High-throughput genotyping of unknown genomic terrain in complex plant genomes: lessons from a case study

Novel high-throughput genotyping technologies have facilitated rapid genotyping of single nucleotide polymorphisms in non-model organisms. Most plant species have complex genomes with a large proportion of their genes having one or more paralogous copies due to single gene duplications and ancient or recent polyploidization events. These paralogous gene copies are potential sources of genotyping errors, and hence genotyping of plant genomes is inherently difficult. Here we present a case study that exemplifies paralog-related problems in high-throughput genotyping of plant genomes. We used the MassARRAY genotyping platform to genotype the LpIRI locus in L. perenne populations; this gene is thought to be involved in low-temperature stress tolerance. The dissection of the molecular genetics underlying the genotyping results provides a good example of how unknown paralogs can mask the true genotype of the locus, instructive to the non-specialist plant researcher and breeder.     

Metapopulation structure for perpetuation of Francisella tularensis tularensis

Background  

Outbreaks of Type A tularemia due to Francisella tularensis tularensis are typically sporadic and unstable, greatly hindering identification of the determinants of perpetuation and human risk. Martha's Vineyard, Massachusetts has experienced an outbreak of Type A tularemia which has persisted for 9 years. This unique situation has allowed us to conduct long-term eco-epidemiologic studies there. Our hypothesis is that the agent of Type A tularemia is perpetuated as a metapopulation, with many small isolated natural foci of transmission. During times of increased transmission, the foci would merge and a larger scale epizootic would occur, with greater likelihood that humans become exposed.     

Neutral N-glycans of the gastropod Arion lusitanicus.

The neutral N-glycan structures of Arion lusitanicus (gastropod) skin, viscera and egg glycoproteins were examined after proteolytic digestion, release of the glycans from the peptides, fluorescent labelling with 2-aminopyridine and fractionation by charge, size and hydrophobicity to obtain pure glycan structures. The positions and linkages of the sugars in the glycan were analysed by two dimensional HPLC (size and hydrophobicity) and MALDI-TOF mass spectrometry before and after digestion with specific exoglycosidases. The most striking feature in the adult tissues was the high amount of oligomannosidic and small paucimannosidic glycans terminated with 3-O-methylated mannoses. The truncated structures often contained modifications of the inner core by beta1,2-linked xylose to the beta-mannose residue and/or an alpha-fucosylation (mainly alpha1,6-) of the innermost GlcNAc residue. Skin and viscera showed predominantly the same glycans, however, in different amounts. Traces of large structures carrying 3-O-methylated galactoses were also detected. The egg glycans contained mainly (approximately 75%) oligomannosidic structures and some paucimannosidic structures modified by xylose or alpha1,6-fucose, but in this case no methylation of any monosaccharide was detected. Thus, gastropods seem to be capable of producing many types of structures ranging from those typical in human to structures similar to those found in nematodes, and therefore will be a valuable model to understand the regulation of glycosylation. Furthermore, this opens the way for using this organism as a host for the production of recombinant proteins. The detailed knowledge on glycosylation also may help to identify targets for pest control.     

Evidence for the Involvement of the Small Subunit of HIV-1 Reverse Transcriptase (RT) in the TSAO-Resistance

Abstract

By introducing the TSAO-resistance mutation 138Glu→Lys in only the p51 subunit of HIV-1 RT, we obtained compelling evidence for a structural and functional role of the p51 subunit in the sensitivity and/or resistance of the enzyme to the TSAO-derivatives.     

A simple method for separating unbound and bound cortisol in a radioimmunoassay

A cortisol radioimmunoassay in which unbound cortisol is partitioned into the organic phase of a toluene: water scintillation fluid mix at 0 to 5 degrees C is described. Antibody-bound cortisol remained in the aqueous phase. Since liquid scintillation spectrometers detect photons generated from the [3H]cortisol only in the organic phase, the system effectively separates antibody bound from unbound [3H]cortisol. Regression coefficients including linear, quadratic, and cubic components of standard curves were between 0.980 and 0.999. Cross-reactivity was 3% or less with 11 other steroids and cholesterol except for cortisone (16%) and prednisone (12%). Intra- and interassay coefficients of variation were 8 and 13%, respectively. The lower limit of sensitivity of the assay was 1.4 ng/ml. Recoveries of added mass averaged 97.5%. The correlation between concentrations of glucocorticoids assayed by competitive binding to dog plasma and the current procedure was 0.90. The assay procedure described simplifies separation of unbound from antibody-bound cortisol.