Protein phosphorylation: technologies for the identification of phosphoamino acids

Protein phosphorylation plays a central role in many biological and biomedical phenomena. In this review, while a brief overview of the occurrence and function of protein phosphorylation is given, the primary focus is on studies related to the detection and analysis of phosphorylation both in vivo and in vitro. We focus on phosphorylation of serine, threonine and tyrosine, the most commonly phosphorylated amino acids in eukaryotes. Technologies such as radiolabelling, antibody recognition, chromatographic methods (HPLC, TLC), electrophoresis, Edman sequencing and mass spectrometry are reviewed. We consider the speed, simplicity and sensitivity of tools for detection and identification of protein phosphorylation, as well as quantitation and site characterisation. The limitations of currently available methods are summarised.     

Is insurance for children enough? The link between parents'' and children''s health care use revisited

The gutless hydrothermal tubeworm Riftia pachyptila Jones relies mainly on its chemoautotrophic bacterial symbionts to supply nutrients in the form of secreted organic compounds resulting from fixation and incorporation of CO2. In this study, symbionts were purified, tested for viability, and incubated in the presence of labeled CO2. We demonstrated that purified symbionts can be used as a viable alternative to experiments with bacterial cultures. Several organic acids, sugars, and amino acids were labeled, but their fraction of the total label stayed generally constant during the incubation times used. However, increasing fractions of succinate and, to a lesser degree, glutamate were excreted into the incubation medium, indicating that these are probably the main carbon-containing compounds transferred from the symbionts to the host. Glutamate could also account for the transport of nitrogen from the symbionts to the host.     

Double blind, randomised, placebo controlled study of oral vancomycin in prevention of necrotising enterocolitis in preterm, very low birthweight infants

AIMS: To evaluate the effectiveness of oral vancomycin in the prophylaxis of necrotising enterocolitis in preterm, very low birthweight infants. METHODS: A prospective, double blind, randomised, placebo controlled study in a tertiary referral centre of a university teaching hospital was conducted on 140 very low birthweight infants consecutively admitted to the neonatal unit. The babies were randomly allocated to receive oral vancomycin (15 mg/kg every 8 hours for 7 days) or an equivalent volume of placebo solution. Prophylaxis was started 24 hours before the start of oral feeds. All suspected cases of necrotising enterocolitis were investigated with a full sepsis screen and serial abdominal radiographs. Necrotising enterocolitis was diagnosed and staged according to modified Bell's criteria. RESULTS: Nine of 71 infants receiving oral vancomycin and 19 of 69 infants receiving the placebo solution developed necrotising enterocolitis (p = 0.035). Infants with necrotising enterocolitis were associated with a significant increase in mortality (p = 0.026) and longer duration of hospital stay (p = 0.002). CONCLUSIONS: Prophylactic oral vancomycin conferred protection against necrotising enterocolitis in preterm, very low birthweight infants and was associated with a 50% reduction in the incidence. However, widespread implementation of this preventive measure is not recommended, as it would only be effective in necrotising enterocolitis caused by Gram positive organisms and could increase the danger of the emergence of vancomycin resistant or dependent organisms. Its use should be restricted to a high prevalence nursery for a short and well defined period in a selected group of high risk patients.     

Aorto-iliac thrombosis in a foal

A six-day-old Missouri foxtrotter colt was examined because it had had diarrhoea since it was 24 hours old. A diagnosis of colitis, septicaemia, and disruption of the arterial blood flow to the pelvic limbs was made on the basis of clinical and laboratory findings. Despite intensive medical therapy, the foal died 13 hours after being examined. Postmortem examination revealed diffuse fibrinous enteritis with lymphoid necrosis, multifocal fibrinonecrotic typhlocolitis, disseminated intravascular coagulation, and a large occluding thrombus at the aortic termination. The results of bacteriological culturing supported the diagnosis of septicaemia leading to activation of the clotting cascade, disseminated intravascular coagulation, aorto-iliac thrombosis and infarction of the pelvic limbs.     

Synthesis and characterization of a new 5-thiol-protected deoxyuridine phosphoramidite for site-specific modification of DNA

A new nucleotide analogue was developed for site-specific incorporation of a reactive thiol group into DNA. This creates a unique site for the post-synthetic modification of that nucleotide with a variety of molecular tags, such as photo-cross-linkers and fluorescent or spin-label moieties. 5'-O-(4,4'-Dimethoxytrityl)-5-[S-(2,4-dinitrophenyl)thio]-2'-deoxyuridin e 3'-O-(2-cyanoethyl N,N'-diisopropylphosphoramidite) was synthesized and incorporated at internal positions in several oligonucleotides using automated DNA synthesis and standard phosphoramidite chemistry. The coupling yield of the analogue was comparable to the coupling yield for a standard phosphoramidite, and no significant differences were observed in the overall yields of the dinitrophenyl-labeled oligonucleotides compared to the corresponding unmodified oligonucleotides. Characterization of the dinitrophenyl-modified oligonucleotides included enzymatic degradation, HPLC chromatography, and gel electrophoresis. Deprotection of the mercaptan group with beta-mercaptoethanol yielded an oligonucleotide containing 5-mercaptodeoxyuridine which was then selectively modified, without purification, by reaction with 5-(iodoacetamido)fluorescein. Incorporation of the dinitrophenyl-modified oligonucleotide into double-stranded DNA was achieved using the polymerase chain reaction. CHaracterization of the dinitrophenyl-labeled product by immunodetection with anti-dinitrophenyl antibodies confirmed the stability of the protecting group to the thermocycling and thus established the use of this thiol-protected mercaptodeoxyuridine phosphoramidite for preparation of site-specifically modified DNA.     

Increasing breast and cervical cancer screening in low-income women

Active cytomegalovirus (CMV) retinitis in patients with acquired immunodeficiency syndrome (AIDS) was treated with an intraocular sustained-release ganciclovir implant. A total number of 19 implants were performed in 15 eyes of 9 AIDS patients. The intraocular sustained-release ganciclovir was effective in preventing reactivation of CMV retinitis in 15 of the 19 implants, ineffective in 3, and undetermined in 1. All ineffective cases had been resistant to ganciclovir therapy before the implants. Vision after the therapy was maintained at better than 0.5 except for one eye. There were no serious ocular complications caused by the therapy. Among 5 patients with unilateral CMV retinitis, 2 unaffected eyes developed CMV retinitis during this therapy. In addition, another patient developed presumed CMV infection in other systemic organs. Based on these data, the intraocular sustained-release ganciclovir implant was considered to be useful for the treatment of CMV retinitis in AIDS.     

Nonradioactive Northern blotting with biotinylated and digoxigenin-labeled RNA probes

The application of nonradioactive RNA probes for Northern blotting offers the advantage of a rapid turn-around time for results without the loss of sensitivity for target mRNA detection. However, a problem that has impeded the widespread use of nonradioactive RNA probes for use in Northern blotting is the difficulty in stripping these probes from nylon membranes after hybridization. In this report we describe two protocols for stripping digoxigenin (Dig)-labeled RNA probes from nylon membranes. One protocol utilizes a phosphate-buffered formamide stripping solution to remove nonchemically modified (regular) RNA probes while the other method utilizes strippable probes that were produced with a chemically modified nucleotide (CTP) and removed by a specific stripping solution. This latter method was developed by Ambion Inc. and is called Strip-EZ. We also describe a protocol for the detection of two separate rat mRNAs using both biotin and digoxigenin-labeled RNA probes that does not require stripping the membrane after hybridization. Finally, we describe the use of another new labeling technology, called Chem-Link, that quickly and conveniently labels RNA for use in Northern blotting.     

Water sorption and diffusion in starch/polyolefin blends

The kinetics of water sorption by starch filled polyolefins has been investigated using blends of commercial starch masterbatch with low density polyethylene (LDPE), high density PE (HDPE), and copolymers of ethylene with methyl acrylate (EMA), ethyl (EEA), AND n-butyl acrylate (EBA). Transient state diffusion coefficients (D) of water in the blends were determined using Fickian analysis of the initial stages of the sorption isotherms. Measured D values were several orders of magnitude lower than values reported for either pure starch of LIDPE by various investigators. Resin effects on D were on the order D_HDPE < D_LDPE ? D_EBA < D_EEA < D_EMA. The resin effects diminished as the starch content increased. The lower magnitude of D in the blends relative to pure LDPE was attributed to the sorption of water by the dry starch particles, in a manner similar to dual-mode sorption in glassy polymers. Copolymer effects were consistent with reduction in crystallinity caused by the comonomers. The dependence of the diffusion coefficient on starch content was not described by mixing models of heterogeneous systems of percolation theory.     

Carbohydrate, enzyme, and hematology dynamics in newborn calves.

The dynamics of 25 blood constituents in newborn calves were monitored. Eight calves were immediately removed from dams following birth. Jugular blood samples for carbohydrate determinations were taken at birth (within 2 min), 1, 3, 6, 8, 12, 18, and 24 h and every 12 h until 144 h of age. Samples for blood chemistries were taken at birth, 1, 3, 6, 12, 24, 48, 72, 120, and 144 h. Colostrum was first fed at either 1 h (group 1) or 12 h (group 2) of age. At birth, plasma glucose concentrations were lower than the plasma fructose in both groups. Plasma glucose increased substantially from birth to 24 h, whereas fructose decreased to nondetectable concentrations by 18 h. Increases in insulin were associated with time of first feeding. Serum cortisol decreased rapidly from birth to 3 h for group 1 and at 15 h for group 2. Colostrum intake resulted in increased activities of serum alkaline phosphatase, gamma-glutamyl transpeptidase, and glutamic oxaloacetic transaminase at 6 h for group 1 and at 15 h for group 2. Activities of these enzymes decreased to "normal" values after 24-h samplings for group 1. Serum glutamic pyruvic transaminase and lactate dehydrogenase increased gradually in activity over the first 24 h in both groups and decreased after 24 h for group 1. Triglycerides and cholesterol increased from birth to 24 h in both groups and continued to increase in group 1 until 144 h. Creatinine decreased and bilirubin increased from birth to 24 h in both groups. These changes indicated that the newborn calves were undergoing many adaptive changes in relation to either maintenance of homeostasis or nutrient intake.     

Dynamic Multiple-Fault Diagnosis With Imperfect Tests

In this paper, we consider a model for the dynamic multiple-fault diagnosis (DMFD) problem arising in online monitoring of complex systems and present a solution. This problem involves real-time inference of the most likely set of faults and their time-evolution based on blocks of unreliable test outcomes over time. In the DMFD problem, there is a finite set of mutually independent fault states, and a finite set of sensors (tests) is used to monitor their status. We model the dependence of test outcomes on the fault states via the traditional D-matrix (fault dictionary). The tests are imperfect in the sense that they can have missed detections, false alarms, or may be available asynchronously. Based on the imperfect observations over time, the problem is to identify the most likely evolution of fault states over time. The DMFD problem is an intractable NP-hard combinatorial optimization problem. Consequently, we decompose the DMFD problem into a series of decoupled subproblems, one for each sample epoch. For a single-epoch MFD, we develop a fast and high-quality deterministic simulated annealing method. Based on the sequential inferences, a local search-and-update scheme is applied to further improve the solution. Finally, we discuss how the method can be extended to dependent faults.