Use of a novel DNA melting profile assay for the identification of PCR-amplified genomic sequences encoding for variant-specific surface proteins from the clonal GS/M-83-H7 line of Giardia lamblia.

During infections, Giardia lamblia undergoes a continuous change of its major surface antigens, the variant-specific surface proteins (VSPs). Many studies on antigenic variation have been performed using G. lamblia clone GS/M-83-H7, which expresses surface antigen VSP H7. The present study was focused on the identification and characterization of vsp gene sequences within the genome of the clonal G. lamblia GS/M-83-H7 line. For this purpose, we applied a PCR which specifically amplified truncated sequences from the 3'-terminal region of the vsp genes. Upon cloning, most of the vsp gene amplification products were shown to be approximately identical in size and thus could not be distinguished from each other by conventional gel electrophoresis. In order to pre-estimate the sequence complexity within the large panel of vsp clones isolated, we elaborated a novel concept which facilitated our large-scale genetic screening approach: PCR products from cloned DNA molecules were generated and then subjected to a DNA melting profile assay based on the use of the LightCycler Instrument. This high-throughput assay system proved to be well suited to monitor sequence differences between the amplification products from closely related vsp genes and thus could be used for the primary, sequence-related discrimination of the corresponding clones. After testing 50 candidates, vsp clones could be divided into five groups, each characterized by an individual DNA melting profile of the corresponding amplification products. Sequence analysis of some of these 50 candidates confirmed data from the aforementioned assay in that clones were demonstrated to be identical within, but different between, the distinct groups. The nucleotide and deduced amino acid sequences of five representative vsp clones showed high similarities both among each other and also with the corresponding gene segment of the variant-specific surface antigen (VSP H7) expressed by the original GS/M-83-H7 variant type. Furthermore, three of the genomic vsp sequences turned out to be identical to vsp sequences that represented previously characterized transcription products from in vivo- or in vitro-switched GS/M-83-H7 trophozoites. In conclusion, the DNA melting profile assay seems to be a versatile tool for the PCR-based genotyping of moderately or highly diversified sequence orthologues.

A Multiplex Real-Time PCR with High Resolution Melting Analysis for the Characterization of Antimicrobial Resistance in Neisseria gonorrhoeae.

Resistance to antibiotics used against Neisseria gonorrhoeae infections is a major public health concern. Antimicrobial resistance (AMR) testing relies on time-consuming culture-based methods. Development of rapid molecular tests for detecting AMR determinants could provide valuable tools for surveillance, epidemiological studies and to inform individual case management. We developed a fast (<1.5 hrs) SYBR-green based real-time PCR method with high resolution melting (HRM) analysis. One triplex and three duplex reactions included two sequences for N. gonorrhoeae identification and seven determinants of resistance to extended-spectrum cephalosporins (ESCs), azithromycin, ciprofloxacin, and spectinomycin. The method was validated by testing 39 previously fully-characterized N. gonorrhoeae strains, 19 commensal Neisseria spp., and an additional panel of 193 gonococcal isolates. Results were compared with culture-based AMR determination. The assay correctly identified N. gonorrhoeae and the presence or absence of the seven AMR determinants. There was some cross-reactivity with non-gonococcal Neisseria species and the detection limit was 10(3)-10(4) gDNA copies/reaction. Overall, the platform accurately detected resistance to ciprofloxacin (sensitivity and specificity, 100%), ceftriaxone (sensitivity 100%, specificity 90%), cefixime (sensitivity 92%, specificity 94%), azithromycin and spectinomycin (both sensitivity and specificity, 100%). In conclusion, our methodology accurately detects mutations generating resistance to antibiotics used to treat gonorrhea. Low assay sensitivity prevents direct diagnostic testing of clinical specimens but this method can be used to screen collections of gonococcal isolates for AMR more quickly than with current culture-based AMR testing.

Geochemistry of ODP Hole 111-504B basalts (Table 2)

Fifty samples of basalt recovered during ODP Leg 111 from the dikes (Layer 2C) of Hole 504B (1350.0-1562.3 m below seafloor) were analyzed by X-ray-fluorescence techniques. All of the samples are highly depleted in magmaphile elements relative to other mid-ocean ridge basalts, with TiO2 = 0.75-1.24 wt%, Na2O = 1.59-2.22 wt%, Zr = 38-64 ppm, Nb = 0.3-1.5 ppm, and Y = 20-30 ppm (for samples containing 0%-2% phenocrysts), but have ratios of highly incompatible elements similar to normal Type I mid-ocean ridge basalts (e.g., Zr/Nb > 30). Abundances of compatible elements are similar to those of typical mid-ocean ridge basalts, with MgO = 7.2-9.2 wt%, Fe2O3* = 9.3-12.5 wt%, Ni = 55-164 ppm, and Cr = 26-388 ppm. Approximately 2% of the samples recovered from the top part of Hole 504B are similar to normal Type I or Type II ocean floor basalts. However, all of the analyzed Leg 111 samples from Hole 504B are depleted basalts. Aphyric dike rocks from Leg 111 are virtually identical to the depleted aphyric samples recovered from the pillow lavas and dikes in the upper 1075 m of Hole 504B during DSDP Legs 69, 70, and 83, with the exception of elements readily altered by seawater (Sr, Rb, and K). These elements reach a maximum in both abundance and variability in the pillow lavas of the upper 571.5 m of Hole 504B and decline to more constant values in the dike system sampled on Legs 83 and 111, apparently as a result of a decrease in porosity and increase in alteration temperatures relative to the pillow lavas. Based on compositional similarities to the vast majority of the pillows and flows, the dikes sampled on Leg 111 appear to be the feeder system for the pillow lavas in the upper part of Hole 504B. The incompatible-element-depleted compositions of the Costa Rica Rift Zone basalts are consistent with multistage melting of a normal mid-ocean ridge source.