Metabolomics meets lipidomics: Assessing the small molecule component of metabolism

Metabolomics, including lipidomics, is emerging as a quantitative biology approach for the assessment of energy flow through metabolism and information flow through metabolic signaling; thus, providing novel insights into metabolism and its regulation, in health, healthy ageing and disease. In this forward-looking review we provide an overview on the origins of metabolomics, on its role in this postgenomic era of biochemistry and its application to investigate metabolite role and (bio)activity, from model systems to human population studies. We present the challenges inherent to this analytical science, and approaches and modes of analysis that are used to resolve, characterize and measure the infinite chemical diversity contained in the metabolome (including lipidome) of complex biological matrices. In the current outbreak of metabolic diseases such as cardiometabolic disorders, cancer and neurodegenerative diseases, metabolomics appears to be ideally situated for the investigation of disease pathophysiology from a metabolite perspective.     

Dual restriction enzyme digest of cationic-gold-coated DNA scaffolds

DNA strands coated with AuNPs were cleaved by restriction enzymes while in solution or on a surface. Enzymatic activity was verified by gel electrophoresis prior to surface analysis. Cleavage results suggest that enzymes can recognize the AuNP-coated strands while on the surfaces, though specificity in digestion has not yet been verified. Development allows for advances in site specific localization of components using biological media.     

Selective placement of templated DNA nanowires between microstructured electrodes

Dip-pen nanolithography is used to selectively modify the SiOx area between microfabricated electrodes. The modified surface is characterized by atomic force microscopy, X-ray photoelectron spectroscopy, force volume imaging, and adhesion maps. The functionalized complex architecture is used for the localization of DNA coated with magnetic nanoparticles. The strategy reported here can become the basis for the construction of a number of functional devices. The devices can utilize the unique recognition properties of the DNA and the magnetic properties of the nanoparticles that template them.     

Comparing soluble and co-immobilized catalysts for 2-ketoaldose production by pyranose 2-oxidase and auxiliary enzymes

The tri-enzyme system pyranose 2-oxidase (P2O), laccase, and catalase was used to study major parameters in the homogeneous and heterogeneous application of a multi-component enzymatic machinery. P2O oxidizes aldoses to 2-ketosugars, which are interesting intermediates in carbohydrate chemistry, and concomitantly reduces oxygen or alternative electron acceptors. The enzyme was immobilized on eleven agarose or acrylic resins using various coupling methods. The binding capacity was determined and an acrylic carrier with the most suitable properties selected for detailed studies. As P2O shows higher turnover numbers with the electron acceptor 1,4-benzoquinone than with oxygen, the use of this alternative electron acceptor was enabled by employing laccase for the continuous reoxidation of hydroquinone. The laccase regeneration system was found to increase the specific productivity up to 3-fold. Catalase was used to disproportionate the formed hydrogen peroxide in close proximity to the oxygen consuming enzymes and applied in different amounts to adjust the hydrogen peroxide concentration, which was found to be the main reason for enzyme deactivation under turnover conditions. In contrast to homogeneous catalysis, the specific productivity of heterogeneous catalysts under the applied experimental conditions was limited primarily by oxygen transfer, an effect significantly reduced by the laccase regeneration system.     

Divergent effects of peripheral and global neuropeptide Y deletion

Objectives:Neuropeptide Y (NPY) is involved in the coordination of bone mass and adiposity. However, multiple NPY sources exist and their individual contribution to the skeleton and adiposity not known. The objectives of our study were to evaluate the effects of peripheral mesenchymal derived NPY to the skeleton and adiposity and to compare them to the global NPY^KO model.Methods:To study the role of mesenchymal-derived NPY, we crossed conditional NPY (NPY^fl/fl) mice with Prx1cre to generate PrxNPY^KO mice. The bone phenotype was assessed using micro-CT. The skeletal phenotype of PrxNPY^KO mice was subsequently compared to global NPY^KO model. We evaluated body weight, adiposity and functionally assessed the feeding response of NPY neurons to determine whether central NPY signaling was altered by Prx1cre.Results:We identified the increase in cortical parameters in PrxNPY^KO mice with no changes to cancellous bone. This was the opposite phenotype to global NPY^KO mice generated from the same conditional allele. Male NPY^KO mice have increased adiposity, while PrxNPY^KO mice showed no difference, demonstrating that local mesenchymal-derived NPY does not influence adiposity.Conclusion:NPY mediates both positive and negative effects on bone mass via separate regulatory pathways. Deletion of mesenchymal-derived NPY had a positive effect on bone mass.     

Intercondylar distances of the human temporomandibular joints

In a sample which included subjects of the Croatian population we made measurements of intercondylar distances between the temporomandibular joints in radiographs. A total of 101 subjects of both sexes ranging in age from 20 to 80 years, mostly residents in Zagreb, were evaluated. We measured the intercondylar distances from the condyle centers in the postero-anterior cranial radiographs which had previously been examined and traced on acetate paper. The measuring points were digitized prior to measurements. A special system of coordinates was devised for each radiograph. The results of our measurements were assessed by ANOVA analysis. The intercondylar distance between the two temporomandibular joints was within the range of 110 and 145 mm, with the mean of 126 mm. In men the intercondylar distance was within the range of 116 and 145 mm, with the mean of 130.2 mm. In women the distance ranged from 110 to 138 mm, with the mean of 123.5 mm. There was a significant difference between the two sexes. From a review of the literature, it is apparent that the results of our measurements do not support the results of similar studies assessed by a number of researchers in other countries. The intercondylar distance in the Croatian sample was 5.25% larger than the maximal values of the same parameters in other populations suggesting larger craniofacial skeletons. The development of this radiographic assessment method should improve evaluation of subjects seeking treatment.     

Duplex sonography of arteriovenous fistula in chronic hemodialysis patients

Duplex sonography was used to assess functional features of arteriovenous fistula (AVF) for hemodialysis (HD). Internal diameter (ID), resistance index (RI) and blood flow (BF) velocity in feeding artery and in vein ofAVF, and venous BF volume were analyzed with purpose to determine the normal values. Presumed normal BF velocities are those of clinically well functioning shunts, allowing BF through HD lines of minimally 250 ml/min. Study included 66 nondiabetic HDpatients (30 women, 36 men), mean age 52-13 years, treated by HD for median 61 (4-252) months. Measurements in 47patients with clinically well functioning AVF were as followed: mean arterial ID 5.2 +/- 1.4 mm, median arterial RI 0.3 (0.3-0.9), median arterial BF velocity 1.5 (0.6-3.6) m/s, mean venous ID 7.6 +/- 2.2 mm, median venous RI 0.3 (0.3-0.9), mean venous BF velocity 1.6 +/- 0.7 m/s, and median venous BF volume 530 (120-1890) ml/min. Patients with poor functioning AVF had significantly less arterial ID, higher arterial RI, less venous ID, less venous BF velocity and volume. Duplex sonography findings obtained for clinically estimated well functioning shunt should be considered as normal Doppler values. Blood vessels' morphologic features depend upon age, and older patients have more pronounced changes.     

Prevalence of antibodies to porcine parvovirus in wild boars (Sus scrofa) in Croatia

Serologic evidence of exposure to porcine parvovirus (PPV) in the wild boar (Sus scrofa) in Croatia was investigated. Serum samples from 219 wild boars captured during 2003 from 12 different locations in the Republic of Croatia were tested by using a commercial enzyme-linked immunoassay (ELISA) and a hemagglutination inhibition (HI) test. Antibodies to PPV were detected in 91 (41.6%) of tested samples and positive results were detected in wild boar from all sample locations. Adults had a significantly higher prevalence (70%) than juveniles (31%; P < 0.01). Our results indicate that wild boar populations throughout the Republic of Croatia are exposed to PPV.     

Caries and oral hygiene in children in postwar Novi Travnik (Bosnia and Herzegovina) and Zabok (Croatia)

The study was performed in 1997 and involved school children between the age of 6 and 12 in Novi Travnik, Bosnia and Herzegovina (n = 203) and Zabok, Croatia (n = 132). OHI-S (Simplified Oral Hygiene Index by Green-Vermillion) and DMF (Decayed, Missing, Filled) index were used as main outcome measures. Prewar data were taken from the respective literature. The value of the DMF/dmf (PERMANENT/deciduous teeth) for six-year-olds in Novi Travnik of the period before the war was: d = 5.6, m = 0.4, f= 0.6 and D = 0.3, F = 0.1 and the average DMF index of twelve-year-olds for the same period were 6.5. The DMF/dmf index in 1997 in Novi Travnik was: d = 9.4+/-4.4; m = 0.7 +/-1.1; D = 1.9+/-1.2 and average DMF index of twelve-year-olds was 9.0+/-4.16. The DMF index of twelve-year-olds in Zabok in 1990 was 3.4 and 4.1+/-2.1 in 1997. Total DMF index for all the examined ages in 1997 for Zabok was 6.1+/-3.7 and for the examinees in Novi Travnik 10.5+/-4.1 (p<0.001). Similarly, the OHI-S in 1997 for Zabok was 1.0+/-0.7 whereas 1.7+/-0.7 (p<0.001) in Novi Travnik. In comparison to prewar data, DMF index in 1997 was considerably higher. Increase of DMF index was higher in Novi Travnik than in Zabok, which can be attributed to the war and wartime conditions.     

nov: a new genetic locus that affects the response of Escherichia coli K-12 to novobiocin

We have identified a new gene locus (nov) affecting the resistance of Escherichia coli K-12 to novobiocin. The gene also affects, although to a lesser extent, tolerance to another gyrase inhibitor coumermycin. Transductional and complementation analysis show that nov is located between att phi 80 and the osmZ (hns) genes at minute 27 of the E. coli K-12 genetic map. In standard laboratory strains of E. coli K-12 nov exists at least in two allelic forms.