Towards a plant model for enigmatic U-to-C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis

Hornworts are crucial to understand the phylogeny of early land plants. The emergence of 'reverse' U-to-C RNA editing accompanying the widespread C-to-U RNA editing in plant chloroplasts and mitochondria may be a molecular synapomorphy of a hornwort-tracheophyte clade. C-to-U RNA editing is well understood after identification of many editing factors in models like Arabidopsis thaliana and Physcomitrella patens, but there is no plant model yet to investigate U-to-C RNA editing. The hornwort Anthoceros agrestis is now emerging as such a model system. We report on the assembly and analyses of the A. agrestis chloroplast and mitochondrial genomes, their transcriptomes and editomes, and a large nuclear gene family encoding pentatricopeptide repeat (PPR) proteins likely acting as RNA editing factors. Both organelles in A. agrestis feature high amounts of RNA editing, with altogether > 1100 sites of C-to-U and 1300 sites of U-to-C editing. The nuclear genome reveals > 1400 genes for PPR proteins with variable carboxyterminal DYW domains. We observe significant variants of the 'classic' DYW domain, in the meantime confirmed as the cytidine deaminase for C-to-U editing, and discuss the first attractive candidates for reverse editing factors given their excellent matches to U-to-C editing targets according to the PPR-RNA binding code.

The Expansion and Diversification of Pentatricopeptide Repeat RNA-Editing Factors in Plants

The RNA-binding pentatricopeptide repeat (PPR) family comprises hundreds to thousands of genes in most plants, but only a few dozen in algae, indicating massive gene expansions during land plant evolution. The nature and timing of these expansions has not been well defined due to the sparse sequence data available from early-diverging land plant lineages. In this study, we exploit the comprehensive OneKP datasets of over 1000 transcriptomes from diverse plants and algae toward establishing a clear picture of the evolution of this massive gene family, focusing on the proteins typically associated with RNA editing, which show the most spectacular variation in numbers and domain composition across the plant kingdom. We characterize over 2 250 000 PPR motifs in over 400 000 proteins. In lycophytes, polypod ferns, and hornworts, nearly 10% of expressed protein-coding genes encode putative PPR editing factors, whereas they are absent from algae and complex-thalloid liverworts. We show that rather than a single expansion, most land plant lineages with high numbers of editing factors have continued to generate novel sequence diversity. We identify sequence variations that imply functional differences between PPR proteins in seed plants versus non-seed plants and variations we propose to be linked to seed-plant-specific editing co-factors. Finally, using the sequence variations across the datasets, we develop a structural model of the catalytic DYW domain associated with C-to-U editing and identify a clade of unique DYW variants that are strong candidates as U-to-C RNA-editing factors, given their phylogenetic distribution and sequence characteristics.

Fern genomes elucidate land plant evolution and cyanobacterial symbioses

Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns-one at the base of 'core leptosporangiates' and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N2-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla-cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.

Seasonal Variation in the Emergency Department Prevalence Of Sepsis

The incidence and mortality of sepsis and severe sepsis in hospitalised patients is seasonal and consistently highest during the winter. The primary aim of this study was to measure the seasonal variation in the prevalence of emergency department (ED) patients with sepsis. This cross-sectional study was performed over two four-week periods in the summer and in the winter, respectively. The clinical records of all patients presenting to the ED during the study periods were retrospectively screened to determine if they met the criteria for “uncomplicated” sepsis and severe sepsis or septic shock. The prevalence of “uncomplicated” sepsis was higher in the winter (43.9 per 1000) compared to the summer (30.7 per 1000). The prevalence of severe sepsis or septic shock was also higher in the winter (17.7 per 1000) compared to the summer (11.7 per 1000). This quantitatively demonstrates the increased ED burden of sepsis in the winter that can be used to inform healthcare planning and resource allocation.

The Prevalence of Severe Sepsis or Septic Shock in an Irish Emergency Department

Severe sepsis and septic shock are among the leading causes of death globally. Despite the central role the emergency department (ED) plays in the early identification of patients presenting to hospital with sepsis, the prevalence of severe sepsis and septic shock in the Irish ED setting has not been described. The primary aim of this study was to measure the prevalence of severe sepsis or septic shock in an Irish adult ED setting. The clinical records of patients presenting to the ED over a four-week period were retrospectively reviewed to determine if they met the current Health Service Executive (HSE) criteria for severe sepsis or septic shock. Overall, 3,585 adult patients attended the ED during the study period, with 42 patients meeting the criteria for severe sepsis or septic shock. The ED prevalence of severe sepsis or septic shock was 11.7 patients (95% CI 8.1 - 15.4%) per 1000 ED attendances.

What Proportion of Patients Meet the Criteria for Uncomplicated Sepsis in an Irish Emergency Department?

Emergency medicine plays a central role in the early recognition of patients presenting to hospital with sepsis. However, the epidemiology of sepsis in the Irish Emergency Department (ED) setting has not been described. The primary aim of this study was to determine the proportion of adult ED patients who meet the current criteria for uncomplicated sepsis. This cross-sectional study was performed in the ED of Beaumont Hospital, Dublin. The clinical records of all patients presenting to the ED over a four-week period were retrospectively screened to determine if they met the current Health Service Executive (HSE) criteria for uncomplicated sepsis. Overall, 3,585 adult patients attended the ED during the study period, with 152 patients meeting the criteria for uncomplicated sepsis. The proportion of ED patients who met the criteria for uncomplicated sepsis was 4.24% (95% CI 3.57-4.91%).

PIK3CA mutation analysis in recurrent breast cancer

11041

Background: Mutations in PIK3CA (encoding p110α catalytic subunit of phosphatidylinositol-3-kinase) are among the most common genetic events identified in breast cancer but the role of these mutations in determining the clinical course of the disease is uncertain. Furthermore the frequency of PIK3CA mutation in metastatic breast cancer samples has not been adequately studied but is an important concern in the design of studies with novel agents designed to inhibit mutant PIK3CA. Methods: We have established a tumor banking protocol for patients (pts) with metastatic breast cancer. In this study, we performed a mutational analysis of exons 9 (HD) and 20 (KD) of the PIK3CA using tumor DNA obtained from pts with recurrent disease and correlated mutational status with clinicopathological features and prognosis. Results: Biopsies were obtained from sites of recurrence in 51 pts with stage 4 disease. The median F/U was 44 (range: 0.9–239) months and death has occurred in 66%. Mutations in PIK3CA were identified in 24.5% (11.3% in HD and 13.2% in KD). PIK3CA mutation was significantly correlated with lower tumor grade (47% in grade 1/2 vs 8% in grade 3, p=0.004), positive ER (35% in ER+ vs 5% in ER-, p=0.017), and PR (37% in PR+ vs 5% in PR-, p=0.011). Overall survival (OS) was 139.5 and 53.7 months for mutation- and non-mutation- carriers respectively (p=0.014). Conclusions: About one quarter of pts with recurrent/advanced breast cancer carry PIK3CA mutations in samples of recurrent disease, which correlated with positive ER/PR status and a more indolent clinical course. These patients are good candidates for experimental protocols that combine endocrine agents with PI3 kinase inhibitors but the slower kinetics of disease progression in PIK3CA mutation carriers may have to be taken into account for statistical designs and power size calculations.

No significant financial relationships to disclose.

New Zealand's epidemic of meningococcal disease described using molecular analysis: implications for vaccine delivery

New Zealand's epidemic of meningococcal disease began in mid 1991. Surveillance of meningococcal disease in New Zealand is based on a combination of disease notification and organism characterisation. Case numbers and population rates rose from 53 (1.5 per 100,000 population) in 1990 to a high of 650 (17.4 per 100,000 population) in 2001. The highest rates of disease occur in Pacific peoples under 20 years but the highest percentages of cases occur in Maori and European New Zealanders. The epidemic has been driven by a strain identified as B:4:P1.7b,4, ST-41/44 complex/Lineage III. The stability of the P1.7b,4 Por A protein has been demonstrated suggesting that the epidemic may be controlled by a strain-specific OMV vaccine.

Effectiveness of a cytokine restraining agent (CRA (TM)) in attenuating disuse deconditioning induced by hindlimb unloading in rats

Spaceflight alters many immune responses and among the regulatory components of an organisms response system that have been to be affected by spaceflight is the cytokine network. Spaceflight, as well as ground-based model systems of spaceflight, have been shown to affect the production and activation of various cytokines including interleukins (IL) and tumor necrosis factor (TNF). Levels of urinary IL-2 are elevated on the first day of spaceflight and again after returning from space. Most results from ground-based studies in rodents indicate either no alterations in cytokines or decreased levels. Results from this experiment indicate that HP 228, a potent cytokine restraining agent (CRA (TM)) was effective in attentuating many of the disuse deconditioning changes induced by the ground-based hindlimb suspension model that simulates weightlessness in rats. HP 228 is a novel heptapeptide with unnatural amino acids and can effectively restrain lipopolysaccharide (LPS)-induced increased levels of several key cytokines, including plasma TNF alpha, IL-1 beta and IL-6. HP 228 has also been shown to be effective in several rodent models of pain, inflammation and LPS-induced lethality, as well as in reducing inducible nitric oxide synthase.

Phosphorus export from an agricultural watershed: linking source and transport mechanisms

Many source and transport factors control P loss from agricultural landscapes; however, little information is available on how these factors are linked at a watershed scale. Thus, we investigated mechanisms controlling P release from soil and stream sediments in relation to storm and baseflow P concentrations at four flumes and in the channel of an agricultural watershed. Baseflow dissolved reactive phosphorus (DRP) concentrations were greater at the watershed outflow (Flume 1; 0.042 mg L(-1)) than uppermost flume (Flume 4; 0.028 mg L(-1)). Conversely, DRP concentrations were greater at Flume 4 (0.304 mg L(-1)) than Flume 1 (0.128 mg L(-1)) during stormflow. Similar trends in total phosphorus (TP) concentration were also observed. During stormflow, stream P concentrations are controlled by overland flow-generated erosion from areas of the watershed coincident with high soil P. In-channel decreases in P concentration during stormflow were attributed to sediment deposition, resorption of P, and dilution. The increase in baseflow P concentrations downstream was controlled by channel sediments. Phosphorus sorption maximum of Flume 4 sediment (532 mg kg(-1)) was greater than at the outlet Flume 1 (227 mg kg(-1)). Indeed, the decrease in P desorption between Flumes 1 and 4 sediment (0.046 to 0.025 mg L(-1)) was similar to the difference in baseflow DRP between Flumes 1 and 4 (0.042 to 0.028 mg L(-1)). This study shows that erosion, soil P concentration, and channel sediment P sorption properties influence streamflow DRP and TP. A better understanding of the spatial and temporal distribution of these processes and their connectivity over the landscape will aid targeting remedial practices.

A critical analysis of on-scene helicopter transport on survival in a statewide trauma system

BACKGROUND

Recently, questions have been raised regarding the effectiveness of helicopters in trauma care. We conducted a retrospective study to evaluate the effect of on-scene helicopter transport on survival after trauma in a statewide trauma system.

METHODS

Data were obtained from a statewide trauma registry of 162,730 patients treated at 28 accredited trauma centers. Patients transported from the scene by helicopter (15,938) were compared with those transported by ground with advanced life support (ALS) (6,473). Interhospital transfers and transports without ALS were excluded. Statistical analysis was performed using one-way analysis of variance and logistic regression.

RESULTS

Patients transported by helicopter were significantly (p < 0.01) younger, were more seriously injured, and had lower blood pressure. They were also more likely to be male and to have systolic blood pressure < 90 mm Hg. Logistic regression analysis revealed that when adjusting for other risk factors, transportation by helicopter did not affect the estimated odds of survival.

CONCLUSION

A reappraisal of the cost-effectiveness of helicopter triage and transport criteria, when access to ground ALS squads is available, may be warranted.

A novel geometry mass spectrometer, the Q-TOF, for low-femtomole/attomole-range biopolymer sequencing

Ultra-high-sensitivity, biopolymer sequencing is a goal in many fields of molecular biology, and collisionally activated decomposition electrospray mass spectrometry (CAD ES MS/MS) using a triple quadrupole mass spectrometer has become a method of choice for work in the high- to mid-femtomole range. However, when the detection of ions becomes statistical, as it may in that range, the mass assignment of fragment ions is inaccurate and either sequencing becomes impossible or ambiguities result due, for example, to the closeness in amino acid residue masses (I/L, N or K/Q, E). Some ambiguities may be resolved by synthesizing possible sequences, but this is unsatisfactory. In considering the limitations of triple quadrupole MS/MS with respect to scanning ion detection, resolution, transmission, and mass accuracy, we reasoned that a novel geometry quadrupole orthogonal acceleration time-of-flight (Q-TOF) instrument would have special merit for ultra-high-sensitivity MS/MS sequencing, and suggested its construction for this purpose some three years ago. A prototype Q-TOF has now been built by Micromass [Morris et al. (1996), Rapid Commun. Mass Spectrom. 10, 889-896], and in the first research on the instrument, including MHC antigen and filarial nematode glycoprotein studies, we demonstrate low-femtomole- and attomole-range sequencing with mass accuracy of better than 0.1 Da throughout the daughter-ion spectrum, thus removing sequencing ambiguities in some of the most challenging work demanding the highest sensitivity.

IL-8 single-chain homodimers and heterodimers: interactions with chemokine receptors CXCR1, CXCR2, and DARC

Covalent single-chain dimers of the chemokine interleukin-8 (IL-8) have been designed to mimic the dimeric form of IL-8 in solution and facilitate the production of heterodimer variants of IL-8. Physical studies indicated that use of a simple peptide linker to join two subunits, while allowing receptor binding and activation, led to self-association of the tethered dimers. However, addition of a single disulfide crosslink between the tethered subunits prevented this multimer from forming, yielding a species of dimer molecular weight. Crosslinked single-chain dimers bind to both IL-8 neutrophil receptors CXCR1 and CXCR2 as well as to DARC, as does a double disulfide-linked dimer with no peptide linker. In addition, neutrophil response to these dimers as measured by chemotaxis or beta-glucuronidase release is similar to that elicited by wild-type IL-8, providing evidence that the dissociation of the dimeric species is not required for these biologically relevant activities. Finally, through construction of single-chain heterodimer mutants, we show that only the first subunit's ELR motif is the single-chain variants.

The multiple carrier model of nonribosomal peptide biosynthesis at modular multienzymatic templates

Gramicidin S synthetase 1 and 2 were affinity-labeled at their thiolation centers either by thioesterification with the amino acid substrate or by specific alkylation with the thiol reagent N-ethylmaleimide in combination with a substrate protection technique. The labeled proteins were digested either chemically by cyanogen bromide or by proteases. An efficient multistep high pressure liquid chromatography methodology was developed and used to isolate the active site peptide fragments of all five thiolation centers of gramicidin S synthetase in pure form. The structures of these fragments are investigated by N-terminal sequencing, mass spectrometry, and amino acid analysis. Each of the active site peptide fragments contains the consensus motif LGG(H/D)S(L/I), which is specific for thioester formation in nonribosomal peptide biosynthesis. It was demonstrated that a 4'-phosphopantetheine cofactor is attached to the central serine of the thiolation motif in each amino acid-activating module of the gramicidin S synthetase multienzyme system forming the thioester binding sites for the amino acid substrates and catalyzing the elongation process. Our data are strong support for a "multiple carrier model" of nonribosomal peptide biosynthesis at multifunctional templates, which is discussed in detail.

Comparison of supercritical fluid extraction and solvent extraction of twenty-two organochlorine pesticides from eggs

The recoveries of twenty-two organochlorine pesticides spiked in egg samples were extracted by supercritical fluid extraction (SFE) using carbon dioxide and solvent extraction using acetonitrile were compared. The extracts were cleaned up with C18 and Florisil SPE columns. At 0.1 ppm spike level, the recoveries were 52 - 100% by SFE and 53 - 93% by solvent extraction. The limits of detection calculated at 0.01 ppm spike level were 0.072 - 0.006 ppm for SFE and 0.06 - 0.006 ppm for solvent extraction. Both methods show improvement in sample preparation time and solvent consumption from the existing Soxhlet extraction method.

Photolabelling of Salmonella typhimurium LT2 sialidase. Identification of a peptide with a predicted structural similarity to the active sites of influenza-virus sialidases

The sialidase from Salmonella typhimurium LT2 was characterized by using photoaffinity-labelling techniques. The well-known sialidase inhibitor 5-acetamido-2,6-anhydro-3,5-dideoxy-D-glycero-D-galacto-non- 2-enonic acid (Neu5Ac2en) was modified to contain an amino group at C-9, which permitted the incorporation of 4-azidosalicylic acid in amide linkage at this position. Labelling of the purified protein with the radioactive (125I) photoprobe was determined to be highly specific for a region within the active-site cavity. This conclusion was based on the observation that the competitive inhibitor Neu5Ac2en in the photolysis mixture prevented labelling of the protein. In contrast, compounds with structural and chemical features similar to the probe and Neu5Ac2en, but which were not competitive enzyme inhibitors, did not affect the photolabelling of the protein. The peptide interacting with the probe was identified by CNBr treatment of the labelled protein, followed by N-terminal sequence analysis. Inspection of the primary structure of the protein, predicted from the cloned structural gene for the sialidase [Hoyer, Hamilton, Steenbergen & Vimr (1992) Mol. Microbiol. 6, 873-884] revealed that the label was incorporated into a 9.6 kDa fragment situated within the terminal third of the molecule near the C-terminal end. Secondary-structural predictions using the Garnier-Robson algorithm [Garnier, Osguthorpe & Robson (1978) J. Mol. Biol. 120, 97-120] of the labelled peptide revealed a structural similarity to the active site of influenza-A- and Sendai-HN-virus sialidases with a repetitive series of alternating beta-sheets connected with loops.

Five years of experience in patients receiving home nutrition support with the implanted reservoir: a comparison with the external catheter

This study examines 5 years (1983-1988) of home parenteral nutrition (HPN) experience in 27 patients using the implanted reservoir for venous access. Their catheter-related complications are compared to two control populations using the external catheter. Group I compares the 46 patients who all started HPN in the same 5-year period, group II compares 17 patients with experience of both types of venous access. For the entire 58 patients the average infusion time was 22 months (1 month-8.2 yr) and the average complication rate was about one complication every 2 years. Analyzing the separate groups however, group I implanted reservoir patients did better than those with the external catheter (p less than 0.05) and group II external catheter patients did better than those with the implanted reservoir (p less than 0.05). A possible explanation for this discrepancy is the greater medical competence of group I patients selecting the reservoir. The data show a clear separation of patients into those who have minimal complications with either device and others who have several complications with both. Two-thirds of the complications were infectious, one third mechanical. The infectious complications were similar with both catheters; clotting was more common with the external catheter and skin erosion was seen only with the reservoir. Eighty % of patients with experience with both type of venous access preferred the implanted reservoir.