Inorganic nutrient utilisation by "adapted" Pseudomonas putida strain used in the bioremediation of agricultural soil polluted with crude petroleum

Garden soil samples polluted with crude petroleum were bioremediated by inorganic nutrient monitoring with appropriate adjustment and inoculation with crude oil-adapted strain of Pseudomonasputida (PP) isolated from oil-impacted soils. Soil samples without PP inoculation served as the control samples to compare the abilities of the native soil microflora with the adapted PP strain in biodegrading crude oil pollutant. In the experimental samples, oil concentration and all the inorganic nutrient sources tested decreased more rapidly with a proportional increase in the population densities of both PP and the native soil microflora than were observed in the control samples. This trend was particularly strong for PO4(3-) and NO3- which eventually became limiting both in all the experimental samples and in some control samples. Inoculation of crude oil-impacted agricultural soils by oil -adapted PP strain with nutrient monitoring and adjustment can be effective as bioremediation methods of agricultural land upon pollution with petroleum or petroleum products.

Characterization of the Net1 cell cycle-dependent regulator of the Cdc14 phosphatase from budding yeast

In the budding yeast Saccharomyces cerevisiae, the multifunctional protein Net1 is implicated in regulating the cell cycle function of the Cdc14 protein phosphatase. Genetic and cell biological data suggest that during interphase and early mitosis Net1 holds Cdc14 within the nucleolus where its activity is suppressed. Upon its transient release from Net1 at late anaphase, active Cdc14 promotes exit from mitosis by dephosphorylating targets in the nucleus and cytoplasm. In this paper we present evidence supporting the proposed role of Net1 in regulating Cdc14 and exit from mitosis. We show that the NH(2)-terminal fragment Net1(1-600) directly binds Cdc14 in vitro and is a highly specific competitive inhibitor of its activity (K(i) = 3 nm) with five different substrates including the physiologic targets Swi5 and Sic1. An analysis of truncation mutants indicates that the Cdc14 binding site is located within a segment of Net1 containing residues 1-341. We propose that Net1 inhibits by occluding the active site of Cdc14 because it acts as a competitive inhibitor, binds to a site located within the catalytic domain (residues 1-374), binds with reduced affinity to a Cdc14 C283S mutant in which an active site Cys is replaced, and is displaced by tungstate, a transition state analog known to bind in the catalytic site of protein-tyrosine phosphatases.

Cell fingerprinting: an approach to classifying cells according to mass profiles of digests of protein extracts

We present a statistical framework for classifying cells according to the set of peptide masses obtained by mass spectrometric analysis of digestions of whole cell protein extracts. The digest is separated by high performance liquid chromatography (HPLC) coupled directly to a mass spectrometer either by an electrospray interface or by collection to a matrix-assisted laser desorption/ionization target plate. Here, the mass to charge ratio, intensity, and HPLC retention time of the peptides are measured. We have used defined bacterial strains to test this approach. For each bacterium, this process is repeated for extracts obtained at different points in the growth curve in order to try and define an invariant set of signals that uniquely identify the bacterium. This paper presents algorithms for the creation of this cell fingerprint database and develops a Bayesian classification scheme for deciding whether or not an unknown bacterium has a match in the database. Our initial testing based on a limited data set of three bacteria indicates that our approach is feasible. Via a jack-knife test, our Bayesian classification scheme correctly identified the bacterium in 67.8% of the cases.

The yeast hsp70 homologue Ssa is required for translation and interacts with Sis1 and Pab1 on translating ribosomes

The 70-kDa heat shock proteins are molecular chaperones that participate in a variety of cellular functions. This chaperone function is stimulated by interaction with hsp40 proteins. The Saccharomyces cerevisiae gene encoding the essential hsp40 homologue, SIS1, appears to function in translation initiation. Mutations in ribosomal protein L39 (rpl39) complement loss-of-function mutations in SIS1 as well as PAB1 (poly(A)-binding protein), suggesting a functional interaction between these proteins. However, while a direct interaction between Sis1 and Pab1 is not detectable, both of these proteins physically interact with the essential Ssa (and not Ssb) family of hsp70 proteins. This interaction is mediated by the variable C-terminal domain of Ssa. Subcellular fractionations demonstrate that the binding of Ssa to ribosomes is dependent upon its C terminus and that its interaction with Sis1 and Pab1 occurs preferentially on translating ribosomes. Consistent with a function in translation, depletion of Ssa protein produces a general translational defect that appears similar to loss of Sis1 and Pab1 function. This translational effect of Ssa appears mediated, at least in part, by its affect on the interaction of Pab1 with the translation initiation factor, eIF4G, which is dramatically reduced in the absence of functional Ssa protein.

Persistent brachial plexus birth palsies

Sixty-six brachial plexus palsies in 64 patients were retrospectively reviewed at the San Francisco Unit of the Shriners Hospital system in a 15-year period from 1973 to 1988. All patients were referred with persistent brachial plexus palsies caused by birth trauma. The distribution of palsies at birth included 34 upper palsies, three lower palsies, and 29 mixed (or global) palsies. At final follow-up, the distribution of palsies had shifted and included 42 upper palsies, 6 lower palsies, and 14 mixed (or global) palsies. One patient had a persistent flail upper extremity. Many previously documented obstetrical risk factors were confirmed. Time to resolution or plateau averaged 4.5 months (range 3 weeks to 18 months). Only two palsies (one patient) resolved completely with time.

Impacts of crude oil on the germination and growth of cress seeds (Lepidium sp.) after bioremediation of agricultural soil polluted with crude petroleum using "adapted" Pseudomonas putida

The impacts of crude oil on the germination, growth and morphology of cress seeds (Lepidium sp.) after bioremediation of agricultural soil polluted with crude petroleum using "adapted" Pseudomonas putida (PP) were examined for 15 days. At day 15 there was 100% germination in the untreated control samples, the mean height of the seedlings was 75.8 +/- 2.6 mm and all appeared to have grown morphologically normal. In the experimental samples treated with oil and PP inoculation, there was 98% germination and the seedlings reached a height of 63.8 +/- 6.9 mm; again, morphologically the seedlings appeared normal. However, in the control samples treated with oil but without PP inoculation, there was 31-38% germination and seedling heights of 34.2 +/- 11.4-42.3 +/- 8.5 mm with abnormal morphology. Treatment of oil-impacted agricultural soil with PP as a bioremediation agent does produce soil which is capable of growing larger and healthier plants than where bioremediation has not taken place.

Protein expression analysis: from "tip of the iceberg" to a global method

In this review I will describe the advances that have recently been made in "traditional" two-dimensional gel based protein expression analysis. A major jump has been made toward the automation of gel image analysis and comparison, one of the major bottlenecks in the analysis chain as well as the automation of spot excision and preparation for mass spectrometric analysis. Currently the gel-based "proteome mapping" approach is highly effective and 300 gels and over 10,000 spots a week can be analysed. Very recently, viable alternatives to the use of two-dimensional gel electrophoresis have emerged and these approaches are discussed here. In combination with the recently developed stable isotopic tagging methods for peptide quantitation and new mass spectrometers, this emerging technology will be a rapid and highly effective alternative to gel-based methods with few of the latter's shortcomings.

Insertion gain measurements using two low-powered analogue hearing aids

Differences between insertion gain measurements and coupler measurements were investigated using two different hearing aids, to assess the accuracy of hearing aid fitting methods which involve the use of real-ear-to-coupler differences (RECDs). The hearing aids used were the NHS BE19 and the Lavis X11. They were allocated alternately to 80 new adult hearing aid users, and insertion gain measurement was carried out with the allocated aid on all subjects, and with both hearing aids on 36 subjects. Coupler measurements were also carried out with both hearing aids, at two different gain settings. Comparison of the coupler measurements and the insertion gain measurements suggests that the differences in insertion gain produced by different hearing aids cannot be predicted accurately from the differences in coupler gain measurements produced by the same aids. Although the use of RECDs measured using insert earphones may accurately predict the real-ear performance of some models of hearing aid, this method may not produce equally satisfactory results with other models.

Quantitation and facilitated de novo sequencing of proteins by isotopic N-terminal labeling of peptides with a fragmentation-directing moiety

We describe a method for comparative quantitation and de novo peptide sequencing of proteins separated either by standard chromatographic methods or by one- and two-dimensional polyacrylamide gel electrophoresis. The approach is based on the use of an isotopically labeled reagent to quantitate (by mass spectrometry) the ratio of peptides from digests of a protein being expressed under different conditions. The method allows quantitation of the changes occurring in spots or bands that contain more than one protein and has a greater dynamic range than most staining methods. Since the reagent carries a fixed positive charge under acidic conditions and labels only the N-terminal of peptides, the interpretation of tandem mass spectra to obtain sequence information is greatly simplified. The sequences can easily be extracted for homology searches instead of using indirect mass spectral-based searches and are independent of posttranslational modifications.

Breakdown of cytoskeletal proteins during meiosis of starfish oocytes and proteolysis induced by calpain

Meiosis reinitiation in starfish oocytes is characterized by Ca(2+) transients in the cytosol and in the nucleus and is accompanied by the disassembly of the nuclear envelope, a process which is likely to be mediated by the cleavage of selected proteins. We have used mass spectrometry analysis (mass profile fingerprinting) on 2D polyacrylamide gels of extracts of oocytes in which meiosis resumption was induced by 1-methyladenine and have identified five proteins that were specifically degraded: alpha-tubulin, lamin B, dynamin, and two kinds of actin. They are all components of the cytoskeleton or associated with it. We then investigated whether calpain, which is activated by the increase in cell Ca(2+), could cleave the same proteins that became degraded under the influence of 1-methyladenine and thus be involved in nuclear membrane breakdown. The investigation was prompted by the finding that microinjection of calpain into the nuclei of prophase arrested oocytes induced meiosis in the absence of 1-methyladenine. Incubation of prophase arrested (disrupted) oocytes with calpain produced a 2D gel protein pattern in which some of the degradation products coincided with those seen in oocytes challenged with 1-methyladenine.

Sequential phosphorylation of protein band 3 by Syk and Lyn tyrosine kinases in intact human erythrocytes: identification of primary and secondary phosphorylation sites

Treatment of intact human erythrocytes with pervanadate induces Tyr (Y)-phosphorylation of the transmembrane protein band 3; in parallel, the activity of the immunoprecipitated tyrosine kinases Syk and Lyn is increased. When erythrocytes are incubated with pervanadate together with PP1, a specific inhibitor of Src kinases, including Lyn, the Y-phosphorylation of band 3 is only partially reduced. Indeed, the PP1-resistant phosphorylation of band 3 precedes and is a prerequisite for its coimmunoprecipitation with Lyn, which interacts with the phosphoprotein via the SH2 domain of the enzyme, as proven by binding competition experiments. Upon recruitment to primarily phosphorylated band 3, Lyn catalyzes the secondary phosphorylation of the transmembrane protein. These data are consistent with the view that band 3 is phosphorylated in intact erythrocytes by both PP1-resistant (most likely Syk) and PP1-inhibited (most likely Lyn) tyrosine kinases according to a sequential phosphorylation process. Similar radiolabeled peptide maps are obtained by tryptic digestion of (32)P-band 3 isolated from either pervanadate-treated erythrocytes or red cell membranes incubated with exogenous Syk and Lyn. It has also been demonstrated by means of mass spectrometry that the primary phosphorylation of band 3 occurs at Y8 and Y21, while the secondary phosphorylation affects Y359 and Y904. (Blood. 2000;96:1550-1557)

Phosphopeptide analysis

In this chapter we review the various methods available to the experimenter to analyse phosphorylated peptides. The initial steps in such an analysis involve the isolation of the phosphopeptides for analysis, and we outline the various current methods such as immobilised metal affinity chromatography, anti-phosphoamino acid antibodies as well as HPLC (High Pressure Liquid Chromatography) and TLC (Thin Layer Chromatography). The isolated peptides can be analysed by chemical modification followed by Edman degradation or by mass spectrometry (MS). We focus on MS methods and give examples illustrating the selective detection and sequencing of phosphopeptides.

Relation between troponin T concentration and mortality in patients presenting with an acute stroke: observational study

OBJECTIVE

To assess whether a raised serum troponin T concentration would be an independent predictor of death in patients with an acute ischaemic stroke.

DESIGN

Observational study.

SETTING

Auckland Hospital, Auckland, New Zealand.

SUBJECTS

All 181 patients with an acute ischaemic stroke admitted over nine months in 1997-8, from a total of 8057 patients admitted to the acute medical service.

MAIN OUTCOME MEASURES

Blood samples for measuring troponin T concentration were collected 12-72 hours after admission; other variables previously associated with severity of stroke were also recorded and assessed as independent predictors of inpatient mortality.

RESULTS

Troponin T concentration was raised (>0.1 microgram/l) in 17% (30) of patients admitted with an acute ischaemic stroke. Thirty one patients died in hospital (12/30 (40%) patients with a raised troponin T concentration v 19/151 (13%) patients with a normal concentration (relative risk 3.2 (95% confidence 1.7 to 5. 8; P=0.0025)). Of 17 possible predictors of death, assessed in a multivariate stepwise model, only a raised troponin T concentration (P=0.0002), age (P=0.0008), and an altered level of consciousness at presentation (P=0.0074) independently predicted an adverse outcome.

CONCLUSIONS

Serum troponin T concentration at hospital admission is a powerful predictor of mortality in patients admitted with an acute ischaemic stroke.

The ssu locus plays a key role in organosulfur metabolism in Pseudomonas putida S-313

Pseudomonas putida S-313 can utilize a broad range of aromatic sulfonates as sulfur sources for growth in sulfate-free minimal medium. The sulfonates are cleaved monooxygenolytically to yield the corresponding phenols. miniTn5 mutants of strain S-313 which were no longer able to desulfurize arylsulfonates were isolated and were found to carry transposon insertions in the ssuEADCBF operon, which contained genes for an ATP-binding cassette-type transporter (ssuABC), a two-component reduced flavin mononucleotide-dependent monooxygenase (ssuED) closely related to the Escherichia coli alkanesulfonatase, and a protein related to clostridial molybdopterin-binding proteins (ssuF). These mutants were also deficient in growth with a variety of other organosulfur sources, including aromatic and aliphatic sulfate esters, methionine, and aliphatic sulfonates other than the natural sulfonates taurine and cysteate. This pleiotropic phenotype was complemented by the ssu operon, confirming its key role in organosulfur metabolism in this species. Further complementation analysis revealed that the ssuF gene product was required for growth with all of the tested substrates except methionine and that the oxygenase encoded by ssuD was required for growth with sulfonates or methionine. The flavin reductase SsuE was not required for growth with aliphatic sulfonates or methionine but was needed for growth with arylsulfonates, suggesting that an alternative isozyme exists for the former compounds that is not active in transformation of the latter substrates. Aryl sulfate ester utilization was catalyzed by an arylsulfotransferase, and not by an arylsulfatase as in the related species Pseudomonas aeruginosa.

GRP94 (endoplasmin) co-purifies with and is phosphorylated by Golgi apparatus casein kinase

A phosphorylatable protein band of about 94 kDa (as judged by SDS-PAGE) which co-purifies and co-immunoprecipitates with Golgi apparatus casein kinase (G-CK) from rat lactating mammary gland has been shown by mass spectrometric sequence analysis to be identical or very similar to the glucose-regulated protein, GRP94. GRP94 is also readily phosphorylated by G-CK (K(m)=0.2 microM) at seryl sites which are different from the sites affected by casein kinase-2 (CK2) in the same protein. A study with peptide substrates would indicate that the G-CK sites in GRP94 conform to the motif S-R/K-E-X (X being different from D and E) which is not recognized by CK2.

A method for the chemical generation of N-terminal peptide sequence tags for rapid protein identification

We describe a method for generating multiple small sequences from the N terminal of peptides in unseparated protein digests by stepwise thioacetylation and acid cleavage. The mass differences between a series of N-terminally degraded peptides give short sequences of defined length. Such short "sequence tags" together with the mass of the parent peptide can be used to identify the protein in a database. The sequence ladders are generated without the use of chain terminators or sample aliquoting and the degradation reagents are water soluble so that the chemistry can be carried out on peptides immobilized on C-18 reversed-phase supports without any peptide loss due to washing with organic solvents as occurs in Edman type sequencing. The entire procedure can be automated, and we describe a prototype device for the parallel analysis of multiple samples. We demonstrate the effectiveness of this chemical tagging method in a comparison with Edman sequencing, peptide mass fingerprinting, and MS/MS analysis of crude protein fractions obtained from an HPLC separation of the Escherichia coli ribosome complex which consists of 57 proteins. We show that chemical tagging is a viable first-pass high-throughput identification method to be used prior to an in depth MS/MS analysis.

'Failure to rescue' as a measure of quality of hospital care: the limitations of secondary diagnosis coding in English hospital data

Although it is widely recognized that quality of care varies between hospitals, a robust and valid measure of outcome that can be used in comparisons has proven elusive. One measure that has recently been proposed by US researchers is the 'failure to rescue' (FTR) rate. This is based on the assumption that, whereas complications may reflect both patient severity and health care factors, the ability to save patients once complications arise is much more closely related to the quality of health care. We describe an evaluation of FTR in a national sample of English hospitals using hospital episode data. We found that the rate of secondary diagnosis recording in England is about one-tenth that in the United States. The FTR rate would be highly sensitive to variations in the completeness of coding of secondary diagnoses. Unless coding is of uniformly high quality, any attempt to compare severity adjusted outcomes will be potentially unreliable.

Proteome mapping, mass spectrometric sequencing and reverse transcription-PCR for characterization of the sulfate starvation-induced response in Pseudomonas aeruginosa PAO1

A set of proteins induced in Pseudomonas aeruginosa PAO1 during growth in the absence of sulfate was characterized by differential two-dimensional electrophoresis and MS. Thirteen proteins were found to be induced de novo or upregulated in P. aeruginosa grown in a succinate/salts medium with sodium cyclohexylsulfamate as the sole sulfur source. Protein spots excised from the two-dimensional gels were analysed by N-terminal Edman sequencing and MS sequencing (MS/MS) of internal protein fragments. The coding sequences for 11 of these proteins were unambiguously identified in the P. aeruginosa genome sequence. Expression of these genes was investigated by reverse transcription-PCR, which confirmed that repression in the presence of sulfate was acting at a transcriptional level. Three classes of sulfur-regulated proteins were found. The first class (five proteins) were high-affinity periplasmic solute-binding proteins with apparent specificity for sulfate and sulfonates. A second class included enzymes involved in sulfonate and sulfate ester metabolism (three proteins). The remaining three proteins appeared to be part of a more general stress response, and included two antioxidant proteins and a putative lipoprotein. This study demonstrates the power of the proteomics approach for direct correlation of the responses of an organism to an environmental stimulus with the genetic structures responsible for that response, and the application of reverse transcription-PCR significantly increases the conclusions that can be drawn from the proteomic study.