The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function

A new microarray method, the isotope array approach, for identifying microorganisms which consume a (14)C-labeled substrate within complex microbial communities was developed. Experiments were performed with a small microarray consisting of oligonucleotide probes targeting the 16S rRNA of ammonia-oxidizing bacteria (AOB). Total RNA was extracted from a pure culture of Nitrosomonas eutropha grown in the presence of [(14)C]bicarbonate. After fluorescence labeling of the RNA and microarray hybridization, scanning of all probe spots for fluorescence and radioactivity revealed that specific signals were obtained and that the incorporation of (14)C into rRNA could be detected unambiguously. Subsequently, we were able to demonstrate the suitability of the isotope array approach for monitoring community composition and CO(2) fixation activity of AOB in two nitrifying activated-sludge samples which were incubated with [(14)C]bicarbonate for up to 26 h. AOB community structure in the activated-sludge samples, as predicted by the microarray hybridization pattern, was confirmed by quantitative fluorescence in situ hybridization (FISH) and comparative amoA sequence analyses. CO(2) fixation activities of the AOB populations within the complex activated-sludge communities were detectable on the microarray by (14)C incorporation and were confirmed independently by combining FISH and microautoradiography. AOB rRNA from activated sludge incubated with radioactive bicarbonate in the presence of allylthiourea as an inhibitor of AOB activity showed no incorporation of (14)C and thus was not detectable on the radioactivity scans of the microarray. These results suggest that the isotope array can be used in a PCR-independent manner to exploit the high parallelism and discriminatory power of microarrays for the direct identification of microorganisms which consume a specific substrate in the environment.     

Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment

For cultivation-independent detection of sulfate-reducing prokaryotes (SRPs) an oligonucleotide microarray consisting of 132 16S rRNA gene-targeted oligonucleotide probes (18-mers) having hierarchical and parallel (identical) specificity for the detection of all known lineages of sulfate-reducing prokaryotes (SRP-PhyloChip) was designed and subsequently evaluated with 41 suitable pure cultures of SRPs. The applicability of SRP-PhyloChip for diversity screening of SRPs in environmental and clinical samples was tested by using samples from periodontal tooth pockets and from the chemocline of a hypersaline cyanobacterial mat from Solar Lake (Sinai, Egypt). Consistent with previous studies, SRP-PhyloChip indicated the occurrence of Desulfomicrobium spp. in the tooth pockets and the presence of Desulfonema- and Desulfomonile-like SRPs (together with other SRPs) in the chemocline of the mat. The SRP-PhyloChip results were confirmed by several DNA microarray-independent techniques, including specific PCR amplification, cloning, and sequencing of SRP 16S rRNA genes and the genes encoding the dissimilatory (bi)sulfite reductase (dsrAB).     

Induction of premature mitosis in root meristem cells of Vicia faba and Pisum sativum by various agents is correlated with an increased level of protein phosphorylation

The intra-S-phase checkpoint response to hydroxyurea (HU)-mediated arrest of DNA replication was analysed in root meristems of two legumes, Pisum sativum and Vicia faba. The obtained results suggest that a molecular signal which invokes mechanisms allowing the cells to override the S-M dependency control system may be generated by caffeine (CF) and a number of alternative, yet related chemical agents, benzyl-6-aminopurine (BAP), 2-aminopurine (2-AP), and 6-dimethylaminopurine (DMAP). A variety of aberrant mitotic divisions included chromosomal breaks and gaps, lost and lagging chromatids and chromosomes, acentric fragments, chromosome bridges and micronuclei. Furthermore, similar effects induced by sodium vanadate, an inhibitor of protein phosphatases, extend the number of inhibitors capable of inducing premature chromosome condensation (PCC) in root meristem cells, as well as the range of possible regulatory pathways leading to the transition from S-phase arrest towards abnormal mitosis. Until preprophase, FITC-conjugated monoclonal antibodies (alpha-Y(a)b-FITC) that specifically recognize phosphorylated form of threonine indicate no evident cell cycle-dependent changes in an overall phosphorylation status of root meristem cells in the control plants. Irrespective of the stage of interphase, alpha-Y(p)ab-FITC was localized basically in the cytoplasm, whereas nuclear staining was considerably weaker, with a significant fluorescence confined merely to nucleolar regions. The intensity of alpha-Y(p)ab-FITC staining in HU/CF-treated seedlings was found higher than that in the control plants (with the exception of G2 cells), suggesting a general increase in the level of protein phosphorylation, a physiological response mediated probably by an enhanced activity of the cdc-like protein kinase(s).     

Immunoexpression of nm23 in advanced esophageal squamous cell carcinoma

The study was undertaken to determine the immunoexpression of protein products of nm23 genes which are thought to be potential metastasis suppressor genes, in esophageal squamous cell carcinoma, and to analyze their relationship to selected clinicopathological features (age, sex, tumour size, depth of invasion, presence of lymph nodes and distant metastasis, pathologic tumor stage, degree of cancer differentiation and vascular/lymphatic invasion), as well as to the overall survival. Immunohistochemical staining with monoclonal antibody against nm23 using LSAB2/HRP method on formalin-fixed, paraffin-embedded sections obtained from 32 tumors was performed. Eight tumors (25%) showed positive nm23 immunoexpression. There were no statistically significant differences between nm23-positive and nm23-negative groups with respect to all clinicopathological features studied. The positive nm23 status was related to a worse prognosis but this was not significant. The results may suggest that nm23-status is not associated with metastatic ability and prognosis in esophageal squamous cell carcinoma, but such thesis requires further study on a larger population.     

AFLP marker polymorphism in cucumber (Cucumis sativus L.) near isogenic lines differing in sex expression

The AFLP technique was used to evaluate the level of polymorphism between two pairs of isogenic cucumber (Cucumis sativus L.) lines (NIL) differing in flower sex expression. The BSA techniques were also applied to find molecular markers linked to sex determination genes (dominant alleles) in those cucumber lines. Sex determination in cucumber is controlled by three main loci F, M and Gy. The interaction of these loci is responsible for the formation of the various phenotypes of flowers in respect to sex in the analyzed lines [corrected]. A female line 2gg with a ff/MM/gygy genotype, isogenic to a monoecious line B10 (genotype ff/MM/GyGy), and a female line Gy3 with a FF/MM/GyGy genotype, isogenic to a hermaphroditic line HGy3 (genotype FF/mm/GyGy). Using 56 combinations of AFLP primers, used for the analysis of lines 2gg and B10, gave 3794 bands, of which 155 (4.1%) were polymorphic. Ten bands distinguished gynoecious and monoecious bulks appearing at the same time in the appropriate parent; they are believed to be linked to the Gy locus. The isogenic lines Gy3 and HGy3 showed a higher level of polymorphism (14.2%). In this case, 55 combinations of primers gave 2996 reaction products, of which 430 showed variation. Twenty bands occurred in one bulk and in one parent, so they are probably associated with the M locus. Using the AFLP technique, the isogenicity of the lines was evaluated. The level of polymorphism (per pair of primer) between lines 2gg and B10 is 0.072% and is four times lower than that between the Gy3 and HGy3 lines (0.27%). The differences in the isogenicity of the lines can result from the degree of their relatedness, which may reflect the way they were derived.     

Diversity of SREBP-1 gene expression in rat adipose tissue depots in response to refeeding after food restriction

The SREBP-1c mRNA level and precursor (microsomal) form of SREBP-1 abundance were significantly higher in epididymal and perirenal than in subcutaneous white adipose tissue of control rats. Moreover, the SREBP-1c mRNA level and an amount of precursor form of SREBP-1 were significantly higher in the epididymal and perirenal white adipose tissue of rats maintained on restricted diet and refed ad libitum for 48 h as compared to the control animals. No significant effects of food restriction/refeeding on SREBP-1c mRNA level and an amount of precursor form of SREBP-1 were found in subcutaneous white adipose tissue. The mature (nuclear) form of SREBP-1 was significantly increased in the epididymal, perirenal and subcutaneous white adipose tissue of the food restricted/refed animals. The activity, protein level and the mRNA abundance of malic enzyme (one of the target genes for SREBP-1) increased significantly in the epididymal, perirenal and subcutaneous white adipose tissue of the food restricted/refed rats as compared to the control animals, however the increase in perirenal and epididymal was higher than in the subcutaneous white adipose tissue. The results presented suggest that SREBP-1c is differently expressed in various rat white adipose tissue depots both under basal (control) and dieting conditions.     

New generation of peptide antibiotics

The increasing antibiotic resistance of pathogenic bacteria calls for the development of alternative antimicrobial strategies. Possible approaches include the development of novel, broad-spectrum antibiotics as well as specific targeting of individual bacterial virulence factors. It is impossible to decide currently which strategy will prove more successful in the future since they both promise different advantages, but also introduce diverse problems. Considering both approaches, our laboratory's research focuses on the evaluation of hemocidins, broad-spectrum antibacterial peptides derived from hemoglobin and myoglobin, and staphostatins, specific inhibitors of staphopains -- Staphylococcus aureus secreted proteases that are virulence factors regarded as possible targets for therapy. The article summarizes recent advances in both fields of study and presents perspectives for further development and possible applications.     

Activity of lysosomal exoglycosidases in submandibular glands of rats intoxicated by cadmium at doses related to human chronic environmental and occupational exposures

Work in cadmium (Cd) smelter and smoking cigarettes damages teeth and oral mucosa which are protected by tissue and salivary glycoconjugates: glycoproteins, glycolipids, and proteoglycans. We worked out a rat model imitating human "environmental" and "occupational" exposure to cadmium using 5 mg Cd and 50 mg Cd/l in drinking water, respectively. In submandibulary glands of exposed to Cd rats, we found the time and dose dependent accumulation of Cd and simultanous decrease in activity of beta-N-acetylhexosaminidase (HEX). In homogenates of submandibulary glands of control rats, beta-N-acetylhexosaminidase showed the highest activity. The activities of alpha-mannosidase and beta-galactosidase were very low. None of these exoglycosidases were inhibited by Cd even at 44 mM concentration.     

Cancer cell detection in tissue sections using AFM

Currently, cancer diagnosis relies mostly on morphological examination of exfoliated, aspirated cells or surgically removed tissue. As long as standard diagnosis is concerned, this classical approach seems to be satisfactory. In the recent years, cancer progression has been shown to be accompanied by alterations in mechanical properties of cells. This offers the detection of otherwise unnoticed cancer cell disregarded by histological analysis due to insignificant manifestations. One of techniques, sensitive to changes in mechanical properties, is the atomic force microscopy, which detects cancer cells through their elastic properties. Such measurements were applied to tissue sections collected from patients suffering from various cancers. Despite of heterogeneity and complexity of cancer cell sections, the use of the Young's modulus as an indicator of cell elasticity allow for detection of cancer cells in tissue slices.