Biochemical characterization of the initial steps of the Kennedy pathway in Trypanosoma brucei:the ethanolamine and choline kinases

Note related output below contains correction of this paper.Ethanolamine and choline are major components of the trypanosome membrane phospholipids, in the form of GPEtn (glycero-phosphoethanolamine) and GPCho (glycerophosphocholine). Ethanolamine is also found as an integral component of the GPI (glycosylpliosphatidylinositol) anchor that is required for membrane attachment of cell-surface proteins, most notably the variant-surface glycoproteins. The de novo synthesis of GPEtn and GPCho starts with the generation of phosphoethanolamine and phosphocholine by ethanolamine and choline kinases via the Kennedy pathway. Database mining revealed two putative C/EKs (choline/ethanolamine kinases) in the Trypanosoma brucei genome, which were cloned, overexpressed, purified and characterized. TbEK 1 (T brucei ethanolamine kinase 1) was shown to be catalytically active as an ethanolamine-specific kinase, i.e. it had no choline kinase activity. The K values for ethanolamine and ATP were found to be 18.4 +/- 0.9 and 219 29 mu M respectively. TbC/EK2 (T brucei choline/ethanolamine kinase 2), on the other hand, was found to be able to phosphorylate both ethanolamine and choline, even though choline was the preferred substrate, with a K-m 80 times lower than that of ethanolamine. The K. values for choline, ethanolamine and ATP were 31.4 +/- 2.6 mu M, 2.56 +/- 0.31 mu M and 20.6 +/- 1.96 mu M respectively. Further substrate specificity analysis revealed that both TbEK1 and TbC/EK2 were able to tolerate various modifications at the amino group, with the exception of a quaternary amine for TbEK1 (choline) and a primary amine for TbC/EK2 (ethanolamine). Both enzymes recognized analogues with substituents oil C-2, but substitutions oil C-1 and elongations of the carbon chain were not well tolerated.Publisher PDFPeer reviewe

Design with a Positive Lens: An affirmative approach to designing information and organizations

Design forms one critical paradigmatic view that pervades organizational studies, management, and information systems research. Building on the discussions in the First Working Conference on Designing Information and Organizations with a Positive Lens, we chart the potential contribution of positive design to the shaping of organizations, work processes, artifacts, communication networks, and information technologies. The figure of speech "Design with a Positive Lens," or in short, "Positive Design," connotes here a distinctive perspective on design that is less focused on the detection of errors associated with gaining control and more concerned with human-centered design associated with the shaping of hopeful organizations and a thriving future. The paper examines how positive design can contribute to the design of information systems and organizations as related to five broad-scale areas: design of high performance work processes; positive design methods and techniques: cooperation and collaboration across boundaries to promote positive change; positive organizational design, and design science and practice. In this paper we aspire to promote the emerging cross-disciplinary discourse between scholars and designers that will foster positive organizational and technological design

Does anxiety moderate the effectiveness of mirtazapine in patients with treatment-resistant depression? A secondary analysis of the MIR trial

BACKGROUND: There is a lack of evidence to guide treatment of comorbid depression and anxiety. Preliminary evidence suggests mirtazapine may be effective in treating patients with both depression and anxiety symptoms. METHODS: We undertook a secondary analysis of mirtazapine (MIR): a placebo-controlled trial of the addition of mirtazapine to a selective serotonin reuptake inhibitor or serotonin-norepinephrine reuptake inhibitor in treatment-resistant depression (TRD) in primary care. We subdivided participants into three groups by baseline generalized anxiety disorder score (GAD-7): severe (GAD-7 ⩾ 16), moderate (GAD-7 = 11-15), no/mild (GAD-7 ⩽ 10). We used linear regression including likelihood-ratio testing of interaction terms to assess how baseline anxiety altered the response of participants to mirtazapine as measured by 12-week GAD-7 and Beck Depression Inventory II (BDI-II) scores. RESULTS: Baseline generalized anxiety moderated mirtazapine's effect as measured by GAD-7 (p = 0.041) and BDI-II (p = 0.088) at 12 weeks. Participants with severe generalized anxiety receiving mirtazapine had lower 12-week GAD-7 score (adjusted difference between means (ADM) -2.82, 95% confidence interval (CI) -0.69 to -4.95) and larger decreases in BDI-II score (ADM -6.36, 95% CI -1.60 to -10.84) than placebo. Conversely, there was no anxiolytic benefit (ADM 0.28, 95% CI -1.05 to 1.60) or antidepressant benefit (ADM -0.17, 95% CI -3.02 to 2.68) compared with placebo in those with no/mild generalized anxiety. CONCLUSIONS: These findings extend the evidence for the effectiveness of mirtazapine to reduce generalized anxiety in TRD in primary care. These results may inform targeted prescribing in depression based on concurrent anxiety symptoms, although these conclusions are constrained by the post-hoc nature of this analysis

Matching experiments across species using expression values and textual information

Motivation: With the vast increase in the number of gene expression datasets deposited in public databases, novel techniques are required to analyze and mine this wealth of data. Similar to the way BLAST enables cross-species comparison of sequence data, tools that enable cross-species expression comparison will allow us to better utilize these datasets: cross-species expression comparison enables us to address questions in evolution and development, and further allows the identification of disease-related genes and pathways that play similar roles in humans and model organisms. Unlike sequence, which is static, expression data changes over time and under different conditions. Thus, a prerequisite for performing cross-species analysis is the ability to match experiments across species

Annotation of the modular polyketide synthase and nonribosomal peptide synthetase gene clusters in the genome of Streptomyces tsukubaensis NRRL18488

et al.The high G+C content and large genome size make the sequencing and assembly of Streptomyces genomes more difficult than for other bacteria. Many pharmaceutically important natural products are synthesized by modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). The analysis of such gene clusters is difficult if the genome sequence is not of the highest quality, because clusters can be distributed over several contigs, and sequencing errors can introduce apparent frameshifts into the large PKS and NRPS proteins. An additional problem is that the modular nature of the clusters results in the presence of imperfect repeats, which may cause assembly errors. The genome sequence of Streptomyces tsukubaensis NRRL18488 was scanned for potential PKS and NRPS modular clusters. A phylogenetic approach was used to identify multiple contigs belonging to the same cluster. Four PKS clusters and six NRPS clusters were identified. Contigs containing cluster sequences were analyzed in detail by using the ClustScan program, which suggested the order and orientation of the contigs. The sequencing of the appropriate PCR products confirmed the ordering and allowed the correction of apparent frameshifts resulting from sequencing errors. The product chemistry of such correctly assembled clusters could also be predicted. The analysis of one PKS cluster showed that it should produce a bafilomycin-like compound, and reverse transcription (RT)-PCR was used to show that the cluster was transcribed. © 2012, American Society for Microbiology.We thank the Government of Slovenia, Ministry of Higher Education, Science and Technology (Slovenian Research Agency [ARRS]), for the award of grant no. J4-9331 and L4-2188 to H.P. We also thank the Ministry of the Economy, the JAPTI Agency, and the European Social Fund (contract no. 102/2008) for the funds awarded for the employment of G.K. This work was also funded by a cooperation grant of the German Academic Exchange Service (DAAD) and the Ministry of Science, Education, and Sports, Republic of Croatia (to J.C. and D.H.), and by grant 09/5 (to D.H.) from the Croatian Science Foundation.Peer Reviewe

Non-Equilibrium Quasiclassical Theory for Josephson Structures

We present a non-equilibrium quasiclassical formalism suitable for studying linear response ac properties of Josephson junctions. The non-equilibrium self-consistency equations are satisfied, to very good accuracy, already in zeroth iteration. We use the formalism to study ac Josephson effect in a ballistic superconducting point contact. The real and imaginary parts of the ac linear conductance are calculated both analytically (at low frequencies) and numerically (at arbitrary frequency). They show strong temperature, frequency, and phase dependence. Many anomalous properties appear near phi = pi. We ascribe them to the presence of zero energy bound states.Comment: 11 pages, 9 figures, Final version to appear in PR

Early Mutants of Polyoma Virus (dl8 and dl23) with Altered Transformation Properties: Is Polyoma Virus Middle T Antigen a Transforming Gene Product?

The questions raised by Dulbecco (1975)—“Is transformation the result of provirus integration … or is it the consequence of the expression of genes present in the provirus?”—have not yet been satisfactorily answered. However, several lines of evidence from recent experiments on many different tumor viruses, as presented in this volume, strongly suggest that viral gene expression is required for transformation, the best evidence still arising from studies on the avian RNA tumor viruses (see Vogt 1977; Hanafusa 1977). With regard to polyoma virus, evidence also exists which indicates that viral gene expression is needed. Studies by Seif and Cuzin (1977) on transformation induced in rat cells by temperature-sensitive tsA mutants of polyoma virus suggest that the transformed phenotype is a complex interplay between various types of controls, including expression of a virus-coded protein, as well as cellular changes induced by the virus or selected for during growth in culture. Data..