Unknown biological mixtures evaluation using STR analytical quantification

Allelic quantification of STRs, where the presence of three or more alleles represents mixtures, provides a novel method to identify mixtures from unknown biological sources. The allelic stutters resulting in slightly different repeat containing products during fragment amplification can be mistaken for true alleles complicating a simple approach to mixture analysis. An algorithm based on the array of estimated stutters from known samples was developed and tuned to maximize the identification of true non-mixtures through the analysis of three pentanucleotide STRs. Laboratory simulated scenarios of needle sharing generated 58 mixture and 38 non-mixture samples that were blinded for determining the number of alleles. Through developing and applying an algorithm that additively estimates stuttering around the two highest peaks, mixtures and non-mixtures were characterized with sensitivity of 77.5, 82.7 and 58% while maintaining the high specificity of 100, 97.4 and 100 for the W, X, and Z STRs individually. When all three STRs were used collectively, the resulting sensitivity and specificity was 91.4 and 97.4%, respectively. The newly validated approach of using multiple STRs as highly informative biomarkers in unknown sample mixture analyses has potential applications in genetics, forensic science, and epidemiological studies.     

Fluctuating flow of an elastico-viscous fluid along an infinite porous plate with an applied magnetic field

The problem of oscillating free stream flow of an elastico-viscous, incompressible, and electrically conducting fluid along an infinite plate with suction varying periodically with time, is considered in the presence of a transverse magnetic field. The effect of the elasticity of the fluid, the magnetic fluid, and the fluctuation of suction velocity on the velocity and the skin friction is examined.     

Molecular biosensing system based on intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) that undergo structural transition upon binding their target molecules are becoming increasingly known. IDPs, because of their binding specificity and induced folding properties, can serve as biological recognition elements for sensing applications. In this paper, BRCA1, an IDP, was utilized as the biological recognition element to detect tumor suppressor protein p53 through the BRCA1/p53 binding interaction to serve as a proof-of-concept for the use of IDPs as recognition elements. The binding resulted in a disordered-to-ordered BRCA1 conformational change, as seen in our circular dichroism (CD) measurements. This conformational change in BRCA1 (residues 219-498) was utilized in the detection of p53 (residues 311-393) via both intrinsic and extrinsic fluorescent probes. Intrinsic tryptophan residues within the BRCA1 sequence detected p53 (311-393) with a detection limit of 0.559 nM (0.112 pmol). Two environmentally sensitive fluorophores, tetramethylrhodamine-5-maleimide (TMR) and 6-((5-dimethylaminonaphthalene-1-sulfonyl)amino)hexanoic acid, succinimidyl ester (dansyl-X, SE) were conjugated to BRCA1 (219-498). Dansyl-X, SE-conjugated BRCA1 (219-498) detected p53 (311-393) with a detection limit of 1.50 nM (0.300 pmol). The sensitivities for TMR and dansyl-X, SE-conjugated BRCA1 for the detection of p53 were nearly threefold and twofold higher, respectively, than the sensitivity reported using intrinsic BRCA1 tryptophan fluorescence. CD measurements did not reveal a disruption of p53/dye-conjugated BRCA1 binding, thus validating the applicability of environmentally sensitive fluorophores as transduction moieties to detect molecules which bind to IDPs and induce a structural change.     

Highly active and reusable hydrotalcite-supported Pd(0) catalyst for Suzuki coupling reactions of aryl bromides and chlorides

A palladium(0) nanocluster supported on hydrotalcite has been prepared and tested for the Suzuki coupling reaction. The prepared catalyst showed very efficient catalytic activity for cross coupling of iodo- and bromoarenes under very mild reaction conditions, affording >90% yield. Under the optimized reaction conditions, chloroarenenes also showed very good reactivity. Transmission electron microscopic imaging data showed the formation of very small Pd(0)-nanoclusters (d = 2.2 ± 0.5 nm) well dispersed on the support, which enhanced the activity and stability of the catalyst for the Suzuki cross-coupling reaction. This catalytic system offers an easy method of preparation with good activity and reusability up to five cycles.     

Reductive conjugate addition of haloalkanes to enones to form silyl enol ethers

A new method is presented for tandem reductive conjugate addition and silyl enol ether formation from cyclic and acyclic enones and enals in the presence of a Mn reductant, a Ni(terpyridine) catalyst, and a trialkylchlorosilane. The addition of secondary, tertiary, and hindered primary haloalkanes is demonstrated. Preliminary studies on the mechanism show that the intermediacy of L1(Ni)(η(3)-1-triethylsilyloxyalkenyl)X or in-situ-formed RMnX is unlikely.     

Self-Assembled Structures of Diglycerol Monolaurate- and Monomyristate in Olive Oil

We have investigated the phase behavior and self-assembled structures of diglycerol monolaurate-and monomyristate (abbreviated as C₁₂G₂ and C₁₄G₂, respectivley) in olive oil over a wide range of temperatures and compositions. At lower temperatures, both the surfactants appear in solid state (α-solid), which does not swell with olive oil. The α-solid transforms into lamellar liquid crystal (L_α) phase upon heating and the solid melting temperature is practically constant at all surfactant/oil compositions, but the C₁₂G₂ melts earlier than the C₁₄G₂. There appear the dispersions of L_α phase and α-solid in the dilute regions of the C₁₂G₂/olive oil and the C₁₄G₂/olive oil systems, respectively, at 25°C. The L_α phase can solubilize some amount of olive oil, but as the oil concentration increases the excess oil separates out from the L_α phase, and there appears L_α dispersion in the dilute surfactant concentration region. The L_α phase eventually transforms into isotropic solutions (reverse micelles) with further heating. The structures (shape and size) of the reverse micelles have been characterized by small-angle x-ray scattering technique. It has found that the C₁₂G₂ and C₁₄G₂ surfactants form reverse rod-like micelles in olive oil above the L_α melting temperature and the micellar size increases with surfactant concentration, but decreases with temperatures.     

Interfacial Properties of Aqueous Nonionic Fluorocarbon Surfactant Solutions

The equilibrium, dynamic surface tensions, and surface dilatational elasticity of aqueous solutions of nonionic fluorocarbon surfactant are reported. The critical micellar concentration, CMC (0.023 mM) and equilibrium surface tension (24.6 m N . m^?1) at CMC were measured by Wilhelmy plate method for aqueous solution of C₈F₁₇SO₂N(C₃H₇)(C₂H₄O)_nH (n=20), abbreviated as EF122A. The surface tension decay is slower for C₈F₁₇SO₂N(C₃H₇)(C₂H₄O)_nH (n=10) system, abbreviated as EF122B compared to the EF122A system over short time region, which indicates the slow transport of the surfactant molecules to the surface. The relaxation time for surface tension decay is estimated by fitting a series of exponentials to the dynamic surface tension data and it decreases with temperature for EF122A. Slow exchange of monomers between bulk and interface is reflected in the high elasticity value of the air‐liquid interface for EF122B compared with EF122A within measured frequency window (0.125–1.25 Hz).     

Temporal variation of atmospheric polycyclic aromatic hydrocarbon concentrations in PM10 from the Kathmandu Valley and their gas-particle concentrations in winter

The concentrations of polycyclic aromatic hydrocarbons (PAHs) in particulate matter (PM) with a diameter <10 µm (PM₁₀, 50% cut off) were investigated in the Kathmandu Valley, Nepal, during 2003. In order to understand the dynamics of atmospheric PAHs in winter, the PAH concentrations in total PM and in the gaseous phase were investigated in the valley in December 2005. Total of 45 PAH compounds (∑45PAHs) were analysed by high-resolution gas chromatography/high-resolution mass spectrometry (HRGC/HRMS). In 2003, the ∑45PAH concentrations in PM₁₀ ranged between 4.3 and 89 ng m^?3 (annual average; 27 ± 24 ng m^?3). The average concentrations of ∑45PAHs in December 2005 were 210 ± 33 ng m^?3 in total PM and 430 ± 90 ng m^?3 in the gaseous phase. The ∑45PAH concentration in PM accounted for more than 30% of the sum of their particulate and gaseous forms. Phenanthrene (Ph) was the most predominant compound in the gaseous phase, whereas four- to seven-ring PAHs were predominant in total PM. The highest values of ∑45PAHs occurred in the winter and spring. Estimates of emission sources based on diagnostic molecular ratios showed that atmospheric PAHs in the Kathmandu Valley mainly originated from the exhaust gas of diesel engine. In the winter and spring, PAH pollution would be accelerated by the operations of brick kilns and the frequent formation of an atmospherically stable layer in the valley.     

Phase behavior of diglycerol fatty acid esters-nonpolar oil systems

Phase behavior of diglycerol fatty acid esters (Qn-D, where n represents the carbon number in the alkyl chain length of amphiphile, n = 10-16) were investigated in different nonpolar oils, liquid paraffin (LP70), squalane, and squalene. There is surfactant solid at lower temperature, and the surfactant solid does not swell in oil, and the melting temperature is almost constant in a wide range of compositions. In all of the systems, a lamellar liquid crystal (L(alpha)) is formed in a concentrated region at a temperature between the solid melting temperature and the isotropic two- or single-phase regions. In the dilute regions, reverse vesicles are formed in L(alpha) + O regions. There are two liquid-phase regions above the L(alpha) present region. This two-phase boundary corresponds to the cloud-point curve of nonionic surfactant aqueous solutions. However, instead of being less soluble in water at high temperature for the cloud point, the surfactant becomes more soluble in the organic solvents at high temperature. Namely, the effect of temperature on the solubility is opposite to the clouding phenomenon. When the hydrocarbon chain of the diglycerol surfactant decreases, the two-phase region becomes wider. In the case of a fixed surfactant, the surfactant is most miscible with squalene (narrowest two-phase regions) and the order of dissolutions tendency is squalene > LP70 > squalane. These results show that the hydrophilic moiety (diglycerol group) is more insoluble in oil compared with that of a conventional poly(oxyethylene)-type nonionic surfactant. Formation of reversed rodlike micelles was confirmed by SAXS scattering curve. When the hydrocarbon chain of surfactant is short, the micellar size becomes larger. In a fixed surfactant system, the reverse micellar size increases by changing oil from squalene to LP70. A small amount of water induces a dramatic elongation of reverse micelles.