Magnetic Hybridization Research Articles

Isolation and characterization of microsatellite loci in the bee Ceratina flavipes

AbstractPolymorphic microsatellite markers can provide essential information on genetic analyses of sociality and mating behaviour of insects. We developed eight microsatellite loci in the small carpenter bee, Ceratina flavipes, using a magnetic bead hybridization enrichment protocol. These loci showed two to eight alleles with expected heterozygosity of 0.21–0.87, and also seemed useful to such congeneric species as Ceratina okinawana distributed in southern Japan. By using these loci, the sociality and mating systems in Ceratina species, that are still controversial, are possible to be analysed.

Detection of lactococcal 936-species bacteriophages in whey by magnetic capture hybridization PCR targeting a variable region of receptor-binding protein genes

To develop PCR assays able to distinguish between groups within lactococcal 936-species bacteriophages, as defined by their different receptor-binding protein (RBP) genes. DNA sequences of RBP genes from 17 lactococcal bacteriophages of the 936-species were compared, and six phage groups were identified. For each phage group a specific primer pair targeting a variable region of the RBP genes was designed. In nine of 20 whey samples, from dairies with recorded phage problems, between one and six phage groups were identified by conventional PCR. The sensitivity and specificity of the method was improved by magnetic capture hybridization (MCH)-PCR using a capture probe targeting an 80-bp highly conserved region just upstream from the RBP gene in all the investigated phages. The MCH-PCR was performed on 100 microl whey samples and the detection limit of the assay was 10(2)-10(3) PFU ml(-1) as opposed to the detection limit of 10(4) PFU ml(-1) for conventional PCR performed on 1-microl whey samples. In this study, PCR assays have been developed to detect six different types of RBP genes in lactococcal 936-species bacteriophages. The PCR assays have practical applications at cheese plants for detection of 936-species phages with different RBP and thereby potentially with different host ranges. This knowledge will make it possible to improve starter culture rotation systems in the dairy industry.

Atlantic capelin (Mallotus villosus) tetranucleotide microsatellites

AbstractTwelve microsatellite loci developed for Atlantic capelin (Mallotus villosus) using magnetic bead hybridization enrichment for tetranucleotide microsatellites revealed five loci composed of single repeat elements and six composed of complex repeats. Forty‐four beach‐spawning females from three different northwestern Atlantic Newfoundland beach‐spawning populations were screened at each locus. Loci were polymorphic (two to 59 alleles per locus) and all but two exhibited high heterozygosity (0.86–1). The loci are considered suitable for addressing questions related to fine‐scale population structure, spawning fidelity and survivorship/kinship issues.

Dinucleotide microsatellite DNA loci from the ant Myrmica scabrinodis

AbstractWe describe the isolation and characterization of five dinucleotide microsatellite loci in the ant Myrmica scabrinodis, which were obtained using a magnetic bead hybridization selection protocol. The PCR primers were tested on nine to 11 individuals. The number of alleles ranged from two to 13, and the observed heterozygosity from 0.200 to 0.778.

Magnetism of UPtAl and UIrAl; [formula omitted] calculations

We report on electronic structure calculations of UPtAl and UIrAl ternary uranium based intermetallic compounds. Calculations were performed in the framework of density functional theory using LDA+U exchange correlation potential. Full relaxation of U and J parameters was performed with the aim of obtaining correct total magnetic moments on uranium site. These parameters are then used in subsequent analysis of magnetic moments (including spin and orbital components) and hybridization effects.

Effect of dimensional and magnetic quantization hybridization in the optical absorption spectra of nanoheterosystems with D (?)-states

The magnetoabsorption of light by quantum dot — D(−)-center complexes synthesized in a transparent dielectric matrix — is theoretically studied with allowance for dispersed quantum dot (QD) sizes. In the effective mass approximation, an analytical expression for the impurity magnetoabsorption coefficient of light polarized in the quantizing magnetic polarization field direction is derived.

Detection of Botrytis aclada in onion seed using magnetic capture hybridization and the polymerase chain reaction

Detection of Botrytis aclada in onion seed using magnetic capture hybridization and the polymerase chain reaction

Two-dimensional Magneto-photonic Crystal Circulators

ABSTRACTPrevious research has demonstrated enhanced Faraday rotation in one-dimensional magnetic photonic crystals, where nonreciprocity in magneto-optical cavities is resonantly enhanced to provide optical isolation in optical paths on the scale of a few microns. In this paper, we study the nonreciprocity of two-dimensional magnetic photonic crystal resonators to allow further miniaturization and monolithic in-plane integration with current integrated optical devices. The nonreciprocal magnetic resonators are constructed by alternating the magnetization directions of the ferromagnetic domains in cavities side-coupled to photonic crystal waveguides. We show analytically that the gyrotropic splitting and the strength of the magnetic hybridization of the cavity modes are determined by the overlap integral between the domain magnetization vector and the modal cross product. With a large overlap obtained from optimizing the domain structures, we circularly hybridize two nearly degenerate modes to form a pair of counter-rotating whispering-gallery like modes, oscillating at different frequencies. As a physical realization, we synthesize two singly-degenerate circularly-hybridized modes in a two-dimensional crystal formed of a triangular air hole lattice in bismuth iron garnet with a TE bandgap. We tune the magnetic splitting and the decay constants of the rotating modes to demonstrate numerically a three-port optical circulator with a 30dB extinction bandwidth of 35GHz at 1550nm. An alternative implementation of a four-port circulator is achieved by side-coupling a point defect to two parallel waveguides. Our numerical experiments are performed with finite-difference time-domain simulations and agree well with the analytical coupled-mode theory predictions.

Magnetism of ultrathin wires suspended in free space and adsorbed on vicinal surfaces

On the basis of total-energy calculations within density functional theory the possibility of magnetic ordering in ultrathin, one or two atom wide nanowires is studied. Specifically, we investigate nanowires composed of fifth and sixth row elements, which are nonmagnetic in the solid phase. At first, the unsupported straight wires are discussed and then, similar to experimental conditions, the wires are placed along step ledges of vicinal surfaces of copper and silver Free-standing wires show only a weak tendency towards magnetic ordering at the equilibrium bond length. In analogy with their 3d homologues Mo, Tc, W, Re are found to order antiferromagnetically, Ru, Rh, and Ir ferromagnetically. Surprisingly, ferromagnetism is also predicted for the early transition metals Zr and Ta and for the simple metals In and Tl. This picture is profoundly modified for supported wires, where the expansion of the bond length enforced through the epitaxial relationship with the substrate favors magnetic ordering but hybridization with the substrate electrons tends to quench magnetism. It turns out that wires on a Cu substrate prefer a ferromagnetic order, whereas on a Ag substrate most elements tend to antiferromagnetism. A second row of atoms added to the wires destroys the magnetism in wires on a Cu substrate, and reduces it in wires on a Ag substrate, except for the late transition metals (Rh, Ir) where an enhancement of magnetic moments is observed. Two possible growth modes of nanowires - a row-by-row growth and island growth - are explored. The results allow us to suggest that Ru, Rh, and Os wires on Ag stepped surfaces are the most promising systems in which magnetism could be verified experimentally.

Magnetic bead hybridization to detect enterotoxigenicEscherichia colistrains associated with cattle in environmental water sources

A magnetic capture hybridization - polymerase chain reaction (MCH-PCR) method was used to increase the detection sensitivity of the enterotoxin gene LTIIa, used as a biomarker for waste in environmental samples. The samples were collected from cow lagoons of different farms and from environmental waters. Total DNA was extracted from colonies grown on mTEC medium or directly from environmental samples. The cow-specific Escherichia coli LTIIa gene was used as a DNA marker. A LTIIa-specific oligonucleotide probe was designed to capture the LTIIa marker during the MCH, followed by PCR. Varying levels of humic acid were added to the DNA extracts to evaluate the sensitivity and effectiveness of MCH-PCR. The minimal detection limit of MCH-PCR for the LTIIa gene was 2.5 ag/muL DNA. In the presence of humic acid, MCH-PCR was able to increase the detection sensitivity 10 000-fold over that of conventional PCR. The MCH-PCR could also detect one cell with the LTIIa DNA marker in a 1-L seeded environmental water sample. Results in this study indicate that MCH-PCR is more sensitive than nested PCR in testing environmental samples.

Isolation and characterization of microsatellite loci in the antMyrmica scabrinodis

AbstractFive polymorphic microsatellite loci were developed for the antMyrmica scabrinodisusing a magnetic bead hybridization selection protocol. The number of alleles per locus varied between three and six. Cross‐species amplification of four of the loci yielded positive amplification products in fourMyrmicaspecies, suggesting their general suitability for microsatellite analysis within this taxonomic group.

Detection of Seedborne Pathogens

Plant pathogens present a serious threat to seedling establishment and the potential for plant disease epidemics under greenhouse conditions is great. Hence, pathogen exclusion by detection and elimination of infested seedlots remains a requisite tactic for seedling production and disease management. Unfortunately, the numbers of contaminated seed within a lot may be low and infested seed may be asymptomatic making their detection difficult. To address these issues seed detection assays have been developed, but many of them have shortcomings that reduce their effectiveness. Examples of frequently used seed assays include visual examination, selective media, seedling grow-out and serological assays which, while appropriate for some pathogens, often display inadequate levels of sensitivity and specificity. Recently, the polymerase chain reaction (PCR) has emerged as a tool for detecting microorganisms in many diverse environments. Thus far, it is clear that DNA-based detection systems exhibit higher levels sensitivity than conventional techniques. Unfortunately, PCR-based seed tests require the extraction of PCR-quality DNA from target organisms in backgrounds of saprophytic organisms and inhibitory seed-derived compounds. The inability to efficiently extract PCR-quality DNA from seeds has restricted the acceptance and application of PCR for seed detection. To overcome these limitations several modified PCR protocols have been developed including selective target colony enrichment followed by PCR (BIO-PCR) and immunomagnetic separation and PCR. These techniques seek to selectively concentrate or increase target organism populations to enhance detection and have been successfully applied for detecting bacteria in seed. Other techniques with great potential for rapid detection of seedborne pathogens include magnetic capture hybridization and PCR, and DNA-chip technology. Ultimately, PCR will be available for the detection of all seedborne pathogens and may supersede conventional detection methods.

Specific features of a magnetic impurity in a correlated electron model with Ising anisotropy

We present the Bethe ansatz solution of a magnetic hybridization impurity in a correlated electron host with Ising-like magnetic anisotropy. On the one hand, the strong correlations between host electrons produce a mixed-valence behavior of the localized electrons. On the other hand, the spin-gap of the low-lying unbound electron states caused by the ``easy-axis'' magnetic anisotropy suppresses the standard Kondo effect. For small enough magnetic fields the magnetic susceptibility of the impurity is zero. The usual Kondo logarithms, characteristic of SU(2)-symmetric systems with gapless spin-carrying excitations, are replaced by square root singularities caused by the closing of the spin gap at a critical field. Similar behavior is predicted for the free edges of an open chain, which again is very different from the isotropic situation. Using the low-lying excitations in the conformal regime we calculate asymptotics of correlation functions.

Magnetic bead-based label-free electrochemical detection of DNA hybridization.

Magnetic bead capture has been used for eliminating non-specific adsorption effects hampering label-free detection of DNA hybridization based on stripping potentiometric measurements of the target guanine at graphite electrodes. In particular, the efficient magnetic separation has been extremely useful for discriminating against unwanted constituents, including a large excess of co-existing mismatched and non-complementary oligomers, chromosomal DNA, RNA and proteins. The new protocol involves the attachment of biotinylated oligonucleotide probes onto streptavidin-coated magnetic beads, followed by the hybridization event, dissociation of the DNA hybrid from the beads, and potentiometric stripping measurements at a renewable graphite pencil electrode. Such coupling of magnetic hybridization surfaces with renewable graphite electrode transducers and label-free electrical detection results in a greatly simplified protocol and offers great promise for centralized and decentralized genetic testing. A new magnetic carbon-paste transducer, combining the solution-phase magnetic separation with an instantaneous magnetic collection of the bead-captured hybrid, is also described. The characterization, optimization and advantages of the genomagnetic label-free electrical protocol are illustrated below for assays of DNA sequences related to the breast-cancer BRCA1 gene.

Isolation of nine novel tetranucleotide microsatellites in Atlantic herring (Clupea harengus)

AbstractNine tetranucleotide microsatellite loci developed for Atlantic herring are presented. Loci were isolated using a magnetic bead hybridization selection protocol that yielded an 80% enrichment for tetranucleotide microsatellites. Fifty Atlantic herring from each of a North‐west and North‐east Atlantic spawning group were screened at each locus. Loci were polymorphic (12–56 alleles per locus) and exhibited high levels of observed heterozygosity (0.66–0.98). These loci are therefore suitable for population studies and the analysis of mating systems.

The potential of soil microorganisms to mineralize atrazine as predicted by MCH-PCR followed by nested PCR.

The potential of soil microorganisms to mineralize atrazine was studied in soil samples collected from fields with various histories of atrazine application. In contrast to many previous studies, which showed no atrazine mineralization activity, all the tested soils mineralized atrazine regardless of their atrazine application history. However, the delay before mineralization and the variation in the subsequent mineralization rate were in agreement with the initial copy number of the atrazine dechlorinaze gene, and the proliferation rate of the degraders. Soils from corn fields, which had up to 100 copies of the atzA gene per gram of soil, had a lag period of 4-5 days before atrazine mineralization started, and final mineralization percentages ranged from 40% to 54%. However, soils from fields that were never amended with atrazine had much longer lag periods (more than 17 days), which decreased after enrichment of the degrader population with high concentrations of atrazine for 15 days. Generally the mineralization rate and the atzA gene copy number increased after the enrichment period. The atrazine mineralization potential was measured by PCR of genes from the atrazine mineralization pathway. Magnetic capture hybridization was the most efficient of the two tested methods for purifying target DNA of PCR inhibitors, without reducing the copy number of the required fragment. Nested PCR proved to be the most effective method for predicting the exact potential of the soil to mineralize the pollutant even without enrichment of a small population with the target genes. This method can complement microcosm studies and eliminate futile efforts when the potential to mineralize the pollutant does not exist in the soil.

Magnetic capture–hybridization method for purification and probing of mRNA for neutral protease of Bacillus cereus

A magnetic capture–hybridization method was assessed for the isolation of prokaryotic mRNA for the neutral protease of B. cereus from liquid culture. A biotin-labeled specific probe was hybridized to the mRNA transcripts and subsequently captured by streptavidin-coated paramagnetic beads. mRNA was detected by dot–blot hybridization with a ds DIG-labeled DNA-probe. The magnetic capture hybridization is a rapid and simple method and has a promising potential for gene expression studies in complex samples.

Superconductivity and magnetism in heavy-fermion UPd2(Al,Ga)3

We present bulk properties (resistivity, specific heat, and susceptibility) of the quasiternary system UPd{sub 2}(Al{sub 1{minus}x}Ga{sub x}){sub 3} and derive the superconducting and magnetic phase diagrams. For low Ga substitution (x{le}0.25) a complete suppression of superconductivity is found, while the magnetic properties are hardly affected. For larger x the magnetic transition temperature T{sub N} gradually decreases, and the mass enhancement of the electrons increases, until at x=0.8{endash}0.9 a crystallographic transition takes place from the PrNi{sub 2}Al{sub 3} to the BaB{sub 2}Pt{sub 3} lattice. At the structural transition T{sub N} discontinuously increases, while the electronic specific heat {gamma} grows smoothly through the transition. We discuss the relationship between the alloying parameter x and the magnetic ordering and electronic hybridization, respectively. The strong suppression of the superconductivity in UPd{sub 2}Al{sub 3} with Ga suggests an unconventional mechanism of superconductivity, most probably related to spin fluctuations mediating the pairing. {copyright} {ital 1997} {ital The American Physical Society}

Development and Application of a Primer Set for Specific Detection of Bacillus thufingiensis and Bacillus cereus in Soil Using Magnetic Capture Hybridization and PCR Amplification

Summary A primer target to the phosphatidylinositol-specific phospholipase C (PI-PLC) gene from Bacillus thuringiensis was shown to differentiate strains of B. cereus and B. thuringiensis from a variety of soil Bacillus spp. and gram-negative bacteria. It was possible to detect the indigenous populations of B. cereus and B. thuringiensis in field rhizosphere soil samples using the magnetic capture hybridization (MCH - PCR) technique. The high specificity of the primer set in B. cereus and B. thuringiensis indicates that the PI-PLC gene can be used as a specific target for MCH-PCR detection in complex environment as soil.

On the possibility of aligning paramagnetic molecules or ions in a magnetic field

Strong magnetic fields can hybridize low rotational states of paramagnetic molecules or molecular ions whose electronic angular momentum is coupled to the molecular axis. The hybridization creates pendular states in which the molecular axis is confined to librate over a limited angular range about the field direction. In this way substantial spatial alignment associated with large Zeeman shifts can be attained for many ground-state radicals or ions and electronically excited states of diatomic or linear molecules. The magnetic hybridization is analogous to that recently demonstrated for polar molecules in electric fields. The magnetic version can only provide ensemble alignment rather than orientation, but offers complementary chemical scope by virtue of its applicability to nonpolar molecules and ions.