Data Mining - Concepts and Techniques.

International Journal of Computer and Applications

When a molecule absorbs a photon of appropriate energy, a chain of photophysical events ensues, such as internal conversion or vibrational relaxation (loss of energy in the absence of light emission), fluorescence, intersystem crossing (from singlet state to a triplet state) and phosphorescence, as shown in the Jablonski diagram for organic molecules (Fig. 1). Each of the processes occurs with a certain probability, characterized by decay rate constants (k). It can be shown that the average length of time τ for the set of molecules to decay from one state to another is reciprocally proportional to the rate of decay: τ = 1/k. This average length of time is called the mean lifetime, or simply lifetime. It can also be shown that the lifetime of a photophysical process is the time required by a population of N electronically excited molecules to be reduced by a factor of e. Correspondingly, the fluorescence lifetime is the time required by a population of excited fluorophores to decrease exponentially to N/e via the loss of energy through fluorescence and other non-radiative processes. The lifetime of photophycal processes vary significantly from tens of femotoseconds for internal conversion1,2 to nanoseconds for fluorescence and microseconds or seconds for phosphorescence.1






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Figure 1


Jablonski diagram and a timescale of photophysical processes for organic molecules.

/pdf/fluorescence-lifetime-measurements-and-biological-imaging-xfalzh4w7e.pdf

Fluorescence Lifetime Measurements and Biological Imaging

Green fluorescent protein (GFP) from the jellyfish Aequorea victoria and its homologs from diverse marine animals are widely used as universal genetically encoded fluorescent labels. Many laboratories have focused their efforts on identification and development of fluorescent proteins with novel characteristics and enhanced properties, resulting in a powerful toolkit for visualization of structural organization and dynamic processes in living cells and organisms. The diversity of currently available fluorescent proteins covers nearly the entire visible spectrum, providing numerous alternative possibilities for multicolor labeling and studies of protein interactions. Photoactivatable fluorescent proteins enable tracking of photolabeled molecules and cells in space and time and can also be used for super-resolution imaging. Genetically encoded sensors make it possible to monitor the activity of enzymes and the concentrations of various analytes. Fast-maturing fluorescent proteins, cell clocks, and timers further expand the options for real time studies in living tissues. Here we focus on the structure, evolution, and function of GFP-like proteins and their numerous applications for in vivo imaging, with particular attention to recent techniques.

Fluorescent Proteins and Their Applications in Imaging Living Cells and Tissues

Small-molecule fluorescent probes embody an essential facet of chemical biology. Although numerous compounds are known, the ensemble of fluorescent probes is based on a modest collection of modular “core” dyes. The elaboration of these dyes with diverse chemical moieties is enabling the precise interrogation of biochemical and biological systems. The importance of fluorescence-based technologies in chemical biology elicits a necessity to understand the major classes of small-molecule fluorophores. Here, we examine the chemical and photophysical properties of oft-used fluorophores and highlight classic and contemporary examples in which utility has been built upon these scaffolds.

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Bright Ideas for Chemical Biology

Base catalysis of chromophore formation in Arg96 and Glu222 variants of green fluorescent protein.

The mature form of green fluorescent protein (GFP) is generated by a spontaneous self-modification process that is essentially irreversible. A key step in chromophore biosynthesis involves slow air oxidation of an intermediate species, in which the backbone atoms of residues 65−67 have condensed to form a five-membered heterocycle. We have investigated the kinetics of hydrogen peroxide evolution during in vitro GFP maturation and found that the H2O2 coproduct is generated prior to the acquisition of green fluorescence at a stoichiometry of 1:1 (peroxide/chromophore). The experimental progress curves were computer-fitted to a three-step mechanism, in which the first step proceeds with a time constant of 1.5 (±1.1) min and includes protein folding and peptide cyclization. Kinetic data obtained by HPLC analysis support a rapid cyclization reaction that can be reversed upon acid denaturation. The second step proceeds with a time constant of 34.0 (±1.5) min and entails rate-limiting protein oxidation, as suppo...

Reaction progress of chromophore biogenesis in green fluorescent protein.

To meet the growing demand for synthetic genes more robust, scalable and inexpensive gene assembly technologies must be developed. Here, we present a protocol for high-quality gene assembly directly from low-cost marginal-quality microarray-synthesized oligonucleotides. Significantly, we eliminated the time- and money-consuming oligonucleotide purification steps through the use of hybridization-based selection embedded in the assembly process. The protocol was tested on mixtures of up to 2000 oligonucleotides eluted directly from microarrays obtained from three different chip manufacturers. These mixtures containing 95% pure column-synthesized oligonucleotides by the standard protocol. Both averaged only 2.7 errors/kb, and genes assembled from microarray-eluted material without clonal selection produced only 30% less protein than sequence-confirmed clones. This report represents the first demonstration of cost-efficient gene assembly from microarray-synthesized oligonucleotides. The overall cost of assembly by this method approaches 5¢ per base, making gene synthesis more affordable than traditional cloning.

High-quality gene assembly directly from unpurified mixtures of microarray-synthesized oligonucleotides

The aim of the present investigation was to evaluate microemulsion as a vehicle for dermal drug delivery and to develop microemulsion-based gel of terbinafine for the treatment of onychomycosis. D-optimal mixture experimental design was adopted to optimize the amount of oil (X
 1), Smix (mixture of surfactant and cosurfactant; X
 2) and water (X
 3) in the microemulsion. The formulations were assessed for globule size (in nanometers; Y
 1) and solubility of drug in microemulsion (in milligrams per milliliter; Y
 2). The microemulsion containing 5.75% oil, 53.75% surfactant–cosurfactant mixture and 40.5% water was selected as the optimized batch. The globule size and solubility of the optimized batch were 18.14 nm and 43.71 mg/ml, respectively. Transmission electron microscopy showed that globules were spherical in shape. Drug containing microemulsion was converted into gel employing 0.75% w/w carbopol 934P. The optimized gel showed better penetration and retention in the human cadaver skin as compared to the commercial cream. The cumulative amount of terbinafine permeated after 12 h was 244.65 ± 18.43 μg cm−2 which was three times more than the selected commercial cream. Terbinafine microemulsion in the gel form showed better activity against Candida albicans and Trichophyton rubrum than the commercial cream. It was concluded that drug-loaded gel could be a promising formulation for effective treatment of onychomycosis.

/pdf/microemulsion-based-gel-of-terbinafine-for-the-treatment-of-2sbxggtol5.pdf

Microemulsion-Based Gel of Terbinafine for the Treatment of Onychomycosis: Optimization of Formulation Using D-Optimal Design

icient locating the fruit on the tree is one of the major requirements for the fruit harvesting system. This paper presents the fruit detection using improved multiple features based algorithm. To detect the fruit, an image processing algorithm is trained for efficient feature extraction. The algorithm is designed with the aim of calculating different weights for features like intensity, color, orientation and edge of the input test image. The weights of different features represent the approximate locations of the fruit within an image. The Detection Efficiency is achieved up to 90% for different fruit image on tree, captured at different positions. The input images are the section of tree image. The proposed approach can be applied for targeting fruits for robotic fruit harvesting.

/pdf/fruit-detection-using-improved-multiple-features-based-1dqnhuc3yf.pdf

Hetal Patel

Papers

Base catalysis of chromophore formation in Arg96 and Glu222 variants of green fluorescent protein.

Reaction progress of chromophore biogenesis in green fluorescent protein.

High-quality gene assembly directly from unpurified mixtures of microarray-synthesized oligonucleotides

Microemulsion-Based Gel of Terbinafine for the Treatment of Onychomycosis: Optimization of Formulation Using D-Optimal Design

Fruit Detection using Improved Multiple Features based Algorithm