Discovering the mechanism of action of novel antibacterial agents through transcriptional profiling of conditional mutants.

We present a new strategy for predicting novel antibiotic mechanisms of action based on the analysis of whole-genome microarray data. We first built up a reference compendium of Bacillus subtilis expression profiles induced by 14 different antibiotics. This data set was expanded by adding expression profiles from mutants that showed downregulation of genes coding for proven or emerging antibacterial targets. Here, we investigate conditional mutants underexpressing ileS, pheST, fabF, and accDA, each of which is essential for growth. Our proof-of-principle analyses reveal that conditional mutants can be used to mimic chemical inhibition of the corresponding gene products. Moreover, we show that a statistical data analysis combined with thorough pathway and regulon analysis can pinpoint the molecular target of uncharacterized antibiotics. We apply this approach to two novel antibiotics: a recently published phenyl-thiazolylurea derivative and the natural product moiramide B. Our results support recent findings suggesting that the phenyl-thiazolylurea derivative is a novel phenylalanyl-tRNA synthetase inhibitor. Finally, we propose a completely novel antibiotic mechanism of action for moiramide B based on inhibition of the bacterial acetyl coenzyme A carboxylase.

Role of two different glyceraldehyde-3-phosphate dehydrogenases in controlling the reversible Embden-Meyerhof-Parnas pathway in Thermoproteus tenax: regulation on protein and transcript level.

The hyperthermophilic archaeum Thermoproteus tenax uses a variant of the Embden-Meyerhof-Parnas (EMP) pathway as the main route for carbohydrate metabolism. This variant is characterized by a reversible nonallosteric PPi-dependent phosphofructokinase and two glyceraldehyde-3-phosphate dehydrogenases differing in cosubstrate specificity, phosphate dependence, and allosteric behavior. Although the nonphosphorylating NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPN; E.C. 1.2.1.8) fulfills exclusively catabolic purposes, the phosphorylating NADP+-dependent glyceraldehyde-3-phosphate dehydrogenase (NADP+-GAPDH; E.C. 1.2.1.13) exhibits anabolic features. The gene encoding the NADP+-GAPDH was cloned, sequenced, and expressed in Escherichia coli. The deduced protein sequence displayed 47%-53% sequence identity to archaeal phosphorylating GAPDHs. The kinetic parameters of the NADP+-GAPDH showed a clear preference for the reductive reaction with a 5-fold-higher specific activity in the reductive reaction as compared to the oxidative reaction and a 20-fold-lower Km for 1,3-bisphosphoglycerate as compared to glyceraldehyde-3-phosphate. Contrary to GAPN, the enzyme is not allosterically regulated. The coding gene overlaps by 1 bp with a preceding open reading frame coding for 3-phosphoglycerate kinase (PGK; E.C. 2.7.2.3). Northern analyses identified mono- and bicistronic messages of both genes in an equimolar ratio. Transcript levels and specific activity of NADP+-GAPDH and PGK were 3- to 4-fold higher under autotrophic conditions as compared to heterotrophic conditions, whereas transcript abundance and specific activity of GAPN remained constant in autotrophically and heterotrophically grown cells. The different regulation of the two counteracting glyceraldehyde-3-phosphate dehydrogenases is discussed with respect to the flux control of the T. tenax-specific EMP variant.

Crystallization and preliminary X-ray diffraction analysis of the NAD-dependent non--phosphorylating GAPDH of the hyperthermophilic archaeon Thermoproteus tenax.

Recombinant non-phosphorylating NAD(+)-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPN) of the hyperthermophilic crenarchaeote Thermoproteus tenax has been overexpressed, purified and crystallized using the hanging-drop vapour-diffusion technique. Crystals of different habits were obtained from several precipitant solutions (salts and polyethylene glycols). Preliminary X-ray analysis was performed with crystals grown in ammonium formate, which belonged to the primitive hexagonal space group P622, and had unit-cell parameters a = b = 184.8, c = 133.0 A, gamma = 120 degrees. Assuming a molecular weight of 55 kDa, a Matthews parameter of 3.3 A(3) Da(-1) is calculated assuming two molecules per asymmetric unit. The diffraction limit of these crystals is 2.5 A resolution.

[Can detection of cancer cells in bone marrow and peripheral blood be used in diagnosis and patient monitoring?]. / Kan detektion af karcinomceller i knoglemarv og perifert blod benyttes til diagnostik og som recidivmarkør?

The prognosis of patients with carcinomas is determined by whether there is dissemination of the primary tumour at the time of diagnosis. A substantial number of patients develop recurrent carcinoma, even though there were no clinical signs of dissemination at the time of primary surgery. Standard methods of tumor staging fail to identify those patients, who are at risk of recurrent disease. Recently several studies have demonstrated that the presence of occult metastatic carcinoma cells in the bone marrow increases the risk of recurrence. This risk is independent of traditional tumour staging, although the findings do not necessarily indicate later development of solid metastases. This review outlines the range of current applications of immunological and molecular methods for detecting disseminated carcinoma cells in blood and bone marrow aspirations, and discusses the applicability and significance of the findings.

[New prognostic markers in colorectal cancer]. / Nye prognostiske markører ved kolorektal cancer.

The majority of patients diagnosed as having colorectal cancer do not survive five years, although 70%-80% undergo curative surgery. Only a minority of the patients receive additional adjuvant chemo-, radio- and/or immunotherapy, which has proven its efficiency in a minor part of patients with Dukes C disease. Therefore, adjuvant therapy has only an insignificant impact on overall survival improvement. The present treatment of patients with colorectal cancer is far from sufficient, and this has led to considerations of how to optimize both surgical and adjuvant medical treatment strategy. Current biotechnological research in tumour biology has led to the development of several new treatment modalities, and within few years some of these will be tested clinically. It cannot be expected that all modalities may prove equally efficient in all patients. Furthermore, half the operated patients are cured by surgery alone, and these should not receive additional adjuvant treatment. Therefore, considerations are required of how to implement new modalities, and of selection of patients who are expected to benefit from a specific modality or a combination of modalities. It is suggested, that new biological markers of development, growth and dissemination of colorectal cancer can be used to predict prognosis either alone or in various combinations, and as selection markers to discriminate between patients who only need surgery and patients who may need adjuvant treatment.

NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase from Thermoproteus tenax. The first identified archaeal member of the aldehyde dehydrogenase superfamily is a glycolytic enzyme with unusual regulatory properties.

The hyperthermophilic archaeum Thermoproteus tenax possesses two glyceraldehyde-3-phosphate dehydrogenases differing in cosubstrate specificity and phosphate dependence of the catalyzed reaction. NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase catalyzes the phosphate-independent irreversible oxidation of D-glyceraldehyde 3-phosphate to 3-phosphoglycerate. The coding gene was cloned, sequenced, and expressed in Escherichia coli. Sequence comparisons showed no similarity to phosphorylating glyceraldehyde-3-phosphate dehydrogenases but revealed a relationship to aldehyde dehydrogenases, with the highest similarity to the subgroup of nonphosphorylating glyceraldehyde-3-phosphate dehydrogenases. The activity of the enzyme is affected by a series of metabolites. All effectors tested influence the affinity of the enzyme for its cosubstrate NAD+. Whereas NADP(H), NADH, and ATP reduce the affinity for the cosubstrate, AMP, ADP, glucose 1-phosphate, and fructose 6-phosphate increase the affinity for NAD+. Additionally, most of the effectors investigated induce cooperativity of NAD+ binding. The irreversible catabolic oxidation of glyceraldehyde 3-phosphate, the control of the enzyme by energy charge of the cell, and the regulation by intermediates of glycolysis and glucan degradation identify the NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase as an integral constituent of glycolysis in T. tenax. Its regulatory properties substitute for those lacking in the reversible nonregulated pyrophosphate-dependent phosphofructokinase in this variant of the Embden-Meyerhof-Parnas pathway.

That was a good meeting!

Good meetings are rare in many organizations. The purposes of meetings include sharing information, decision making, problem solving, education, planning, evaluation, and peer support. The structure of meetings flows from the basic function(s) of the group. Consideration is given to membership, degree of formality, limits of authority, and responsibility. Suggestions for successful meetings focus on establishing an agenda, sticking to the time schedule, appropriately using visual aids, and doing necessary post-meeting follow-up. Responsible and meaningful participation in the group process is an essential aspect of meeting effectiveness and efficiency. When all the elements are managed skillfully, the meeting can be GREAT.

Chemosensitivity of human small cell carcinoma of the lung detected by flow cytometric DNA analysis of drug-induced cell cycle perturbations in vitro.

A method based on detection of drug-induced cell cycle perturbation by flow cytometric DNA analysis has previously been described in Ehrlich ascites tumors as a way to estimate chemosensitivity. The method is extended to test human small-cell carcinoma of the lung. Three tumors with different sensitivities to melphalan in nude mice were used. Tumors were disaggregated by a combined mechanical and enzymatic method and thereafter have incubated with different doses of melphalan. After incubation the cells were plated in vitro on agar, and drug induced cell cycle changes were monitored by flow cytometric DNA analysis. Melphalan produced a dose-related S phase accumulation in the two sensitive tumors, whereas no changes in the cell cycle distribution were found in the resistant tumor. The size of S phase accumulation correlated to the chemosensitivity in vivo. For low concentrations of melphalan, the S phase accumulation was accompanied by G2 + M accumulation. The results indicate that the method may be extended to sensitivity testing of human solid tumors, including screening for new agents.

A joint practice council in action.

A nurse/physician joint practice council, patterned after the activities and recommendations of the National Joint Practice Commission, was developed at a community hospital to provide a forum for nurse-physician dialogue regarding roles and practice issues. Clear objectives, good communications, utilization of resource persons, and equal physician and nurse representation and critical elements of the council's success. In operation, the council's focus is evolving from conflict resolution to a medium for planning and implementing change.