Early warning of footpad dermatitis and hockburn in broiler chicken flocks using optical flow, bodyweight and water consumption.

Footpad dermatitis and hockburn are serious welfare and economic issues for the production of broiler (meat) chickens. The authors here describe the use of an inexpensive camera system that monitors the movements of broiler flocks throughout their lives and suggest that it is possible to predict, even in young birds, the cross-sectional prevalence at slaughter of footpad dermatitis and hockburn before external signs are visible. The skew and kurtosis calculated from the authors' camera-based optical flow system had considerably more power to predict these outcomes in the 50 flocks reported here than water consumption, bodyweight or mortality and therefore have the potential to inform improved flock management through giving farmers early warning of welfare issues. Further trials are underway to establish the generality of the results.

Comparison of naturally and synthetically baited spruce beetle trapping systems in the central Rocky Mountains.

We compared naturally baited trapping systems to synthetically baited funnel traps and fallen trap trees for suppressing preoutbreak spruce beetle, Dendroctonus rufipennis Kirby, populations. Lures for the traps were fresh spruce (Picea spp.) bolts or bark sections, augmented by adding female spruce beetles to create secondary attraction. In 2003, we compared a naturally baited system ("bolt trap") with fallen trap trees and with synthetically baited funnel traps. Trap performance was evaluated by comparing total beetle captures and spillover of attacks into nearby host trees. Overall, the trap systems did not significantly differ in spruce beetle captures, although bolt traps caught 6 to 7 times more beetles than funnel traps during the first 4 wk of testing. Funnel traps with synthetic lures had significantly more spillover than either trap trees or bolt traps. The study was repeated in 2004 with modifications including an enhanced blend synthetic lure. Again, trap captures were generally similar among naturally and synthetically baited traps, but naturally baited traps had significantly less spillover. Although relatively labor-intensive, the bolt trap could be used to suppress preoutbreak beetle populations, especially when spillover is undesirable. Our work provides additional avenues for management of spruce beetles and suggests that currently used synthetic lures can be improved.

Cytoplasmic deposition of NFkappaB decoy oligonucleotides is insufficient to inhibit bleomycin-induced pulmonary inflammation.

Lung inflammation leads to severe tissue destruction and ultimately organ failure in a number of diseases, including cystic fibrosis (CF). The transcription factor nuclear factor kappa B (NFkappaB) regulates expression of many pro-inflammatory mediators. We have assessed the effect of topical administration of NFkappaB decoys in a bleomycin model of acute lung inflammation. Using fluorescein-labelled decoy oligonucleotides (ODN) (80 microg/mouse) we have shown that lipid-complexed and 'naked' ODN transfect conducting airway epithelium in a comparable manner (approximately 65% of cells). However, the ODN were detectable in the cytoplasm, but not in the nucleus of transfected cells. An increase of ODN dose to 500 microg/mouse did not increase nuclear transfection significantly. We determined the effect of cytoplasmic NFkappaB decoys on bleomycin-induced inflammation. We transfected mice with 'naked' decoy and scrambled ODN (500 microg) 1 h before intratracheal administration of bleomycin. We measured IL6 secretion in BALF and lung homogenates and total and differential cell counts in BALF 5 days after bleomycin administration. We did not detect a difference between NFkappaB decoy and scrambled ODN-treated animals in any of the parameters tested. We suggest that access of ODN to the nucleus of airway epithelial cells is a key problem, limiting the efficacy of such decoy strategies, as well as attempts at gene repair.

Structural and functional roles of the N1- and N3-protons of psi at tRNA's position 39.

Pseudouridine at position 39 (Psi(39)) of tRNA's anticodon stem and loop domain (ASL) is highly conserved. To determine the physicochemical contributions of Psi(39)to the ASL and to relate these properties to tRNA function in translation, we synthesized the unmodified yeast tRNA(Phe)ASL and ASLs with various derivatives of U(39)and Psi(39). Psi(39)increased the thermal stability of the ASL (Delta T (m)= 1.3 +/- 0.5 degrees C), but did not significantly affect ribosomal binding ( K (d)= 229 +/- 29 nM) compared to that of the unmodified ASL (K (d)= 197 +/- 58 nM). The ASL-Psi(39)P-site fingerprint on the 30S ribosomal subunit was similar to that of the unmodified ASL. The stability, ribosome binding and fingerprint of the ASL with m(1)Psi(39)were comparable to that of the ASL with Psi(39). Thus, the contribution of Psi(39)to ASL stability is not related to N1-H hydrogen bonding, but probably is due to the nucleoside's ability to improve base stacking compared to U. In contrast, substitutions of m(3)Psi(39), the isosteric m(3)U(39)and m(1)m(3)Psi(39)destabilized the ASL by disrupting the A(31)-U(39)base pair in the stem, as confirmed by NMR. N3-methylations of both U and Psi dramatically decreased ribosomal binding ( K (d)= 1060 +/- 189 to 1283 +/- 258 nM). Thus, canonical base pairing of Psi(39)to A(31)through N3-H is important to structure, stability and ribosome binding, whereas the increased stability and the N1-proton afforded by modification of U(39)to Psi(39)may have biological roles other than tRNA's binding to the ribosomal P-site.

Use of cross-links to study the conformational dynamics of triplex DNA.

The conformational dynamics of a 34-base-long pyrimidine purine-pyrimidine motif intramolecular DNA triple helix possessing three cytosine residues in the Hoogsteen strand (1) and a disulfide cross-linked analog (2) were studied by two-dimensional exchange and NOE spectroscopy and by measuring base-catalyzed imino proton exchange rates. Under acidic conditions that stabilize triplexes containing Hoogsteen strand cytosines (pH 6.0 and 1 degree C), sequences 1 and 2 exhibit a small and identical degree of conformational heterogeneity. However, at a higher temperature (pH 6.0 and 37 degrees C), 1 exhibits much more extensive conformational heterogeneity than 2. The exchange times for Watson-Crick imino protons are approximately 1 h for both triplexes. However, the Hoogsteen base-pair lifetimes of 1 could not be measured because this sequence is conformationally labile under the alkaline conditions necessary to conduct these experiments. Because of the extraordinary pH stability conferred by the cross-link, it is possible to estimate the base-pair lifetimes for 2. The lifetimes of the Hoogsteen base pairs range from about 3 to 370 ms, and in all cases are shorter than that of the Watson-Crick base pair contained in the same triplet. These experiments represent the first measurement of base-pair lifetimes within Hoogsteen triplets. The ability to measure individual base-pair lifetimes may prove useful in studies that attempt to modulate triplex properties through rational design.

The effect of cross-links on the conformational dynamics of duplex DNA.

The base pair lifetimes and apparent dissociation constants of a 21 base DNA hairpin and an analog possessing a disulfide cross-link bridging the 3'- and 5'-terminal bases were determined by measuring imino proton exchange rates as a function of exchange catalyst concentration and temperature. A comparison of the lifetimes and apparent dissociation constants for corresponding base pairs of the two hairpins indicates that the cross-link neither increases the number of base pairs involved in fraying nor alters the lifetime, dissociation constant, or the opened structure from which exchange occurs for the base pairs that are not frayed. The cross-link does, however, stabilize the frayed penultimate base pair of the stem duplex. Significantly, it appears that the disulfide cross-link is more effective at preventing fraying of the penultimate base pair than is the 5 base hairpin loop. Because this disulfide cross-link can be incorporated site specifically, and does not adversely affect static or dynamic properties of DNA, it should prove very useful in studies of nucleic acid structure and function.

Solution structure of a DNA hairpin and its disulfide cross-linked analog.

The solution structures of a 21 base long DNA hairpin derived from the ColE1 cruciform, and an analog possessing a disulfide cross-link bridging the terminal bases, have been determined by NMR spectroscopy. The 8 bp long stem of these sequences adopts a B-form helix whereas the five base long single-stranded loop appears to be flexible and cannot be represented by a unique static conformation. NOESY cross-peak volumes, proton and phosphorus chemical shifts, and both homo- and heteronuclear coupling constants for the cross-linked hairpin are virtually identical to those measured for the unmodified sequence, even for the residues that are proximal to the cross-link. These results indicate that both hairpins are structurally isomorphous. Because this cross-link can be incorporated site specifically in a sequence independent manner, and does not appear to alter native conformation, it should prove broadly applicable in studies of DNA structure and function.

Conformational studies of hairpin sequences from the ColE1 cruciform.

Inverted repeat sequences derived from the ColE1 cruciform were investigated by nuclear magnetic resonance (NMR) and UV spectroscopy. It was shown that 15 different sequences exist as stable hairpin structures over a range of buffer conditions and DNA concentrations. Experiments with six oligomers (1-6) containing the native stem sequence and five base loops, found that the two hairpins with the wild-type loops (1-2) served as upper and lower bounds for the thermodynamic stability of all the other sequences. NMR experiments, including rotational correlation time measurements and NOESY spectra, were then performed on 1, the most stable hairpin sequence to begin to uncover a structural basis of its stability.

Basal cell carcinoma of the nipple. Report of two cases.

Two cases of basal cell carcinoma of the nipple are presented, bringing the total number of reported cases to 15. The majority, including our two patients, are elderly men. This finding suggests a causal role of exposure to ultraviolet radiation. In our cases excision was curative.

Radiographs in clinical periodontal trials.

Fifty-eight patients were selected from an ongoing study of periodontal therapy at The University of Michigan. Pre-and post-treatment series of full mouth radiographs obtained by conventional paralleling long cone technique were available. Mesial and distal radiographic bone height was scored using the technique developed by Björn et al. A total of 1416 teeth were scored from the itial radiographs, and subsequently at one, two, three, and four years after the treatment. Radiographic bone height scores were compared with level of attachment and pocket depth scores for the same teeth at the same time. Statistical significance and correlation coefficients were derived using computer analysis of the data. The data were analyzed using three different data groupings: individual teeth, patient means, and half-mouth treatment methods. High positive correlations were found between initial measurements of radiographic bone height and attachment level as well as pocket depth. The correlations between changes in measurements of radiographic bone height and attachment level after treatment were markedly lower but are statistically significant. A highly significant correlation between radiographic bone heights and measurements of attachment level also appeared in follow-up data one to four years after treatment. The method of data grouping resulted in different correlation coefficients. Highest correlations were found if the data were pooled for patients. Lowest correlations were found if the data for individual teeth were analyzed. When the data were combined to produce patient scores, sample variation is reduced and correlations increase in magnitude. The generally high correlations between radiographic bone height and attachment level scores before and after treatment tend to confirm the fact that radiographic assessment of alveolar bone height using the method of Björn et al. can provide fairly accurate assessment of interproximal periodontal support.