Assimilation of toluene carbon along a bacteria-protist food chain determined by 13C-enrichment of biomarker fatty acids

A food chain consisting of toluene, toluene-degrading Pseudomonas sp. PS+ and a bacterivorous flagellated amoebae Vahlkampfia sp. was established in a batch culture. This culture was amended with [U-13C]toluene and served as a model system to elucidate the flux of carbon in the food chain by quantifying bacterial biovolumes and 13C enrichment of phospholipid fatty acid (PLFA) biomarkers of the bacteria and the heterotrophic protists. Major PLFA detected in the batch co-culture included those derived from Pseudomonas sp. PS+ (16:1omega7c and 18:1omega7c) and Vahlkampfia sp. (20:4omega6c and 20:3omega6c). A numerical model including consumption of toluene by the bacteria and predation of the bacteria by the heterotrophic protists was adjusted to the measured toluene carbon, bacterial carbon and delta13C values of bacterial and protist biomass. Using this model, we estimated that 28+/-7% of the consumed toluene carbon was transformed into bacterial biomass, and 12+/-4% of the predated bacterial carbon was incorporated into heterotrophic protist biomass. Our study showed that the 13C enrichment of PLFA biomarkers coupled to biomass determination via biovolume calculations is a suitable method to trace carbon fluxes in protist-inclusive microbial food chains because it does not require the separation of protist cells from bacterial cells and soil particles.     

Quantitative analysis of protein phosphorylation status and protein kinase activity on microarrays using a novel fluorescent phosphorylation sensor dye

Ultrasensitive detection of minute amounts of phosphorylated proteins and peptides is a key requirement for unraveling many of the most important signal transduction pathways in mammalian systems. Protein microarrays are potentially useful tools for sensitive screening of global protein expression and post-translational modifications, such as phosphorylation. However, the analysis of signaling pathways has been hampered by a lack of reagents capable of conveniently detecting the targets of protein kinases. Historically, phosphorylation detection methods have relied upon either radioisotopes ((gamma-(32)P)ATP(gamma-(33)P)ATP labeling) or phosphoamino acid-selective antibodies. Both of these methods suffer from relatively well-known shortcomings. In this study, a small molecule fluorophore phosphosensor technology is described, referred to as Pro-Q Diamond dye, which is capable of ultrasensitive global detection and quantitation of phosphorylated amino acid residues in peptides and proteins displayed on microarrays. The utility of the fluorescent Pro-Q Diamond phosphosensor dye technology is demonstrated using phosphoproteins and phosphopeptides as well as with protein kinase reactions performed in miniaturized microarray assay format. Instead of applying a phosphoamino acid-selective antibody labeled with a fluorescent or enzymatic tag for detection, a small, fluorescent probe is employed as a universal sensor of phosphorylation status. The detection limit for phosphoproteins on a variety of different commercially available protein array substrates was found to be 312-625 fg, depending upon the number of phosphate residues. Characterization of the enzymatic phosphorylation of immobilized peptide targets with Pro-Q Diamond dye readily permits differentiation between specific and non-specific peptide labeling at picogram to subpicogram levels of detection sensitivity.     

Maximal strength testing in healthy children

Strength training has become an accepted method of conditioning in children. However, there is concern among some observers that maximal strength testing may be inappropriate or potentially injurious to children. The purpose of this study was to evaluate the safety and efficacy of 1 repetition maximum (1RM) strength testing in healthy children. Thirty-two girls and 64 boys between 6.2 and 12.3 years of age (mean age 9.3 +/- 1.6 years) volunteered to participate in this study. All subjects were screened for medical conditions that could worsen during maximal strength testing. Under close supervision by qualified professionals, each subject performed a 1RM test on 1 upper-body (standing chest press or seated chest press) and 1 lower-body (leg press or leg extension) exercise using child-size weight training machines. No injuries occurred during the study period, and the testing protocol was well tolerated by the subjects. No gender differences were found for any upper- or lower-body strength test. These findings demonstrate that healthy children can safely perform 1RM strength tests, provided that appropriate procedures are followed.     

TIP,a T-cell factor identified using high-throughput screening increases survival in a graft-versus-host disease model

A coordinated effort combining bioinformatic tools with high-throughput cell-based screening assays was implemented to identify novel factors involved in T-cell biology. We generated a unique library of cDNAs encoding predicted secreted and transmembrane domain-containing proteins generated by analyzing the Human Genome Sciences cDNA database with a combination of two algorithms that predict signal peptides. Supernatants from mammalian cells transiently transfected with this library were incubated with primary T cells and T-cell lines in several high-throughput assays. Here we describe the discovery of a T cell factor, TIP (T cell immunomodulatory protein), which does not show any homology to proteins with known function. Treatment of primary human and murine T cells with TIP in vitro resulted in the secretion of IFN-gamma, TNF-alpha, and IL-10, whereas in vivo TIP had a protective effect in a mouse acute graft-versus-host disease (GVHD) model. Therefore, combining functional genomics with high-throughput cell-based screening is a valuable and efficient approach to identifying immunomodulatory activities for novel proteins.     

Bacteroides thetaiotaomicron: a dynamic, niche-adapted human symbiont

The coevolution of humans with their intestinal microflora has resulted in cooperative relationships that have shaped the biology and the genomes of these symbiotic partners. Bacteroides thetaiotaomicron is one such bacterial symbiont that is a dominant member of the intestinal microbiota of humans and other mammals. The recent report of the genome sequence of B. thetaiotaomicron is the first reported for an abundant Gram-negative organism of the human colonic microbiota and, as such, provides the first glimpse on a genomic scale of the genetic arsenal used by a Gram-negative symbiont to dominate in this ecosystem. The genome has revealed large expansions of many paralogous groups of genes that encode products essential to the organism's ability to successfully compete in this environment. Most noteable is the organism's abundant machinery for utilizing a large variety of complex polysaccharides as a source of carbon and energy. The proteome also reveals the organism's extensive ability to adapt and regulate expression of its genes in response to the changing ecosystem. These factors, as well as others highlighted below, suggest an incredibly flexible and adaptable organism that is exquisitely equipped to dominate in its challenging and competitive niche.     

Integrin and Cadherin Synergy Regulates Contact Inhibition of Migration and Motile Activity

Integrin receptors play a central role in cell migration through their roles as adhesive receptors for both other cells and extracellular matrix components. In this study, we demonstrate that integrin and cadherin receptors coordinately regulate contact-mediated inhibition of cell migration. In addition to promoting proliferation (Sastry, S., M. Lakonishok, D. Thomas, J. Muschler, and A. Horwitz. 1996. J. Cell Biol. 133:169–184), ectopic expression of the α5 integrin in cultures of primary quail myoblasts promotes a striking contact-mediated inhibition of cell migration. Myoblasts ectopically expressing α5 integrin (α5 myoblasts) move normally when not in contact, but upon contact, they show inhibition of migration and motile activity (i.e., extension and retraction of membrane protrusions). As a consequence, these cells tend to grow in aggregates and do not migrate to close a wound. This phenotype is also seen with ectopic expression of β1 integrin, paxillin, or activated FAK (CD2 FAK) and therefore appears to result from enhanced integrin-mediated signaling. The contact inhibition observed in the α5 myoblasts is mediated by N-cadherin, whose expression is upregulated more than fivefold. Perturbation studies using low calcium conditions, antibody inhibition, and ectopic expression of wild-type and mutant N-cadherins all implicate N-cadherin in the contact inhibition of migration. Ectopic expression of N-cadherin also produces cells that show inhibited migration upon contact; however, they do not show suppressed motile activity, suggesting that integrins and cadherins coordinately regulate motile activity. These observations have potential importance to normal and pathologic processes during embryonic development and tumor metastasis.     

Comparative mapping of the wheat chromosome 5A Vrn-A1 region with rice and its relationship to QTL for flowering time

 The vernalization gene Vrn-A1 on chromosome 5A is the predominant gene determining the spring/winter habit difference in bread wheat. Vrn-A1 was physically mapped using a set of deletion lines which located it to the region of chromosome 5A flanked by deletion breakpoints 0.68 and 0.78. This interval was shown to be homoeologous to a region of rice chromosome 3 that contains the flowering-time QTL Hd-6, previously mapped in a Nipponbare×Kasalath cross, and FLTQ1, a novel QTL identified by analysis of 78 F₃ families derived from a cross of ‘IR20’ב63–83’. Possible relationships between Vrn-A1 and rice QTL are discussed. Analysis of the chromosome 5A deletion lines showed evidence for a second, more proximal flowering-time effect located between deletion breakpoints 0.56 and 0.64. The proximal part of chromosome 5A is homoeologous to rice chromosome 9, on which two QTL were detected in the ‘IR20ב63–83’ cross. The possible relationship between these effects is also discussed. Received: 23 December 1997 / Accepted: 12 January 1998     

Comparison of three methods of acute administration of progesterone on ovarian follicular development and the timing and synchrony of ovulation in Bos indicus heifers

The aim of this study was to induce the formation of a persistent dominant ovarian follicle and to compare the effects of 3 methods of acute administration of P4 on ovarian follicular development and on the timing and synchrony of ovulation. Stage of the estrous cycle was initially synchronized in Bos indicus heifers with a norgestomet implants (3 mg) for 10 d and with an analogue of PGF2 alpha (15 mg) on the first and last day of norgestomet treatment. Eight days after removal of the implants, heifers were randomly assigned to 4 groups. All heifers received a norgestomet implant (Day 0), which was removed 17 d later (Day 17); PGF2 alpha was administered on Days 0 and 4. Heifers in the control group (n = 5) received no other treatment. On Day 10 heifers in Group P4C (n = 5) were treated with a CIDR for 24 h; heifers in Group P4O (n = 5) were administered 100 mg i.m. of P4 in oil, while heifers in Group P4S (n = 5) were administered 100 mg i.m. of P4 in saline/alcohol. Data were analyzed using bootstrap estimates of location (mean) and spread (standard deviation; SD). Compared with the control heifers, day of emergence of the ovulatory follicle was delayed, and age and duration of dominance of the ovulatory follicle were reduced in the P4C and P4O heifers (P < 0.05) but not in the P4S heifers (P > 0.05). In all groups treated with P4 both the mean and variability (SD) in the timing of ovulation did not differ with that of the control group (P > 0.05) but there was less variability in the day of emergence, age, duration of dominance and diameter of the ovulatory follicle than in the control group (P < 0.05). Delayed timing and reduced synchrony (SD) of ovulation and greater age of the ovulatory follicle (P < 0.05) occurred in P4S heifers than in P4C heifers. We conclude that administration of 100 mg of P4 in oil is as effective as treatment with a CIDR for synchronizing emergence and ovulation of a newly recruited dominant follicle. However, reduced synchrony of ovulation, greater age of the ovulatory follicle and delayed timing of ovulation occurred following administration 100 mg of P4 in saline/alcohol compared with the CIDR device.     

Optimization of transient gene expression in mammalian cells and potential for scale-up using flow electroporation

The goals of this study were to identify mammalian cell lines which could be efficiently transiently-transfected and scaled-up for protein production. The transfection efficiencies of eight cell lines (NSO, NSO-TAg, CV-1, COS-7, CHO, CHO-TAg, HEK 293, and 293-EBNA) were measured using electroporation for DNA delivery and green fluorescent protein (Evans, 1996) as the reporter gene. In addition, we have evaluated the effects of stable expression of viral proteins, cell cycle manipulation, and butyrate post-treatment in small scale experiments. The cell lines varied widely in their GFP transfection efficiencies. Stable expression of simian virus 40 large T-antigen or Epstein Barr nuclear antigen failed to significantly increase transfection efficiency above that seen in the parental lines. Aphidicolin (a DNA polymerase inhibitor), which blocked cells from S or G2/M, brought about an increase in transfection efficiency in two cell lines. The primary effect of butyrate (a histone deacetylase inhibitor) post-treatment was an increased intensity of the fluorescent signal of green fluorescent protein, as measured by flow cytometry (1.0 to 4.2-fold, depending on the cell line). The combined use of aphidicolin pretreatment followed by butyrate treatment post- electroporation yielded increases in fluorescence intensities ranging from 0.9 to 6.8-fold. Based on their high transfection efficiencies in small scale experiments, rapid growth, and ability to grow in suspension culture, CHO, CHO-TAg, and 293-EBNA were selected to assess the feasibility of using flow electroporation for large-scale transfections. Using secreted placental alkaline phosphatase as a reporter, 293-EBNA cells produced the highest protein levels in both the presence and absence of butyrate. These data indicate that flow electroporation provides an efficient method of DNA delivery into large numbers of cells for mammalian protein production. This revised version was published online in August 2006 with corrections to the Cover Date.     

Should inhaled anticholinergics be added to β2 agonists for treating acute childhood and adolescent asthma? A systematic review

Objectives To estimate the therapeutic and adverse effects of addition of inhaled anticholinergics to β₂ agonists in acute asthma in children and adolescents.Design Systematic review of randomised controlled trials of children and adolescents taking β₂ agonists for acute asthma with or without the addition of inhaled anticholinergics.Main outcome measures Hospital admission, pulmonary function tests, number of nebulised treatments, relapse, and adverse effects.Results Of 37 identified trials, 10 were relevant and six of these were of high quality. The addition of a single dose of anticholinergic to β₂ agonist did not reduce hospital admission (relative risk 0.93, 95% confidence interval 0.65 to 1.32). However, significant group differences in lung function supporting the combination treatment were observed 60 minutes (standardised mean difference −0.57, −0.93 to −0.21) and 120 minutes (−0.53, −0.90 to −0.17) after the dose of anticholinergic. In contrast, the addition of multiple doses of anticholinergics to β₂ agonists, mainly in children and adolescents with severe exacerbations, reduced the risk of hospital admission by 30% (relative risk 0.72, 0.53 to 0.99). Eleven (95% confidence interval 5 to 250) children would need to be treated to avoid one admission. A parallel improvement in lung function (standardised mean difference −0.66, −0.95 to −0.37) was noted 60 minutes after the last combined inhalation. In the single study where anticholinergics were systematically added to every β₂ agonist inhalation, irrespective of asthma severity, no group differences were observed for the few available outcomes. There was no increase in the amount of nausea, vomiting, or tremor in patients treated with anticholinergics.Conclusions Adding multiple doses of anticholinergics to β₂ agonists seems safe, improves lung function, and may avoid hospital admission in 1 of 11 such treated patients. Although multiple doses should be preferred to single doses of anticholinergics, the available evidence only supports their use in school aged children and adolescents with severe asthma exacerbation.

Key messages

• The addition of multiple doses of anticholinergics to β₂ agonist inhalations seems indicated in the initial management of children and adolescents with severe exacerbations of asthma (⩽55% of predicted FEV₁)
• For the larger group of children and adolescents with mild to moderate asthma exacerbations, there is no apparent benefit from adding a dose of anticholinergics to β₂ agonists
• Little evidence exists to support the systematic addition of anticholinergics to every β₂ agonist inhalation, irrespective of patients’ disease severity