Development and validation of real-time PCR screening methods for detection of cry1A.105 and cry2Ab2 genes in genetically modified organisms

Primers and probes were developed for the element-specific detection of cry1A.105 and cry2Ab2 genes, based on their DNA sequence as present in GM maize MON89034. Cry genes are present in many genetically modified (GM) plants and they are important targets for developing GMO element-specific detection methods. Element-specific methods can be of use to screen for the presence of GMOs in food and feed supply chains. Moreover, a combination of GMO elements may indicate the potential presence of unapproved GMOs (UGMs). Primer-probe combinations were evaluated in terms of specificity, efficiency and limit of detection. Except for specificity, the complete experiment was performed in 9 PCR runs, on 9 different days and by testing 8 DNA concentrations. The results showed a high specificity and efficiency for cry1A.105 and cry2Ab2 detection. The limit of detection was between 0.05 and 0.01 ng DNA per PCR reaction for both assays. These data confirm the applicability of these new primer-probe combinations for element detection that can contribute to the screening for GM and UGM crops in food and feed samples.     

Finite perturbation theory-density functional theory calculation of the spin-dipolar contribution to NMR spin-spin coupling constants

In this work an implementation of the FPT-DFT approach for calculating the spin-dipolar contribution to NMR spin-spin coupling constants is presented. This method was tested in a set of small molecules, giving results in excellent agreement when comparing them with values taken from the literature, which were obtained with state-of-the-art calculations. To obtain an insight into the relative importance of the spin-dipolar contribution in unsaturated compounds, calculations of J(F,C), J(F,F) and J(F,H) couplings in 1,2-, 1,3-, and 1,4-difluorobenzenes were performed. An important spin-dipolar contribution to ³ J(F, F) and ⁵ J(F,F) was found, suggesting that this term might be important in some cases. When performing DFT calculations the non-singlet instabilities usually found in unsaturated compounds are overcome.     

Orbital contributions to relativistic corrections of the NMR nuclear magnetic shielding tensor originated in scalar field-dependent operators

In this work relativistic corrections to the magnetic shielding constant (σM), which arise from scalar field-dependent operators (both linear and bilinear), are calculated and decomposed into contributions from molecular orbitals (MOs). Numerical results for the magnetic shielding constant of the heavy nucleus X in closed shell atomic ions X^? and HX compounds (X = F, Cl, Br, I) are presented. The relative importance of inner-shell and valence electrons in the definition of each one of these terms is thus assessed and its relation with their sensitivity to changes in a chemical environment is discussed.     

Synthesis of a Val-Pro diaminodiol dipeptide isostere by epoxyamine cyclization

[reaction: see text] The stereoselective synthesis of a novel proline-containing dipeptide isostere is described. Starting from l-valine, three new contiguous stereocenters are generated by asymmetric induction and epoxide chemistry, while the pyrrolidine ring of proline is introduced in the final step via intramolecular ring opening of the amino acid derived epoxyamine. Proline-containing peptidomimetics are potentially attractive as selective inhibitors of proline-specific enzymes, such as PPIases and retroviral proteases, and as analogues of bioactive peptides.     

Experimental, Theoretical and Biological Activity Study on the Acyl-Substituted Benzo-18-crown-6, Dibenzo-18-crown-6 and Dibenzo-24-crown-8

Hexadecanoyl, dihexadecanoyl, dioctadecaneoyl, di-10-undecenoyl, and dicis-9-octadecenoyl derivatives of benzo[18]crown-6, dibenzo[18]crown-6 and dibenzo[24]-8 were synthesized by the condensation of carboxylic acids (palmitic, stearic, oleic and undecenoic acid) with benzo and dibenzo crown ethers in the presence of zinc chloride. The extraction equilibrium constants of such macrocyclic ethers with long side chains were estimated using chloroform/water and dichloromethane/water membranes transfer of Na-PAR (4-(2-pyridylazo)-resorcinol mono sodium monohydrate) with UV–Vis spectroscopy. It was found that they were in the range of 10.88–11.71 in dichloromethane and 8.04–11.77 in chloroform. These results actually show that the Na+ binding effect of macrocyclic ethers depends on the type and the length of side chains. The geometrical properties of the molecules were studied employing semi-empirical calculations by simulated annealing technique. The frontier molecular orbital energies and dipole moments were also examined. The biological activity results showed that the synthesized crown ethers have no activity against the studied microorganisms.     

A high-throughput method for GMO multi-detection using a microfluidic dynamic array

The ever-increasing production of genetically modified crops generates a demand for high-throughput DNA-based methods for the enforcement of genetically modified organisms (GMO) labelling requirements. The application of standard real-time PCR will become increasingly costly with the growth of the number of GMOs that is potentially present in an individual sample. The present work presents the results of an innovative approach in genetically modified crops analysis by DNA based methods, which is the use of a microfluidic dynamic array as a high throughput multi-detection system. In order to evaluate the system, six test samples with an increasing degree of complexity were prepared, preamplified and subsequently analysed in the Fluidigm system. Twenty-eight assays targeting different DNA elements, GM events and species-specific reference genes were used in the experiment. The large majority of the assays tested presented expected results. The power of low level detection was assessed and elements present at concentrations as low as 0.06 % were successfully detected. The approach proposed in this work presents the Fluidigm system as a suitable and promising platform for GMO multi-detection.     

FLUSHING TIME IN THE CIENFUEGOS BAY,CUBA

We use a high‐resolution numerical model to analyze the hydrodynamical exchange processes of the Cienfuegos Bay with the Caribbean Sea. Results show that freshwater inputs and wind are the main factors controlling the water exchange in the bay. Nine simulation case studies with three wind conditions and three freshwater inputs were carried out. The main conclusion is that the Cienfuegos Bay system has a slow exchange rate, with an average flushing time of 39 days during the rainy period and 50 days during the dry one, for the most probable wind direction. Two new temporary scales for Cienfuegos Bay are discussed: the local e‐flushing time and the flushing lag. The results obtained for these new variables validate the slow exchange capacity of the bay.     

Molecular Interactions and Thermodynamic Aspects of the Complexation Reaction between Gentian Violet and Several Cyclodextrins

The complexation process between gentian violet (CV+) and four different cyclodextrins (-, -, -, and HP--CDs) has been investigated under different reaction conditions (pH, solvent, and temperature) by electronic absorption and 1H NMR (NOE and NOESY) spectroscopies. All the binding constants were determined by the direct spectroscopic method. The H and S complexation values have been evaluated and discussed according to the diverse factors that affect the chemical interactions in these systems. A simple association takes place between the secondary hydroxyl or the hydroxypropyl groups of and HP--cycloamyloses, respectively, with the amine group of the gentian violet, while the binding between CV+ and - or -CDs corresponds to a real inclusion. Also, a CV22+ dimmeric species within the -CD cavity was detected in aqueous solution, while two molecules of -CD react with one molecule of gentian violet in DMSO at 294 K. In all the reaction media the -CD forms 1 : 1 complexes, but in the buffered aqueous solution at pH 7.5 the inclusion is deeper than in the other solvents. It is important to point out that the solvophobic effect is the most important binding factor in the complexation of the CV+ with the - and HP--CDs, while the complexes with -, and -cyclodextrins are mainly stabilized by van der Waals interactions between the guest and the host cavity. In all cases, the inclusion orientation is probably determined by the ion-dipole interactions between gentian violet and the solvent.     

A catalytic antibody programmed for torsional activation of amide bond hydrolysis

Amidase antibody 312d6, obtained against the sulfonamide hapten 4 a that mimics the transition state for hydrolysis of a distorted amide, accelerates the hydrolysis of the corresponding amides 1 a-3 a by a factor of 10(3) at pH 8. The mechanisms of both the uncatalyzed and antibody-catalyzed reactions were studied. Between pH 8 and 12 the uncatalyzed hydrolysis of N-toluoylindoles 1 a and 3 a shows a simple first-order dependence on [OH(-)], while hydrolysis of 3 a is zeroth-order in [OH(-)] below pH 8. The pH profile for hydrolysis of the corresponding tryptophan amide 2 a is more complex due to the dissociation of the zwitterion into an anion with pK(a) 9.74; hydrolysis of the zwitterionic and the anionic form of 2 a both show simple first-order dependence on [OH(-)]. Absence of (18)O exchange between H(2) (18)O/(18)OH(-) and the substrate, a normal SKIE for both 1 a (k(H)/k(D)=1.12) and 3 a (k(H)/k(D)=1.24) and the value of the Hammett constant rho for hydrolysis of p-substituted amides 3 a-e are consistent with an ester-like mechanism in which formation of the tetrahedral intermediate is rate-determining and the amine departs as anion. The 312d6-catalyzed hydrolysis of 3 a was studied between pH 7.5 and 9, and its independence of pH in this range indicates that water is the reacting nucleophile. Hydrolysis of 3 a is only partially inhibited by the sulfonamide hapten, and this indicates that non-specific catalysis by the protein accompanies the specific process. Only the nonspecific process is observed in the hydrolysis of amides 3 with para substituents other than methyl. Binding studies on the corresponding series of p-substituted sulfonamides 5 a-e confirm the high specificity of antibody 312d6 for p-methyl substituted substrates.     

半导体纳米激光

半导体纳米激光的研究是目前纳米技术（或纳米光子学）和半导体激光交汇产生的研究前沿。本文将综述这一领域最近一些最激动人心的进展。我们将集中讨论两种半导体纳米结构的纳米激光：自下而上生长而成的纳米线和自上而下刻蚀制成的纳米柱状结构。本文将综述这些纳米激光器的特殊特征,特别是利用表面等离子效应而成制成的金属{半导体等离子体激光,即目前世界上最小激光器的最新进展。由于这些纳米激光器的微小的尺寸以及对光在空间限制增强,我们必须重新检验半导体激光器中某些熟悉的概念在纳米尺度上的正确性和含义,例如模式增益和光限制因子（CF）的概念。本文将从统一的观点解释光限制因子在电介质和等离子体纳米激光器中的某些似乎反常的行为。在本文的通篇论述中,我们将尝试回答究竟激光器的尺寸能够小到什么程度,或者激光器的尺寸是否存在一个最小极限等基本问题。