2d Regional Correlation Analysis Of Single-molecule Time Trajectories

We report a new approach of 2D regional correlation analysis capable of analyzing fluctuation dynamics of complex multiple correlated and anticorrelated fluctuations under a noncorrelated noise background. Using this new method, by changing and scanning the start time and end time along a pair of fluctuation trajectories, we are able to map out any defined segments along the fluctuation trajectories and determine whether they are correlated, anticorrelated, or noncorrelated; after which, a cross-correlation analysis can be applied for each specific segment to obtain a detailed fluctuation dynamics analysis. We specifically discuss an application of this approach to analyze single-molecule fluorescence resonance energy transfer (FRET) fluctuation dynamics where the fluctuations are often complex, although this approach can be useful for analyzing other types of fluctuation dynamics of various physical variables as well

Probing Single-molecule Interfacial Geminate Electron-cation Recombination Dynamics

Interfacial electron-cation recombination in zinc-tetra (4-carboxyphenyl) porphyrin (ZnTCPP)/TiO(2) nanoparticle system has been probed at the single-molecule level by recording and analyzing photon-to-photon pair times of the ZnTCPP fluorescence. We have. developed a novel approach to reveal the hidden single-molecule interfacial electron-cation recombination dynamics by analyzing the autocorrelation function and a proposed convoluted single-molecule interfacial electron-cation recombination model. Our results suggest that the fluctuations of the interfacial electron transfer (ET) reactivity modulate the ET cycles as well as the interfacial electron-cation recombination dynamics. On the basis of this model, the single-molecule electron-cation recombination time of ZnTCPP/-TiO(2) system is deduced to be at time scale of 10(-5) s. The autocorrelation of photon-to-photon pair times as well as the convoluted ET model has been further demonstrated by simulation and interpreted in terms of the interfacial ET reactivity fluctuation and blinking. Our approach not only can effectively probe the single-molecule interfacial electron-cation dynamics but also can be applied to other single-molecule ground-state regeneration dynamics occurring at interfaces and within condensed phases

Suspended Lipid Bilayer For Optical And Electrical Measurements Of Single Ion Channel Proteins

Making and holding an artificial lipid bilayer horizontally in an aqueous solution within the microscopic working distance of similar to 100 mu m are essential for simultaneous single molecule imaging and single ion-channel electrical current recording. However, preparation of such a lipid bilayer without a solid support is technically challenging. In a typical supported lipid bilayer, the asymmetric local environments and the strong perturbation of the underneath solid or dense surface can diverge the normal behavior of membrane proteins and lipids. On the other hand, the suspended lipid bilayers can provide a native local environment for the membrane proteins and lipids by having fluids on both sides. In this technical report, we present a simple and novel methodology for making a suspended lipid bilayer that can be used for recording the single-molecule diffusion and single ion-channel electrical measurements of ion-channel proteins. Our approach has a higher validity for studying the molecular diffusions and conformational fluctuations of membrane proteins without having perturbations from supporting layers. We demonstrate the feasibility of such an approach on simultaneous single-molecule fluorescence imaging and electric current measurements of ion channel proteins

Probing Single-molecule Interfacial Electron Transfer Dynamics Of Porphyrin On Tio2 Nanoparticles

Single-molecule interfacial electron transfer (ET) dynamics has been studied by using single-molecule fluorescence spectroscopy and microscopic imaging. For a single-molecule zinc-tetra (4-carboxyphenyl) porphyrin (ZnTCPP)/TiO2 nanoparticle system, the single-molecule fluorescence trajectories show strong fluctuation and blinking between bright and dark states. The intermittency and fluctuation of the single-molecule fluorescence are attributed to the variation of the reactivity of interfacial electron transfer. The nonexponential autocorrelation function and the power-law distribution of the probability density of dark times imply the dynamic and static inhomogeneities of the interfacial ET dynamics. On the basis of the power-law analysis, the variation of single-molecule interfacial ET reactivity is analyzed as a fluctuation according to the Levy statistics

Gattini 2010: Cutting Edge Science at the Bottom of the World

The high altitude Antarctic sites of Dome A and the South Pole offer intriguing locations for future large scale optical astronomical Observatories. The Gattini project was created to measure the optical sky brightness, large area cloud cover and aurora of the winter-time sky above such high altitude Antarctic sites. The Gattini-DomeA camera was installed on the PLATO instrument module as part of the Chinese-led traverse to the highest point on the Antarctic plateau in January 2008. This single automated wide field camera contains a suite of Bessel photometric filters (B, V, R) and a long-pass red filter for the detection and monitoring of OH emission. We have in hand one complete winter-time dataset (2009) from the camera that was recently returned in April 2010. The Gattini-South Pole UV camera is a wide-field optical camera that in 2011 will measure for the first time the UV properties of the winter-time sky above the South Pole dark sector. This unique dataset will consist of frequent images taken in both broadband U and B filters in addition to high resolution (R similar to 5000) long slit spectroscopy over a narrow bandwidth of the central field. The camera is a proof of concept for the 2m-class Antarctic Cosmic Web Imager telescope, a dedicated experiment to directly detect and map the redshifted lyman alpha fluorescence or Cosmic Web emission we believe possible due to the unique geographical qualities of the site. We present the current status of both projects

Reprogramming to pluripotency using designer TALE transcription factors targeting enhancers

The modular DNA recognition code of the transcription-activator-like effectors (TALEs) from plant pathogenic bacterial genus Xanthomonas provides a powerful genetic tool to create designer transcription factors (dTFs) targeting specific DNA sequences for manipulating gene expression. Previous studies have suggested critical roles of enhancers in gene regulation and reprogramming. Here, we report dTF activator targeting the distal enhancer of the Pou5f1 (Oct4) locus induces epigenetic changes, reactivates its expression, and substitutes exogenous OCT4 in reprogramming mouse embryonic fibroblast cells (MEFs) to induced pluripotent stem cells (iPSCs). Similarly, dTF activator targeting a Nanog enhancer activates Nanog expression and reprograms epiblast stem cells (EpiSCs) to iPSCs. Conversely, dTF repressors targeting the same genetic elements inhibit expression of these loci, and effectively block reprogramming. This study indicates that dTFs targeting specific enhancers can be used to study other biological processes such as transdifferentiation or directed differentiation of stem cells. © 2013 The Authors.Link_to_subscribed_fulltex

Formyl-methionyl-leucyl-phenylalanine–Induced Dopaminergic Neurotoxicity via Microglial Activation: A Mediator between Peripheral Infection and Neurodegeneration?

BackgroundParkinson disease (PD), a chronic neurodegenerative disease, has been proposed to be a multifactorial disorder resulting from a combination of environmental mechanisms (chemical, infectious, and traumatic), aging, and genetic deficits. Microglial activation is important in the pathogenesis of PD.ObjectivesWe investigated dopaminergic (DA) neurotoxicity and the underlying mechanisms of formyl-methionyl-leucyl-phenylalanine (fMLP), a bacteria-derived peptide, in relation to PD. METHODS: We measured DA neurotoxicity using a DA uptake assay and immunocytochemical staining (ICC) in primary mesencephalic cultures from rodents. Microglial activation was observed via ICC, flow cytometry, and superoxide measurement.ResultsfMLP can cause selective DA neuronal loss at concentrations as low as 10−13 M. Further, fMLP (10−13 M) led to a significant reduction in DA uptake capacity in neuron/glia (N/G) cultures, but not in microglia-depleted cultures, indicating an indispensable role of microglia in fMLP-induced neurotoxicity. Using ICC of a specific microglial marker, OX42, we observed morphologic changes in activated microglia after fMLP treatment. Microglial activation after fMLP treatment was confirmed by flow cytometry analysis of major histocompatibility antigen class II expression on a microglia HAPI cell line. Mechanistic studies revealed that fMLP (10−13 M)-induced increase in the production of extracellular superoxide from microglia is critical in mediating fMLP-elicited neurotoxicity. Pharmacologic inhibition of NADPH oxidase (PHOX) with diphenylene-iodonium or apocynin abolished the DA neurotoxicity of fMLP. N/G cultures from PHOX-deficient (gp91PHOX−/ −) mice were also insensitive to fMLP-induced DA neurotoxicity.ConclusionfMLP (10−13 M) induces DA neurotoxicity through activation of microglial PHOX and subsequent production of superoxide, suggesting a role of fMLP in the central nervous system inflammatory process

Radiosensitizing and Hyperthermic Properties of Hyaluronan Conjugated, Dextran-Coated Ferric Oxide Nanoparticles: Implications for Cancer Stem Cell Therapy

Cytotoxicity, radiosensitivity, and hyperthermia sensitivity of hyaluronan-mediated dextran-coated super paramagnetic iron oxide nanoparticles (HA-DESPIONs) were assessed in CD44-expressing head and neck squamous cell carcinoma (HNSCC) cell lines at clinically relevant radiation dose and temperatures. Low-passage HNSCC cells were exposed to HA-DESPIONs and cytotoxicity was assessed using MTT assay. Radiosensitizing properties of graded doses of HA-DESPIONs were assessed in both unsorted and CD44-sorted cells using clonogenic assay in combination with 2 Gy exposure to X-rays. Hyperthermia-induced toxicity was measured at 40°C, 41°C, and 42°C using clonogenic assay. Cell death was assessed 24 hours after treatment using a flow cytometry-based apoptosis analysis. Results showed that HA-DESPIONs were nontoxic at moderate concentrations and did not directly radiosensitize the cell lines. Further, there was no significant difference in the radiosensitivity of CD44high and CD44low cells. However, HA-DESPIONs enhanced the effect of hyperthermia which resulted in reduced cell survival that appeared to be mediated through apoptosis. We demonstrated that HA-DESPIONs are nontoxic and although they do not enhance radiation sensitivity, they did increase the effect of local hyperthermia. These results support further development of drug-attached HA-DESPIONs in combination with radiation for targeting cancer stem cells (CSCs) and the development of an alternating magnetic field approach to activate the HA-DESPIONs attached to CSCs

Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: Knowledge of the structure of gene expression is essential for mammalian transcriptomics research. We analyzed a collection of more than one million porcine expressed sequence tags (ESTs), of which two-thirds were generated in the Sino-Danish Pig Genome Project and one-third are from public databases. The Sino-Danish ESTs were generated from one normalized and 97 non-normalized cDNA libraries representing 35 different tissues and three developmental stages. RESULTS: Using the Distiller package, the ESTs were assembled to roughly 48,000 contigs and 73,000 singletons, of which approximately 25% have a high confidence match to UniProt. Approximately 6,000 new porcine gene clusters were identified. Expression analysis based on the non-normalized libraries resulted in the following findings. The distribution of cluster sizes is scaling invariant. Brain and testes are among the tissues with the greatest number of different expressed genes, whereas tissues with more specialized function, such as developing liver, have fewer expressed genes. There are at least 65 high confidence housekeeping gene candidates and 876 cDNA library-specific gene candidates. We identified differential expression of genes between different tissues, in particular brain/spinal cord, and found patterns of correlation between genes that share expression in pairs of libraries. Finally, there was remarkable agreement in expression between specialized tissues according to Gene Ontology categories. CONCLUSION: This EST collection, the largest to date in pig, represents an essential resource for annotation, comparative genomics, assembly of the pig genome sequence, and further porcine transcription studies.Published versio

Winter sky brightness and cloud cover at Dome A, Antarctica

At the summit of the Antarctic plateau, Dome A offers an intriguing location for future large scale optical astronomical observatories. The Gattini Dome A project was created to measure the optical sky brightness and large area cloud cover of the winter-time sky above this high altitude Antarctic site. The wide field camera and multi-filter system was installed on the PLATO instrument module as part of the Chinese-led traverse to Dome A in January 2008. This automated wide field camera consists of an Apogee U4000 interline CCD coupled to a Nikon fisheye lens enclosed in a heated container with glass window. The system contains a filter mechanism providing a suite of standard astronomical photometric filters (Bessell B, V, R) and a long-pass red filter for the detection and monitoring of airglow emission. The system operated continuously throughout the 2009, and 2011 winter seasons and part-way through the 2010 season, recording long exposure images sequentially for each filter. We have in hand one complete winter-time dataset (2009) returned via a manned traverse. We present here the first measurements of sky brightness in the photometric V band, cloud cover statistics measured so far and an estimate of the extinction