Evidence for differential binding of isoniazid by Mycobacterium tuberculosis KatG and the isoniazid-resistant mutant KatG(S315T)

Isoniazid is a mainstay of antibiotic therapy for the treatment of tuberculosis, but its molecular mechanism of action is unclear. Previous investigators have hypothesized that isoniazid is a prodrug that requires in vivo activation by KatG, the catalase-peroxidase of Mycobacterium tuberculosis, and that resistance to isoniazid strongly correlates with deletions or point mutations in KatG. One such mutation, KatG(S315T), is found in approximately 50% of clinical isolates exhibiting isoniazid resistance. In this work, 1H nuclear magnetic resonance T1 relaxation measurements indicate that KatG and KatG(S315T) each bind isoniazid at a position approximately 12 A from the active site heme iron. Electron paramagnetic resonance spectroscopy revealed heterogeneous populations of high-spin ferric heme in both wild-type KatG and KatG(S315T) with the ratios of each species differing between the two enzymes. Small changes in the proportions of these high-spin species upon addition of isoniazid support the finding that isoniazid binds near the heme periphery of both enzymes. Titration of wild-type KatG with isoniazid resulted in the appearance of a "type I" substrate-induced difference spectrum analogous to those seen upon substrate binding to the cytochromes P450. The difference spectrum may result from an isoniazid-induced change in a portion of the KatG heme iron from 6- to 5-coordinate. Titration of KatG(S315T) with isoniazid failed to produce a measurable difference spectrum indicating an altered active site configuration. These results suggest that KatG(S315T) confers resistance to isoniazid through subtle changes in the isoniazid binding site.     

A framework for traversing dense annotation lattices

Pattern matching, or querying, over annotations is a general purpose paradigm for inspecting, navigating, mining, and transforming annotation repositories—the common representation basis for modern pipelined text processing architectures. The open-ended nature of these architectures and expressiveness of feature structure-based annotation schemes account for the natural tendency of such annotation repositories to become very dense, as multiple levels of analysis get encoded as layered annotations. This particular characteristic presents challenges for the design of a pattern matching framework capable of interpreting ‘flat’ patterns over arbitrarily dense annotation lattices. We present an approach where a finite state device applies (compiled) pattern grammars over what is, in effect, a linearized ‘projection’ of a particular route through the lattice. The route is derived by a mix of static grammar analysis and runtime interpretation of navigational directives within an extended grammar formalism; it selects just the annotations sequence appropriate for the patterns at hand. For expressive and efficient pattern matching in dense annotations stores, our implemented approach achieves a mix of lattice traversal and finite state scanning by exposing a language which, to its user, provides constructs for specifying sequential, structural, and configurational constraints among annotations.     

GEOCHEMICAL CHARACTERISTICS OF CRUDE OILS FROM THE SHARARA-C OIL FIELD,MURZUQ BASIN,SOUTHWESTERN LIBYA

Crude oil samples from the Sharara-C oil field (Concession NC-115, Murzuq Basin, SW Libya) were analysed by organic geochemical methods in order to infer the geochemical characteristics of their respective source rocks. Aromatic hydrocarbons were analysed by gas chromatography – mass spectrometry (GC-MS), and gas chromatography – tandem mass spectrometry (GC-MS-MS) was used to analyse saturated biomarkers. The Sharara-C oils are interpreted to have been generated by marine shales containing mixed terrigenous and marine organic materials deposited in an intermediate (suboxic) environment. Age-specific biomarker ratios indicated that the oils are older than Cretaceous, and maturation-related parameters pointed to their high thermal maturity. Consistent with previous studies, source rocks are inferred to be “hot” shales in the Lower Silurian Tanezzuft Formation. Almost all the parameter ratios calculated varied over a very narrow range, indicating that the investigated oils were compositionally similar. The only significant difference that was noted concerned the sterane/hopane ratios whose variation suggested that there was some variability in the composition of the source organic material. The organic geochemical parameters determined for the Sharara-C crude oils were compared with published data on other crude oils from Concession NC-115. Almost all the parameters agreed well with previously published data on oils from this part of the Murzuq Basin. The greatest deviation concerned the values of some of the maturity parameters. This tended to confirm the conclusions of previous studies concerning the presence of a number of distinct oil families and sub-families in the Sharara oil field area which are genetically related but which have different maturities.     

Epidemiology of end‐stage renal disease and hemodialysis treatment in Serbia at the turn of the millennium

The study presents the epidemiological features of patients treated with renal replacement therapy (RRT) in Serbia from 1997 to 2009 and compares the results of hemodialysis treatment in 1999 and 2009. Epidemiological data were obtained from the National Registry of RRT patients and data on hemodialysis treatment from special surveys conducted in 1999 and 2009. Within the period 1997–2009 the incidence of patients on RRT increased from 108 to 179 per million population (pmp), prevalence rose from 435 to 699 pmp, while mortality rate fell from 20.7% to 16.7%. The frequency of patients with glomerulonephritis decreased, while that of patients with diabetes and hypertensive nephropathy increased. In late 2009 there were 5208 patients receiving RRT in Serbia. Within the examined period new hemodialysis and reverse osmosis equipment were purchased, high‐flux dialyzers with synthetic membranes were increasingly used and the number of patients receiving hemodiafiltration increased to 17.6%. Kt/V greater than 1.2 was recorded in 16% of the patients in 1999 but 52% in 2009. Options for correction of anemia and mineral disorders have also improved. The percentage of patients with HbsAg (13.8% vs. 4.8%) as well as anti‐hepatitis C virus antibodies positive patients (23.2% vs. 12.7%) was significantly lower in 2009 than in 1999. Both the incidence and prevalence of RRT patients in Serbia are rising continuously, while the mortality rate is falling. More favorable conditions for dialysis treatment have brought about significant improvement in the results over the last 10 years.     

32P-postlabeling analysis of the DNA adducts of 6-fluorobenzo[a]pyrene and 6-methylbenzo[a]pyrene formed in vitro

Studies of benzo[a]pyrene (BP) and selected derivatives are part of the strategy to elucidate mechanisms of tumor initiation by polycyclic aromatic hydrocarbons. Substitution of BP at C-6 with fluorine to form 6-fluorobenzo[a]pyrene (6-FBP) or a methyl group to form 6-methylbenzo[a]pyrene (6-CH3BP) decreases tumorigenicity compared to BP. BP, 6-FBP, and 6-CH3BP formed adducts with DNA when (1) they were activated by 3-methylcholanthrene-induced rat liver microsomes, (2) they were activated by horseradish peroxidase (HRP), (3) their 7,8-dihydrodiols were activated by microsomes, or (4) the radical cation of BP, 6-FBP, or 6-CH3-BP was directly reacted with DNA. With microsomes, 6.5 mumol of [3H]6-FBP/mol of DNA-P and 10 mumol of [14C]6-CH3BP/mol of DNA-P were bound vs 15 mumol of [3H]BP. With microsomes, two major 6-FBP adducts and some minor adducts were obtained. One major adduct coincided with that from 6-FBP-7,8-dihydrodiol. With microsomes, the minor 6-FBP adducts coincided with the adducts obtained from 6-FBP radical cation plus DNA and the major adduct of HRP-activated 6-FBP. With microsomes, 6-CH3BP showed adducts similar to some formed with HRP and one from 6-CH3BP radical cation. 6-CH3BP-7,8-dihydrodiol produced a small amount of one adduct that did not coincide with any from 6-CH3BP. The adducts of 6-FBP appear to be formed mostly through the diolepoxide pathway, whereas those of 6-CH3BP appear to arise mostly via one-electron oxidation.     

Building co-operative bibliographic databases in European bioethics: a contribution from EU New Member States

The paper presents a web-based application, developed as a part of the Eurethnet database network, which is being used by project partners from EU New Member States to collect bibliographic records from bioethics domains. The application development was focused mainly on records compatibility with other Eurethnet databases, support for all European character sets, minimalisation of network traffic, and security issues. The time window available for the system development was very small and this problem was solved with our own software for automatic application generation.     

Diameter-dependent elastic modulus supports the metastable-catalyst growth of carbon nanotubes

We measured the elastic modulus of individual multiwalled carbon nanotubes (MWCNTs) grown by catalytic chemical vapor deposition (CVD) over a broad diameter range (10-25 nm). Alternating current (ac) dielectrophoresis was used for efficient tube deposition, and atomic force microscope (AFM) force-displacement curve technique was used for stiffness measurements. The elastic modulus exhibits a strong diameter dependence, showing a difference of nearly 2 orders of magnitude in the 10-20 nm diameter range (thinner MWCNTs have higher elastic modulus). Our results support the metastable-catalyst model in which the catalyst's molten skin plays a key role.     

Croatian scientific publications in top journals according to the Science Citation Indexfor the 1980–2000 Period

A top journal is defined as a journal which is within the first 10% of journals ranked by impact factor in the SCI list, within a particular scientific subfield, for the year considered. Journals which were for 11 or more years within the first 10% were considered top journals during the whole period even though they were not within the first 10%, in some of the years covered by this study.In the period from 1980 to 2000, the Croatian scientists affiliated with research institutions within the Republic of Croatia, published a total of 13,021 papers in journals covered by the Science Citation Index (SCI). Out of these papers, only 2,720 were published in top journals. This amounts to 20.9% of the total, and this is below the world average of 29.5% for the same scientific subfields. Out of the above 2,720 publications, 1,250 (46.0%) were published in international collaboration, and 335 (12.3%) papers were Meeting Abstracts. The Croatian scientists were most productive in the main scientific fields: Physics (875 papers; 32.2%), Medicine (786 papers; 28.9%), and Chemistry (580 papers; 21.3%). All others fields, taken together, comprised 17.6% of the total scientific output. Of the 786 medical papers, 290 were Meeting Abstracts, or 36.9% of the total output in the field of Medicine, and medical Meeting Abstracts represent 86.6% of the total number of abstracts (335). Articles (2,060) represent 75.7% of the total Croatian scientific output in top journals. This revised version was published online in June 2006 with corrections to the Cover Date.     

Voltammetric measurements of aminosalicylate drugs using bismuth film electrode

A bismuth film electrode (BiFE) prepared ex-situ on a supporting glassy carbon electrode exhibited convenient electroanalytical performance for voltammetric measurement of selected aminosalycilate drugs. The reduction behaviour of aminosalycilate drugs was studied in aqueous solutions within the pH range of 4–6. The voltammetric responses were compared with those obtained at the bare glassy carbon electrode under identical conditions. In the square-wave voltammetric operation mode the BiFE showed a linear response in the concentration range of 5 × 10⁻⁶ to 3.5 × 10⁻⁴ and 1 × 10⁻⁶ to 5 × 10⁻⁴ M for sulfasalazine and olsalazine, respectively. Its electrode surface revealed auspiciously high stability and remarkable reproducibility in the rapid analysis of aminosalycilate drugs. Finally, the BiFE was satisfactorily applied for direct quantitation of azo prodrugs in real pharmaceutical samples.     

Optimization: Microwave irradiation effect on polyphenolic compounds extraction from winter savory (Satureja montana L.)

Microwave-assisted extraction of polyphenols with elevated antioxidant activity from winter savory was optimized by simultaneous maximization of total phenolics, total flavonoids yields, and antioxidant activity (measured by two assays—DPPH and reducing power assay). For optimization of microwave assisted extraction, Box–Behnken experimental design coupled with response surface methodology was applied. Independent variables were extraction time, ethanol concentration, and irradiation power. Analysis of variance was used to evaluate model fitness and determine optimal conditions.