaborate on those results; it is really a kinetic problem, since the probe deforms and introduces voids in the ion and electron distribution functions. A new code, the Plasma-Object Simulator with Iterated Trajectories (POSIT) has been developed to self-consistently compute the steady-state six-dimensional ion and electron distribution functions in the perturbed plasma. Particle trajectories are integrated backwards in time to the domain boundary, where arbitrary background distribution functions can be specified. This allows POSIT to compute the ion and electron density at each node of its unstructured mesh, update the potential based on those densities, and then iterate until convergence. POSIT is used to study the impact of a background density gradient on transverse Mach probe measurements, and the results compared to the previous fluid theory. C.B. Haakonsen was supported in part by NSF/DOE Grant No. DE-FG02-06ER54512, and in part by an SCGF award administered by ORISE under DOE Contract No. DE-AC05-06OR23100.

Kinetic modeling of active plasma resonance spectroscopy

NASA Astrophysics Data System (ADS)

Oberrath, Jens

2016-09-01

The term ``active plasma resonance spectroscopy'' (APRS) refers to a plasma diagnostic method which employs the natural ability of plasmas to resonate close to the plasma frequency. Essential for this method is an appropriate model to determine the relation between the resonance parameters and demanded plasma parameters. Measurements with these probes in plasmas of a few Pa typically show a broadening of the spectrum that cannot be predicted by a fluid model. Thus, a kinetic model is necessary. A general kinetic model of APRS probes, which can be described in electorstatic approximation, valid for all pressures has been presented. This model is used to analyze the dynamic behavior of such probes by means of functional analytic methods. One of the main results is, that the system response function Y (ω) is given in terms of the matrix elements of the resolvent of the dynamic operator evaluated for values on the imaginary axis. The spectrum of this operator is continuous which implies a new phenomenon related to anomalous or non-collisional dissipation. Based on the scalar product, which is motivated by the kinetic free energy, the non-collisional damping can be interpreted: In a periodic state, the probe constantly emits plasma waves which propagate to ``infinity''. The free energy simply leaves the ``observation range'' of the probe which is recorded as damping. The kinetic damping, which depends on the mean kinetic energy of the electrons, is responsible for the broadening of a resonance peak in the measured spectrum of APRS probes. The ultimate goal is to determine explicit formulas for the relation between the broadening of the resonance peak and the ``equivalent electron temperature'', especially in the case of the spherical Impedance Probe and the Multipole Resonance Probe. Gratitude is expressed to the internal funding of Leuphana University, the BMBF via PluTO+, the DFG via Collaborative Research Center TR 87, and the Ruhr University Research School.

Pivot methods for global optimization

NASA Astrophysics Data System (ADS)

Stanton, Aaron Fletcher

A new algorithm is presented for the location of the global minimum of a multiple minima problem. It begins with a series of randomly placed probes in phase space, and then uses an iterative redistribution of the worst probes into better regions of phase space until a chosen convergence criterion is fulfilled. The method quickly converges, does not require derivatives, and is resistant to becoming trapped in local minima. Comparison of this algorithm with others using a standard test suite demonstrates that the number of function calls has been decreased conservatively by a factor of about three with the same degrees of accuracy. Two major variations of the method are presented, differing primarily in the method of choosing the probes that act as the basis for the new probes. The first variation, termed the lowest energy pivot method, ranks all probes by their energy and keeps the best probes. The probes being discarded select from those being kept as the basis for the new cycle. In the second variation, the nearest neighbor pivot method, all probes are paired with their nearest neighbor. The member of each pair with the higher energy is relocated in the vicinity of its neighbor. Both methods are tested against a standard test suite of functions to determine their relative efficiency, and the nearest neighbor pivot method is found to be the more efficient. A series of Lennard-Jones clusters is optimized with the nearest neighbor method, and a scaling law is found for cpu time versus the number of particles in the system. The two methods are then compared more explicitly, and finally a study in the use of the pivot method for solving the Schroedinger equation is presented. The nearest neighbor method is found to be able to solve the ground state of the quantum harmonic oscillator from a pure random initialization of the wavefunction.

Distinctive gene expression profiles characterize donor biopsies from HCV-positive kidney donors.

PubMed

Mas, Valeria R; Archer, Kellie J; Suh, Lacey; Scian, Mariano; Posner, Marc P; Maluf, Daniel G

2010-12-15

Because of the shortage of organs for transplantation, procurement of kidneys from extended criteria donors is inevitable. Frequently, donors infected with hepatitis C virus (HCV) are used. To elucidate an initial compromise of molecular pathways in HCV graft, gene expression profiles were evaluated. Twenty-four donor allograft biopsies (n=12 HCV positive (+) and n=12 HCV negative (-)) were collected at preimplantation time and profiled using microarrays. Donors were age, race, gender, and cold and warm ischemia time matched between groups. Probe level data were read into the R programming environment using the affy Bioconductor package, and the robust multiarray average method was used to obtain probe set expression summaries. To identify probe sets exhibiting differential expression, a two sample t test was performed. Molecular and biologic functions were analyzed using Interaction Networks and Functional Analysis. Fifty-eight probe sets were differentially expressed between HCV (+) versus HCV (-) donors (P<0.001). The molecular functions associated with the two top scored networks from the analysis of the differentially expressed genes were connective tissue development and function and tissue morphology (score 34), cell death, cell signaling, cellular assembly, and organization (score 32). Among the differentially affected top canonical pathways, we found the role of RIG1-like receptors in antiviral innate immunity (P<0.001), natural killer cell signaling (P=0.007), interleukin-8 signaling (P=0.048), interferon signaling (P=0.0 11; INFA21, INFGR1, and MED14), ILK signaling (P=0.001), and apoptosis signaling. A unique gene expression pattern was identified in HCV (+) kidney grafts. Innate immune system and inflammatory pathways were the most affected.

A multi writable thiophene-based selective and reversible chromogenic fluoride probe with dual -NH functionality

NASA Astrophysics Data System (ADS)

Vishwakarma, Siddharth; Kumar, Ajit; Pandey, Abha; Upadhyay, K. K.

2017-01-01

A chromogenic fluoride probe bearing bis imine groups having dual -NH functionality (BSB) has been designed, synthesised and structurally characterized by its single crystal X-ray diffraction studies. The BSB could visually and spectroscopically recognise F- with high selectivity over other anions by exhibiting intense chromogenic response (from colourless to red) for F- in acetonitrile solution. The UV-visible titration and 1H NMR titration experiments indicated that the observed changes occur via a combined process including hydrogen bonding and deprotonation between the BSB and F-. Moreover theoretical calculations at the Density Functional Theory (DFT) level shed further light upon probe design strategy and the nature of interactions between BSB and F-. The limit of detection and binding constant of BSB towards F- were found to be 6.9 × 10- 7 M and 1.42 ± 0.069 × 108 M- 2 respectively. Finally, by using F- and H+ as chemical inputs and the absorbance as output, a INHIBIT logic gate was constructed, which exhibits "Multi-write" ability without obvious degradation in its optical output.

Coherent fifth-order visible-infrared spectroscopies: ultrafast nonequilibrium vibrational dynamics in solution.

PubMed

Lynch, Michael S; Slenkamp, Karla M; Cheng, Mark; Khalil, Munira

2012-07-05

Obtaining a detailed description of photochemical reactions in solution requires measuring time-evolving structural dynamics of transient chemical species on ultrafast time scales. Time-resolved vibrational spectroscopies are sensitive probes of molecular structure and dynamics in solution. In this work, we develop doubly resonant fifth-order nonlinear visible-infrared spectroscopies to probe nonequilibrium vibrational dynamics among coupled high-frequency vibrations during an ultrafast charge transfer process using a heterodyne detection scheme. The method enables the simultaneous collection of third- and fifth-order signals, which respectively measure vibrational dynamics occurring on electronic ground and excited states on a femtosecond time scale. Our data collection and analysis strategy allows transient dispersed vibrational echo (t-DVE) and dispersed pump-probe (t-DPP) spectra to be extracted as a function of electronic and vibrational population periods with high signal-to-noise ratio (S/N > 25). We discuss how fifth-order experiments can measure (i) time-dependent anharmonic vibrational couplings, (ii) nonequilibrium frequency-frequency correlation functions, (iii) incoherent and coherent vibrational relaxation and transfer dynamics, and (iv) coherent vibrational and electronic (vibronic) coupling as a function of a photochemical reaction.

Institute for Science and Engineering Simulation (ISES)

DTIC Science & Technology

2015-12-18

performance and other functionalities such as electrical , magnetic, optical, thermal, biological, chemical, and so forth. Structural integrity...transmission electron microscopy (HRSTEM) and three-dimensional atom probe (3DAP) tomography , the true atomic scale structure and change in chemical...atom probe tomography (3DAP) techniques, has permitted characterizing and quantifying the multimodal size distribution of different generations of γ

Putative and unique gene sequence utilization for the design of species specific probes as modeled by Lactobacillus plantarum

USDA-ARS?s Scientific Manuscript database

The concept of utilizing putative and unique gene sequences for the design of species specific probes was tested. The abundance profile of assigned functions within the Lactobacillus plantarum genome was used for the identification of the putative and unique gene sequence, csh. The targeted gene (cs...

Simultaneous measurement of liquid absorbance and refractive index using a compact optofluidic probe.

PubMed

Malak, Maurine; Marty, Frédéric; Bourouina, Tarik; Angelescu, Dan

2013-07-21

We present a novel optical technique for simultaneously measuring the absorbance and the refractive index of a thin film using an infrared optofluidic probe. Experiments were carried on two different liquids and the results agree with the bibliographical data. The ultimate goal is to achieve a multi-functional micro-optical device for analytical applications.