Comparison of responses by bacteriophages and bacteria to pressures on the base composition of open reading frames

Differences in the base composition of genomes can occur because of GC pressure, purine-loading pressure (AG pressure) and RNY pressure, for which there are possible functional explanations, and because of the more abstract pressures exerted by individual bases. The graphical approach of Muto and Osawa was used to analyse how bacteriophages and bacteria balance potentially conflicting pressures on their genomes. Phages generally respond to AG pressure by increasing A while keeping T constant, and by decreasing C while keeping G constant. In contrast, bacteria generally increase both A and T, the former more so, and decrease both G and C, the latter more so. These differences largely occur at third codon positions, which are more responsive than first and second codon positions to AG pressure and GC pressure. Phages respond to AG pressure more in the third codon position than bacteria, whereas bacteria respond more in the first codon position than phages. Conversely, bacteria respond to GC pressure more in the third codon position than phages, whereas phages respond more in the first codon position than bacteria. As GC pressure increases, A is traded for C and AG pressure decreases; first and second codon positions, having more A than T, are most responsive to this negative effect of increased GC pressure; third positions either do not respond (phages) or respond weakly (bacteria). In a set of 48 phage-host pairs, degrees of purine loading were less correlated between phage and host than were GC percentages. These results suggest that pressures on conventional and genome phenotypes operate differentially in phages and bacteria, generating both general differences in base composition and specific differences characteristic of particular phage-host pairs. The reciprocal relationship between GC pressure and AG pressure implies that effects attributed to GC pressure may actually be due to AG pressure, and vice versa.     

Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles

Genome-wide expression profiles contain global patterns that evade visual detection in current gene clustering analysis. Here, a Gene Expression Dynamics Inspector (GEDI) is described that uses self-organizing maps to translate high-dimensional expression profiles of time courses or sample classes into animated, coherent and robust mosaics images. GEDI facilitates identification of interesting patterns of molecular activity simultaneously across gene, time and sample space without prior assumption of any structure in the data, and then permits the user to retrieve genes of interest. Important changes in genome-wide activities may be quickly identified based on 'Gestalt' recognition and hence, GEDI may be especially useful for non-specialist end users, such as physicians. AVAILABILITY: GEDI v1.0 is written in Matlab, and binary Matlab.dll files which require Matlab to run can be downloaded for free by academic institutions at http://www.chip.org/~ge/gedihome.html Supplementary information: http://www.chip.org/~ge/gedihome.html     

Metabolic flux analysis of halogenated monoterpene biosynthesis in microplantlets of the macrophytic red alga Ochtodes secundiramea

The bioprocess engineering of marine macroalgae (i.e. seaweeds) for the production of secondary metabolites is an emerging area of marine biotechnology. One novel system is the biosynthesis of halogenated monoterpenes by "microplantlet" suspension cultures derived from the red alga Ochtodes secundiramea. This biosynthetic platform has three principal components: elaboration of myrcene from geranyl diphosphate (GPP); bromonium-ion promoted halogenation of myrcene to 10E-bromomyrcene, 3-chloro-10E-bromo-alpha-myrcene, and 3,10E-dibromomyrcene; bromonium-ion promoted cyclization of myrcene to Apakaochtodene B. In this study, a metabolic flux analysis on halogenated monoterpene biosynthesis was performed. To facilitate this effort, a "bromine free" cell line of O. secundiramea microplantlets was developed where biohalogenation was temporarily disabled but myrcene biosynthesis was still enabled. This cell line was cultivated within an airlift photobioreactor under nutrient medium perfusion. Halogenated monoterpene biosynthesis was "turned on" by coordinated addition of bromide and vanadate (a co-factor for vanadium bromoperoxidase) to the perfusion medium. From these experiments, the effects of bromide and vanadate delivery on the metabolic flux of each metabolite were determined. Bromination of myrcene at its Delta(6-10) olefinic bond was the dominant branch of the bioreaction network, whereas chlorination steps in the pathway were "weakly rigid". This study represents the first application of metabolic engineering principles to the analysis and manipulation of secondary metabolism in macrophytic marine organisms.     

Nitrogen Dynamics in Ice Storm-Damaged Forest Ecosystems: Implications for Nitrogen Limitation Theory

Despite the widely recognized importance of disturbance in accelerating the loss of elements from land, there have been few empirical studies of the effects of natural disturbances on nitrogen (N) dynamics in forest ecosystems. We were provided the unusual opportunity for such study, partly because the intensively monitored watersheds at the Hubbard Brook Experimental Forest (HBEF), New Hampshire, experienced severe canopy damage following an ice storm. Here we report the effects of this disturbance on internal N cycling and loss for watershed 1 (W1) and watershed 6 (W6) at the HBEF and patterns of N loss from nine other severely damaged watersheds across the southern White Mountains. This approach allowed us to test one component of N limitation theory, which suggests that N losses accompanying natural disturbances can lead to the maintenance of N limitation in temperate zone forest ecosystems. Prior to the ice storm, fluxes of nitrate (NO₃ ^–) at the base of W1 and W6 were similar and were much lower than N inputs in atmospheric deposition. Following the ice storm, drainage water NO₃ ^– concentrations increased to levels that were seven to ten times greater than predisturbance values. We observed no significant differences in N mineralization, nitrification, or denitrification between damaged and undamaged areas in the HBEF watersheds, however. This result suggests that elevated NO₃ ^- concentrations were not necessarily due to accelerated rates of N cycling by soil microbes but likely resulted from decreased plant uptake of NO₃ ^-. At the regional scale, we observed high variability in the magnitude of NO₃ ^- losses: while six of the surveyed watersheds showed accelerated rates of NO₃ ^– loss, three did not. Moreover, in contrast to the strong linear relationship between NO₃ ^– loss and crown damage within HBEF watersheds [r ²: (W1 = 0.91, W6 = 0.85)], stream water NO₃ ^– concentrations were weakly related to crown damage (r ² = 0.17) across our regional sites. The efflux of NO₃ ^– associated with the ice storm was slightly higher than values reported for soil freezing and insect defoliation episodes, but was approximately two to ten times lower than NO₃ ^– fluxes associated with forest harvesting. Because over one half of the entire years worth of N deposition was lost following the ice storm, we conclude that catastrophic disturbances contribute synergistically to the maintenance of N limitation and widely observed delays of N saturation in northern, temperate zone forest ecosystems. Present address: Department of Ecology and Evolutionary Biology, Princeton University, Guyot Hall, Princeton, New Jersey 08544, USA.     

Development of a novel method of lytic phage delivery by use of a bacteriophage P22 site-specific recombination system

Bacteriophage therapy represents a potential alternative to the use of antibiotics to control proliferation of pathogenic bacteria. As an alternative to the strategy where a limited number of doses of large numbers of lytic bacteriophages are administered, a novel method delivery system was developed so that phages are continually released into the culture. Specifically, a non-pathogenic Escherichia coli strain was constructed that was lysogenic for a lytic mutant of bacteriophage lambda. This lysogen was shown to be effective at decreasing the number of lambda-sensitive E. coli in vitro. Construction of this E. coli strain was accomplished by development of a plasmid-based system utilizing the site-specific recombination machinery of bacteriophage P22 to integrate DNA constructs into the host chromosome. This recombination system is useful for strain construction and other genetic manipulations in both E. coli and Salmonella enterica serovars.     

The wbiA locus is required for the 2-O-acetylation of lipopolysaccharides expressed by Burkholderia pseudomallei and Burkholderia thailandensis

Burkholderia pseudomallei and Burkholderia thailandensis express similar O-antigens (O-PS II) in which their 6-deoxy-alpha-L-talopyranosyl (L-6dTalp) residues are variably substituted with O-acetyl groups at the O-2 or O-4 positions. In previous studies we demonstrated that the protective monoclonal antibody, Pp-PS-W, reacted with O-PS II expressed by wild-type B. pseudomallei strains but not by a B. pseudomallei wbiA null mutant. In the present study we demonstrate that WbiA activity is required for the acetylation of the L-6dTalp residues at the O-2 position and that structural modification of O-PS II molecules at this site is critical for recognition by Pp-PS-W.     

Overall survival in advanced breast cancer: relevance of progesterone receptor expression and DNA ploidy in fine-needle aspirates of 392 patients

Fine-needle aspiration cytology (FNAC) is essential for making a diagnosis in advanced breast cancer. The determination of hormone receptors in the material obtained is useful for predicting patient response to endocrine therapy, but the prognostic value of hormone receptor expression as well as the clinical utility of DNA flow cytometry are controversial. The aim of this prospective study with long-term follow-up (median: 81 months) was to evaluate these biomarkers in relation to overall survival in a series of 392 patients with advanced breast cancer (stage IIB, n=106; IIIA, n=66; IIIB, n=174; and IV, n=46) using FNAC. Estrogen and progesterone receptor expression was found in 65.1% and 46.1% of the tumors, respectively. Hormone receptors were not found to be associated with clinical staging. DNA aneuploidy was present in 70.9% of the cases and the median S-phase fraction (SPF) was 9.4%. There was a significant correlation of aneuploidy and high SPF with lack of hormone receptors. In univariate analysis, advanced disease stage, absence of hormone receptors, DNA aneuploidy and high SPF showed a statistically significant correlation with poor clinical outcome. In multivariate analysis, disease stage, progesterone receptors and DNA ploidy retained independent prognostic significance in relation to overall survival. These data indicate that progesterone receptor expression and DNA ploidy are independent prognostic factors in advanced breast cancer.     

A method for reconstructing three-dimensional dive profiles of marine mammals using geomagnetic intensity data: results from two lactating Weddell seals

The under-ice behavior of two free-ranging female Weddell seals (Leptonychotes weddellii) was studied using geomagnetic, acceleration and velocity sensors at Big Razorback Island in McMurdo Sound, Antarctica. The seals' body angle and posture were calculated from the acceleration data and the heading from the geomagnetic intensity data. Together with swim speed, the seals' three-dimensional underwater dive path, heading and even posture were reconstructed for each dive. Each instrument was deployed for 2 days, during which time these females made multiple, deep (₞ m) dives, with average maximum depths of 236ᆯ m (n=4) and 244끁 m (n=40). Each seal appeared to choose a particular heading on which to descend. These headings were significantly different between seals and bouts (Watson's U² test, P<0.05). These new instruments and methodologies are shown to provide valuable information on the fine-scale and complex movements of diving animals.     

Nucleotide variation,haplotype structure,and association with end-stage renal disease of the human interleukin-1 gene cluster

A dense gene-based SNP map was constructed across a 360-kb region containing the interleukin-1 gene cluster (IL1A, IL1B, and IL1RN), focusing on IL1RN. In total, 95 polymorphisms were confirmed or identified primarily by direct sequencing. Polymorphisms were precisely mapped to completed BAC and genomic sequences spanning this region. The polymorphisms were typed in 443 case-control subjects from Caucasian and African American groups. Consecutive pair-wise marker linkage disequilibrium was not strictly correlated with distance and ranged from D'=0.0079 to 1.000 and D'=0.0521 to 1.0000 in Caucasians and African Americans, respectively. Single markers and haplotypes in IL1 cluster genes were evaluated for association with end-stage renal disease (ESRD). Eleven SNPs show some evidence of association with ESRD, with the strongest associations in two IL1A variants, one SNP, rs1516792-3, in intron 5 (p=0.0015) and a 4-bp insertion/deletion within the 3'UTR, rs16347-2 (p=0.0024), among African Americans with non-T2DM-associated ESRD.     

Shaping and stretching life by autophagy

In a recent study published in Science, demonstrate that genes required for autophagy act downstream of insulin-like signaling, and are involved in the expression of major life history traits, including dauer larva development and adult life span.