An algorithm for analyzing linkages affected by heterozygous translocations: QuadMap

Heterozygous chromosome rearrangements such as reciprocal translocations are most accurately displayed as two-dimensional linkage maps. Standard linkage mapping software packages, such as MapMaker, generate only one-dimensional maps and so reciprocal translocations appear as clusters of markers, even though they originate from two nonhomologous chromosomes. To more accurately map these regions, researchers have developed statistical methods that use the variance in map distance to distinguish among the four segments (two translocation, two interstitial) of the translocation. In this study, we describe modifications to one of these protocols, that proposed by Livingstone et al. (2000). We also introduce QuadMap, a new software application for dissecting heterozygous translocation-affected linkage maps.     

Microaerophilic–aerobic sequential decolourization/biodegradation of textile azo dyes by a facultative Klebsiella sp. strain VN-31

Four different azo dyes were decolourized and biodegraded in a sequential microaerophilic–aerobic treatment by a facultative Klebsiella sp. strain VN-31, a bacterium isolated from activated sludge process of the textile industry. Dye decolourization was performed under microaerophilic conditions until no colour was observed (decolourization percentage >94%). The medium was then aerated to promote the biodegradation of the amines produced. The presence of aromatic amine in the microaerophilic stage and its absence in the aerobic stage demonstrate azo bond reduction and an oxidative biodegradation process, respectively. Total Organic Carbon (TOC) reduction for the growth medium plus dyes was ～50% in the microaerophilic stage and ～80% in the aerobic stage. The degradation products were also characterized by FT-IR and UV–vis techniques and their toxicity measured using Daphnia magna. The results provide evidence that the successive microaerophilic/aerobic stages, using a single Klebsiella sp. strain VN-31 in the same bioreactor, were able to form aromatic amines by the reductive break down of the azo bond and to oxidize them into non-toxic metabolites.     

New methods to identify conserved microsatellite loci and develop primer sets of high cross-species utility - as demonstrated for birds

We have developed a new approach to create microsatellite primer sets that have high utility across a wide range of species. The success of this method was demonstrated using birds. We selected 35 avian EST microsatellite loci that had a high degree of sequence homology between the zebra finch Taeniopygia guttata and the chicken Gallus gallus and designed primer sets in which the primer bind sites were identical in both species. For 33 conserved primer sets, on average, 100% of loci amplified in each of 17 passerine species and 99% of loci in five non-passerine species. The genotyping of four individuals per species revealed that 24-76% (mean 48%) of loci were polymorphic in the passerines and 18-26% (mean 21%) in the non-passerines. When at least 17 individuals were genotyped per species for four Fringillidae finch species, 71-85% of loci were polymorphic, observed heterozygosity was above 0.50 for most loci and no locus deviated significantly from Hardy-Weinberg proportions. This new set of microsatellite markers is of higher cross-species utility than any set previously designed. The loci described are suitable for a range of applications that require polymorphic avian markers, including paternity and population studies. They will facilitate comparisons of bird genome organization, including genome mapping and studies of recombination, and allow comparisons of genetic variability between species whilst avoiding ascertainment bias. The costs and time to develop new loci can now be avoided for many applications in numerous species. Furthermore, our method can be readily used to develop microsatellite markers of high utility across other taxa.     

Mutation of the Chlamydomonas reinhardtii analogue of residue M210 of the Rhodobacter sphaeroides reaction center slows primary electron transfer in Photosystem II

Primary charge separation within Photosystem II (PS II) is much slower (time constant 21 ps) than the equivalent step in the related reaction center (RC) found in purple bacteria ( 3 ps). In the case of the bacterial RC, replacement of a specific tyrosine residue within the M subunit (at position 210 in Rhodobacter sphaeroides), by a leucine residue slows down charge separation to 20 ps. Significantly the analogous residue in PS II, within the D2 polypeptide, is a leucine not a tyrosine (at position D2-205, Chlamydomonas reinhardtii numbering). Consequently, it has been postulated [Hastings et al. (1992) Biochemistry 31: 7638–7647] that the rate of electron transfer could be increased in PS II by replacing this leucine residue with tyrosine. We have tested this hypothesis by constructing the D2-Leu205Tyr mutant in the green alga, Chlamydomonas reinhardtii, through transformation of the chloroplast genome. Primary charge separation was examined in isolated PS II RCs by time-resolved optical spectroscopy and was found to occur with a time constant of 40 ps. We conclude that mutation of D2-Leu205 to Tyr does not increase the rate of charge separation in PS II. The slower kinetics of primary charge separation in wild type PS II are probably not due to a specific difference in primary structure compared with the bacterial RC but rather a consequence of the P680 singlet excited state being a shallower trap for excitation energy within the reaction center.     

An atomic level model for the interactions of molybdenum nitrogenase with carbon monoxide, acetylene, and ethylene

A combination of density functional theory and molecular mechanics calculations has been used to study the possible interactions of CO, C(2)H(2), and C(2)H(4) with the central Fe and terminal Mo sites of the iron-molybdenum cofactor of nitrogenase. The most favorable binding mode for CO on the central section of the FeMoco appears to be end-on to a single Fe and results in a change from high to low spin for the ligating Fe atom. If a coordination site for CO is available on the Mo, this becomes the preferred CO binding site. Calculated nu(CO) infrared frequencies are compared with the experimental values given in the literature. C(2)H(2) binds weakly in a side-on orientation to a single Fe site; addition of a single H(+)/e(-) couple to the substrate results in spontaneous migration of the resulting -CH=CH(2) group from Fe to a central S atom of the cofactor. Further reduction liberates C(2)H(4) or alternatively can give an S=CHCH(3) intermediate, which then goes on to produce C(2)H(6). A model for C(2)H(2) reduction by nitrogenase is proposed, based on the results of the calculations and the extensive literature on this process.     

Potato virus Y NIa protease activity is not sufficient for elicitation of Ry-mediated disease resistance in potato

Ry confers extreme resistance (ER) to all strains of potato virus Y (PVY). In previous work, we have shown that the protease domain of the nuclear inclusion a protease (NIaPro) from PVY is the elicitor of the Ry-mediated resistance and that integrity of the protease active site is required for the elicitation of the resistance response. Two possibilities arise from these results: first, the structure of the active protease has elicitor activity; second, NIa-mediated proteolysis is required to elicit the resistance response. To resolve these possibilities, the NIaPro from PVY was randomly mutagenised and the clones obtained were screened for elicitation of cell death as an indicator of resistance and proteolytic activity. We did not find any mutants that had retained the ability to elicit cell death but had lost protease activity, as measured by processing of the NIa cleavage site in the viral genome. This was consistent with the idea that protease activity is necessary for elicitor activity. However, protease activity was not sufficient because we found three elicitor-defective mutants in which there was a high level of protease activity in this assay.     

Papanicolaou staining of exfoliated vaginal epithelial cells facilitates the prediction of ovulation in the giant panda

The giant panda is seasonally monoestrus, experiencing a single estrous with spontaneous ovulation in the spring. Therefore, accurate monitoring of the estrous cycle to pinpoint the time of ovulation is critical for the success of timed mating or artificial insemination. Analysis of exfoliated vaginal epithelial cells is a simple technique that rapidly yields information about the estrous status of a panda. Vaginal swabs were obtained during five estrous cycles of two nulliparous females. Cells were stained with the trichrome Papanicolaou and classified as basophils, intermediates or superficials. The color of stained cells, basophilic, acidophilic or keratinized, was recorded as a characteristic independent of the three standard cell types. The day urinary conjugates of estrogen fell from peak levels was considered the day of ovulation. A chromic shift occurred 8-9 days before ovulation when the majority of exfoliated vaginal cells changed from basophilic (blue) to acidophilic (pink) without accompanying nuclear or cytoplasmic changes. A second chromic shift was consistently observed 2 days prior to ovulation when keratinized (orange) cells replaced acidophils as the majority of vaginal cells. Monochrome staining of vaginal cells is sufficient to quantify superficial cells, which is a useful adjunct to behavioral and endocrinological data in determining estrous in the giant panda. However, the timing and duration of superficial cell elevations are substantially different between and within individual females, which limits the accuracy of timing ovulation for artificial insemination. The predictive value of vaginal cytology was greatly enhanced with the trichrome stain and evaluation of cell color.     

A patch of surface-exposed residues mediates negative regulation of immune signaling by tomato Pto kinase

Tomato (Lycopersicon esculentum) Pto kinase specifically recognizes the Pseudomonas effector proteins AvrPto and AvrPtoB, leading to induction of defense responses and hypersensitive cell death. Structural modeling of Pto combined with site-directed mutagenesis identified a patch of surface-exposed residues required for native regulation of signaling. Mutations in this area resulted in constitutive gain-of-function (CGF) forms of Pto that activated AvrPto-independent cell death via the cognate signaling pathway. The patch overlaps the peptide binding region of the kinase catalytic cleft and is part of a broader region required for interaction with bacterial effectors. We propose that the negative regulatory patch is normally occupied by a peptide that represses Pto signaling. Furthermore, we found that Pto kinase activity was required for Avr-dependent activation but dispensable for signaling by CGF forms of Pto. This suggests that Pto signals by a conformational change rather than phosphorylation of downstream substrates in the defense signaling pathway.     

Epitope tagging of legume root nodule extensin modifies protein structure and crosslinking in cell walls of transformed tobacco leaves

Root nodule extensins (RNEs) are highly glycosylated plant glycoproteins localized in the extracellular matrix of legume tissues and in the lumen of Rhizobium-induced infection threads. In pea and other legumes, a family of genes encode glycoproteins of different overall length but with the same basic composition. The predicted polypeptide sequence reveals repeating and alternating motifs characteristic of extensins and arabinogalactan proteins. In order to monitor the behavior of individual RNE gene products in the plant extracellular matrix, the coding sequence of PsRNE1 from Pisum sativum was expressed in insect cells and in tobacco leaves. RNE products extracted from tobacco tissues were of high molecular weight (in excess of 80 kDa), indicating extensive glycosylation similar to that in pea tissues. Epitope-tagged derivatives of PsRNE1 could be localized in cell walls. However, the introduction of epitope tags at the C-terminus of RNE altered the behavior of RNE in the extracellular matrix, apparently preventing intermolecular crosslinking of RNE molecules and their covalent association with other cell wall components. These observations are discussed in the light of a computational model for the RNE glycoprotein that is consistent with an extended rod-like structure. It is proposed that RNE can undergo three classes of tyrosine-based crosslinking. Intramolecular crosslinking of vicinal Tyr residues is rod stiffening, end-to-end linkage is rod lengthening, and side-to-side intermolecular crosslinking is rod bundling. The control of these interconversions could have important implications for the biomechanics of infection thread growth.     

Linkage disequilibrium mapping via cladistic analysis of phase-unknown genotypes and inferred haplotypes in the Genetic Analysis Workshop 14 simulated data

We recently described a method for linkage disequilibrium (LD) mapping, using cladistic analysis of phased single-nucleotide polymorphism (SNP) haplotypes in a logistic regression framework. However, haplotypes are often not available and cannot be deduced with certainty from the unphased genotypes. One possible two-stage approach is to infer the phase of multilocus genotype data and analyze the resulting haplotypes as if known. Here, haplotypes are inferred using the expectation-maximization (EM) algorithm and the best-guess phase assignment for each individual analyzed. However, inferring haplotypes from phase-unknown data is prone to error and this should be taken into account in the subsequent analysis. An alternative approach is to analyze the phase-unknown multilocus genotypes themselves. Here we present a generalization of the method for phase-known haplotype data to the case of unphased SNP genotypes. Our approach is designed for high-density SNP data, so we opted to analyze the simulated dataset. The marker spacing in the initial screen was too large for our method to be effective, so we used the answers provided to request further data in regions around the disease loci and in null regions. Power to detect the disease loci, accuracy in localizing the true site of the locus, and false-positive error rates are reported for the inferred-haplotype and unphased genotype methods. For this data, analyzing inferred haplotypes outperforms analysis of genotypes. As expected, our results suggest that when there is little or no LD between a disease locus and the flanking region, there will be no chance of detecting it unless the disease variant itself is genotyped.