Improving identification of differentially expressed genes by integrative analysis of Affymetrix and Illumina arrays

Together with the widely used Affymetrix microarrays, the recently introduced Illumina platform has become a cost-effective alternative for genome-wide studies. To efficiently use data from both array platforms, there is a pressing need for methods that allow systematic integration of multiple datasets, especially when the number of samples is small. To address these needs, we introduce a meta-analytic procedure for combining Affymetrix and Illumina data in the context of detecting differentially expressed genes between the platforms. We first investigate the effect of different expression change estimation procedures within the platforms on the agreement of the most differentially expressed genes. Using the best estimation methods, we then show the benefits of the integrative analysis in producing reproducible results across bootstrap samples. In particular, we demonstrate its biological relevance in identifying small but consistent changes during T helper 2 cell differentiation.     

Superantigen types inStaphylococcus aureus isolated from patients with cystic fibrosis

The screening of 17 SAg genes of S. aureus isolated from the sputum of cystic fibrosis (CF) patients revealed that among 47 genetically different strains, 39 (83 %) carried SAg genes. Superantigens forming enterotoxin gene cluster were detected in 20 strains. The 2nd most common superantigen type was selk detected in 13 strains. In 9 strains, selk occurred together with the sea gene. Out of 74 strains recovered from nasal carriers, 56 (75 %) were found to carry SAg genes, 38 carried egc genes, while selk was detected in 5 strains. The predominant SAg types in both investigated S. aureus populations were egc and selk/sea, but selk gene frequency was significantly higher in the CF-derived strains.     

Prevention of infection transmission during stem cell transplantation

Group of 152 patients (investigated before autologous transplantation) and 35 healthy donors for allogeneic transplantation was examined for the risk of infection transmission that can be associated with the infusion of cryopreserved peripheral blood progenitor cells to the patient and/or cross-contamination of stored grafts. No laboratory signs of active infection were found in 22 donors (63 %) and in 91 patients (60%). The most common was active infection by herpes viruses--50 cases in patients, 21 cases in donors; hepatitis B was found in only two cases. The rate of clinically unsuspected (but dangerous) infections in donors and patients thus remains relatively high in spite of the fact that the system of donor search and the whole transplantation procedure have improved in the last years. The system of safety assurance is extremely important and the whole palette of preventive tests according to EBMT (European Blood and Marrow Transplantation Group) and ISHAGE (International Society for Hemotherapy and Graft Engineering) is fully justified.     

Primary fluorescence (Autofluorescence) of fruiting bodies of the wood-rotting fungusFomes fomentarius

Autofluorescence of fruiting bodies of the wood-rotting fungus Fomes fomentarius has been observed and is described among native macrofungi for the first time. The strongest yellow autofluorescence with blue excitation was displayed by pith sets, a weaker yellow, yellow-green to yellow-red fluorescence was due to generative thin-walled hyphae while the weakest yellow-reddish fluorescence was emitted by thick-walled skeletal hyphae (though their parts may emit a more intensive yellow fluorescence). This yellow, yellow-green to yellow-red autofluorescence was assessed to be more intensive than the emission described so far in bacteria and fungi (except for lysed hyphae of the fungus Trametes versicolor). With green excitation all F. fomentarius cells emitted strong red autofluorescence.     

Effect of Darkness on Growth and Flowering of Chenopodium rubrum and C. murale Plants in vitro

Chenopodium rubrum, a short-day plant, and C. murale, a long-day plant, were grown in vitro in continuous darkness. Control C. rubrum plants exposed to continuous darkness for 15 d at cotyledonary phase, did not flower, while 80 % of plants flowered on the medium with 5 % glucose and 10 mg dm⁻³ GA₃. Control C. murale plants exposed to continuous darkness for 10 d at the age of 4^th pair of leaves, did not flower, while GA₃ (1 – 5 mg dm⁻³) stimulated flowering up to 65 %. This revised version was published online in July 2006 with corrections to the Cover Date.     

Species Specificity of Aldehyde and Fatty Acid Profiles of Four Family Group Representatives within the Insect Infraorder Pentatomomorpha (Hemiptera: Heteroptera)

Reactive α,β‐unsaturated aldehydes, including 4‐oxoalk‐2‐enals, are known to be present in volatile secretions of numerous heteropteran insect species. Because the aldehydes are likely to originate from metabolism of fatty acids (FAs), the present study aimed to examine and compare the aldehyde and FA profiles of four model heteropteran species. The model species consisted of adult family group representatives within the infraorder Pentatomomorpha (Hemiptera: Heteroptera): seed bug (Lygaeus equestris (Lygaeoidea)), dock leaf bug (Coreus marginatus (Coreoidea)), red firebug (Pyrrhocoris apterus (Pyrrhocoroidea)), and European stink bug (Graphosoma lineatum (Pentatomoidea)). Solid‐phase microextraction combined with two‐dimensional gas‐chromatography/time‐of‐flight mass spectrometry was used to establish the profiles of volatile secretions in stressed living insects. The FA profiles of acylglyceride and phospholipid fractions deposited in fat body and/or hemolymph were obtained by liquid chromatography/mass spectrometry and gas chromatography with flame ionization detection techniques. Our results based on multivariate statistical analyses of the data imply that volatile secretion blends as well as fat body and/or hemolymph lipid profiles are species specific but the differences in volatile blends between different species do not mirror the changes in corresponding fat body and/or hemolymph lipid profiles of stressed and non‐stressed individuals.     

Synthesis and structure–activity relationship study of novel quinazolinone-based inhibitors of MurA

MurA is an intracellular bacterial enzyme that is essential for peptidoglycan biosynthesis, and is therefore an important target for antibacterial drug discovery. We report the synthesis, in silico studies and extensive structure–activity relationships of a series of quinazolinone-based inhibitors of MurA from Escherichia coli. 3-Benzyloxyphenylquinazolinones showed promising inhibitory potencies against MurA, in the low micromolar range, with an IC₅₀ of 8 µM for the most potent derivative (58). Furthermore, furan-substituted quinazolinones (38, 46) showed promising antibacterial activities, with MICs from 1 µg/mL to 8 µg/mL, concomitant with their MurA inhibitory potencies. These data represent an important step towards the development of novel antimicrobial agents to combat increasing bacterial resistance.     

Chemical Profiling and Assessment of Antineurodegenerative and Antioxidant Properties of Veronica teucrium L. and Veronica jacquinii Baumg.

Neuroprotective potential of V. teucrium and V. jacquinii methanol extracts was analyzed. Chemical analysis of investigated extracts showed the presence of phenolic acid derivatives, flavonoids and one secoiridoid. The detected flavonoids derived from flavones (luteolin and isoscutellarein in V. jacquinii ; apigenin, isoscutellarein and luteolin in V. teucrium ) and flavonol (quercetin in V. jacquinii ). Acteoside was the dominant compound in V. jacquinii , while plantamajoside and isoscutellarein 7‐O ‐(6?‐O ‐acetyl)‐β ‐allosyl (1?→2?)‐β ‐glucoside were the major phenolics in V. teucrium . Additionally, the antineurodegenerative activity was tested at concentrations of 25, 50, and 100 μg/ml using acetylcholinesterase (AC hE) and tyrosinase (TYR ) assays. The inhibition of both enzymes was achieved with the investigated extracts, ranging from 22.78 to 35.40% for AC hE and from 9.57 to 16.38% for TYR . There was no statistical difference between the activities of the analyzed extracts. Our data indicate that V. teucrium and V. jacquinii may have beneficial effects against Alzheimer 's and Parkinson 's disease.