A nine-base nucleotide sequence in the porcine circovirus type 2 (PCV2) nucleocapsid gene determines viral replication and virulence

Porcine circovirus type 2 (PCV2) was retrospectively identified by serology in swine populations as an asymptomatic infection at least 25 years prior to the first reported case of PCV2-associated postweaning multisystemit wasting syndrome (PMWS). To investigate the sudden emergence of PMWS, viral sequences were amplified from frozen archived (1970-1971) porcine tissues and the complete genome of archival PCV2 was determined. The ORF1 gene product (viral DNA replicase) was homologous to contemporary PCV2 ORF1. In ORF2 (viral nucleocapsid gene) archival PCV2, a consistent linear nine-base sequence difference at base positions 1331 through 1339 was observed.The deduced amino acid sequence from these base changes alters the nucleocapsid conformation within the second immunogenic epitope from a hydrophobic (contemporary PCV2) to a hydrophilic (archival PCV2) configuration.

The effect of various treatment conditions on natural zeolites: Ion exchange, acidic, thermal and steam treatments

Two different natural zeolites having different phase compositions were obtained from different regions of Turkey and modified by ion-exchange (0.5 M NH4NO3) and acid leaching using 1 M HCl. The natural and modified samples were treated at low temperature (LT), high temperature (HT) and steam (ST) conditions and characterised by XRF, XRD, BET, FTIR, DR-UV-Vis, NH3-TPD and TGA. Ion-exchange with NH4+ of natural zeolites results in the exchange of the Na+ and Ca2+ cations and the partial exchange of the Fe3+ and Mg2+ cations. However, steam and acidic treatments cause significant dealumination and decationisation, as well as loss of crystalline, sintering of phases and the formation of amorphous material. The presence of mordenite and quartz phases in the natural zeolites increases the stability towards acid treatment, whereas the structure of clinoptilolite-rich zeolites is mostly maintained after high temperature and steam treatments. The natural and modified zeolites treated at high temperature and in steam were found to be less stable compared with synthetic zeolites, resulting in a loss of crystallinity, a decrease in the surface area and pore volume, a decrease in the surface acidity as well as dealumination, and decationisation. (C) 2012 Elsevier Inc. All rights reserved.

Measurement of absolute charge-exchange cross sections for He2+ collisions with He and H-2

Reported are total, absolute charge-exchange cross sections for collisions of 3He(2+) ions with He and H-2. Measurements are reported at fixed energies between 0.33 and 4.67 keV/amu. Both the present results and earlier results of others are analyzed in terms of available experimental small-angle differential cross sections as a function of collision energy, and hence the geometry of the exit aperture of the gas-collision cells used by the various experimental groups. In addition, the effective length of gas-collision cells is studied using fluid dynamic and molecular flow simulations to address the density patterns near the cell entrance and exit apertures. When small acceptance-angle corrections were applied, the results of present and previous measurements for the single electron capture in these systems were brought into good accord in the relevant energy ranges. Taken in their entirety, the present data for 3He(2+) with He and H-2 lend themselves to new theoretical calculations of the multichannel charge-exchange cross sections.

Detection of single nucleotide polymorphisms within a sequence of a gene associated with prostate cancer using a fluorophore-tagged DNA probe

Single nucleotide polymorphisms within a sequence of a gene associated with prostate cancer were identified using oligodeoxynucleotide probe sequences bearing internal anthracene fluorophores proximal to the SNP site. Depending upon the nature of the synthesised target sequences, probe-target duplex formation could lead to enhanced or attenuated fluorescence emission from the anthracene, enabling detection of a proximal base-pair as either matching or mismatching. © 2011 Elsevier Ltd. All rights reserved.

Genomewide linkage scan of schizophrenia in a large multicenter pedigree sample using single nucleotide polymorphisms

A genomewide linkage scan was carried out in eight clinical samples of informative schizophrenia families. After all quality control checks, the analysis of 707 European-ancestry families included 1615 affected and 1602 unaffected genotyped individuals, and the analysis of all 807 families included 1900 affected and 1839 unaffected individuals. Multipoint linkage analysis with correction for marker-marker linkage disequilibrium was carried out with 5861 single nucleotide polymorphisms (SNPs; Illumina version 4.0 linkage map). Suggestive evidence for linkage ( European families) was observed on chromosomes 8p21, 8q24.1, 9q34 and 12q24.1 in nonparametric and/or parametric analyses. In a logistic regression allele-sharing analysis of linkage allowing for intersite heterogeneity, genomewide significant evidence for linkage was observed on chromosome 10p12. Significant heterogeneity was also observed on chromosome 22q11.1. Evidence for linkage across family sets and analyses was most consistent on chromosome 8p21, with a one-LOD support interval that does not include the candidate gene NRG1, suggesting that one or more other susceptibility loci might exist in the region. In this era of genomewide association and deep resequencing studies, consensus linkage regions deserve continued attention, given that linkage signals can be produced by many types of genomic variation, including any combination of multiple common or rare SNPs or copy number variants in a region. Molecular Psychiatry (2009) 14, 786-795; doi:10.1038/mp.2009.11; published online 17 February 2009

Contribution of reverse Na+/Ca2+ exchange to spontaneous activity in interstitial cells of cajal in the rabbit urethra

Interstitial cells of Cajal (ICC) isolated from the rabbit urethra exhibit regular Ca2+ oscillations that are associated with spontaneous transient inward currents (STICs) recorded under voltage clamp. Their frequency is known to be very sensitive to external Ca2+ concentration but the mechanism of this has yet to be elucidated. In the present study experiments were performed to assess the role of Na+-Ca2+ exchange (NCX) in this process. Membrane currents were recorded using the patch clamp technique and measurements of intracellular Ca2+ were made using fast confocal microscopy. When reverse mode NCX was enhanced by decreasing the external Na+ concentration [Na+]o from 130 to 13 mM, the frequency of global Ca2+ oscillations and STICs increased. Conversely, inhibition of reverse mode NCX by KB-R7943 and SEA0400 decreased the frequency of Ca2+ oscillations and STICs. Application of caffeine (10 mM) and noradrenaline (10 microM) induced transient Ca2+-activated chloride currents (I(ClCa)) at -60 mV due to release of Ca2+ from ryanodine- and inositol trisphosphate (IP3)-sensitive Ca2+ stores, respectively, but these responses were not blocked by KB-R7943 or SEA0400 suggesting that neither drug blocked Ca2+-activated chloride channels or Ca2+ release from stores. Intact strips of rabbit urethra smooth muscle develop spontaneous myogenic tone. This tone was relaxed by application of SEA0400 in a concentration-dependent fashion. Finally, single cell RT-PCR experiments revealed that isolated ICC from the rabbit urethra only express the type 3 isoform of the Na+-Ca2+ exchanger (NCX3). These results suggest that frequency of spontaneous activity in urethral ICC can be modulated by Ca2+ entry via reverse NCX.

Na+/H+ exchange inhibitor cariporide attenuates skeletal muscle infarction when administered before ischemia or reperfusion

Administration of Na(+)/H(+) exchange isoform-1 (NHE-1) inhibitors before ischemia has been shown to attenuate myocardial infarction in several animal models of ischemia-reperfusion injury. However, controversy still exists as to the efficacy of NHE-1 inhibitors in protection of myocardial infarction when administered at the onset of reperfusion. Furthermore, the efficacy of NHE-1 inhibition in protection of skeletal muscle from infarction (necrosis) has not been studied. This information has potential clinical applications in prevention or salvage of skeletal muscle from ischemia-reperfusion injury in elective and trauma reconstructive surgery. The objective of this research project is to test our hypothesis that the NHE-1 inhibitor cariporide is effective in protection of skeletal muscle from infarction when administered at the onset of sustained ischemia or reperfusion and to study the mechanism of action of cariporide. In our studies, we observed that intravenous administration of cariporide 10 min before ischemia (1 or 3 mg/kg) or reperfusion (3 mg/kg) significantly reduced infarction in pig latissimus dorsi muscle flaps compared with the control, when these muscle flaps were subjected to 4 h of ischemia and 48 h of reperfusion (P <0.05; n = 5 pigs/group). Both preischemic and postischemic cariporide treatment (3 mg/kg) induced a significant decrease in muscle myeloperoxidase activity and mitochondrial-free Ca(2+) content and a significant increase in muscle ATP content within 2 h of reperfusion (P <0.05; n = 4 pigs/group). Preischemic and postischemic cariporide treatment (3 mg/kg) also significantly inhibited muscle NHE-1 protein expression within 2 h of reperfusion after 4 h of ischemia, compared with the control (P <0.05; n = 3 pigs/group). These observations support our hypothesis that cariporide attenuates skeletal muscle infarction when administered at the onset of ischemia or reperfusion, and the mechanism involves attenuation of neutrophil accumulation and mitochondrial-free Ca(2+) overload and preservation of ATP synthesis in the early stage of reperfusion.

Levels and patterns of population genetic diversity in the red seaweed Chondrus crispus (Florideophyceae): a direct comparison of single nucleotide polymorphisms and microsatellites

Single nucleotide polymorphisms (SNPs) are predicted to supersede microsatellites as the marker of choice for population genetic studies in the near future. To date, however, very few studies have directly compared both marker systems in natural populations, particularly in non-model organisms. In the present study, we compared the utility of SNPs and microsatellites for population genetic analysis of the red seaweed Chondrus crispus (Florideophyceae). Six SNP loci yielded very different patterns of intrapopulation genetic diversity compared to those obtained using seven moderately (mean 5.2 alleles) polymorphic microsatellite loci, although Bayesian clustering analysis gave largely congruent results between the two marker classes. A weak but significant pattern of isolation-by-distance was observed across scales from a few hundred metres to approximately 200?km using the combined SNP and microsatellite data set of 13 loci. Over larger scales, however, there was little correlation between genetic divergence and geographical distance. Our findings suggest that even a moderate number of SNPs is sufficient to determine patterns of genetic diversity across natural populations, and also highlight the fact that patterns of genetic variation in seaweeds arise through a complex interplay of short- and long-term natural processes, as well as anthropogenic influence.

Macroscopic limit of time-dependent density-functional theory for adiabatic local approximations of the exchange-correlation kernel

Time-dependent density-functional theory is a rather accurate and efficient way to compute electronic excitations for finite systems. However, in the macroscopic limit (systems of increasing size), for the usual adiabatic random-phase, local-density, or generalized-gradient approximations, one recovers the Kohn-Sham independent-particle picture, and thus the incorrect band gap. To clarify this trend, we investigate the macroscopic limit of the exchange-correlation kernel in such approximations by means of an algebraical analysis complemented with numerical studies of a one-dimensional tight-binding model. We link the failure to shift the Kohn-Sham spectrum of these approximate kernels to the fact that the corresponding operators in the transition space act only on a finite subspace.