Afr Health Sci, 2003 Dec, 3(3), 131 - 135 Imaging features of brain tuberculoma in Tanzania: case report and literature review; Lwakatare FA et al.; Brain tubercluomas are a rare manifestation of mycobacterium tuberculosis infection usually resulting from hematogenous spread of the bacteria from a primary focus elsewhere in the body . A 29-year-old female with no history of pulmonary tuberculosis or signs of pulmonary infection presented with signs and symptoms of raised intracranial pressure . She underwent CT and MR imaging where multiple enhancing lesions were revealed in the brain parenchyma . The features of tuberculoma on CT and MR imaging may mimic the appearance of several other brain lesions . Histological diagnosis of tuberculoma was obtained . In areas where tuberculosis is endemic, the imaging features of brain tuberculoma have to be readily recognized by attending doctors. Curr Opin Struct Biol, 2003 Dec, 13(6), 665 - 73 Molecular shredders: how proteasomes fulfill their role; Groll M et al.; The 20S proteasome is a large, cylinder-shaped protease that is found in all domains of life and plays a crucial role in cellular protein turnover . It has multiple catalytic centers located within the hollow cavity of a molecular cage . This architecture prevents unwanted degradation of endogenous proteins and promotes processive degradation of substrates by restricting the dissociation of partially digested polypeptides . Although this kind of self-compartmentalization is generally conserved, the proteasomes of bacteria, archaea and eukaryotes show many differences in architecture, subunit composition and regulation . The structure of the 20S proteasome and its inherent role in the regulation of proteasome function are gradually being elucidated. Stat Med, 2003 Dec 30, 22(24), 3713 - 24 Estimating the incidence of subclinical infections with Legionella Pneumonia using data augmentation: analysis of an outbreak in The Netherlands; Nagelkerke NJ et al.; Infections with Legionella bacteria can cause a potentially lethal form of pneumonia known as legionnaires' disease . In 1999 a major outbreak, causing 31 deaths, occurred among visitors and exhibitors of a consumer fair in The Netherlands . The epidemiology of subclinical infections is largely unknown, as there is no reliable method to diagnose such infections . To explore the incidence of subclinical infections, IgG and IgM antibody levels among exhibitors were compared to those among a representative sample of the Dutch population . As exhibitors were assumed to comprise both infected and uninfected individuals, their antibody levels were modelled as a mixture distribution . As infected individuals are expected to cluster around a point source, the spatial aspect of the spread of infections was taken into account . To estimate the distribution of antibody levels among infected individuals and to impute infection status among exhibitors, data augmentation was used . Subclinical infection appeared to be very common and its frequency declined with the distance from the putative source of the outbreak . Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai), 2003 Dec, 35(12), 1061 - 5 Evolution of phenylalanyl-tRNA synthetase by domain losing; Lin J et al.; The gene duplication, fusion and horizontal transfer are the frequent events during evolution of many proteins, including the aminoacyl-tRNA synthetases (AARSs) . However, in this work, it was shown that the main event during evolution of phenylalanyl-tRNA synthetase (PheRS) is a domain loss, and the function/activity of PheRS is not affected by domain losing . Generally, the size of genome and number of genes are increased during evolution from bacteria to eukaryote, but the interesting thing is that the type and number of PheRS domains in eukaryote are obviously less than those in bacteria . The evolution of PheRS by domain losing seems to be related to the functional evolution of some AARSs from the multiple specificities to the single specificity. J Neurosci, 2003 Dec 10, 23(36), 11479 - 88 Effects of neurotoxic and neuroprotective agents on peripheral nerve regeneration assayed by time-lapse imaging in vivo; Pan YA et al.; A direct histological assay of axonal regeneration would have many advantages over currently available behavioral, electrophysiological, and radiometric assays . We show that peripheral sensory axons marked with the yellow fluorescent protein in transgenic mice can be viewed transcutaneously in superficial nerves . Degenerating and regenerating axons can be followed in live animals with a dissecting microscope and then, after fixation, studied at high resolution by confocal microscopy . Using this approach, we document differences in regenerative ability after nerve transection, crush injury, and crush injury after a previous "conditioning" lesion . We also show that the chemotherapeutic drug vincristine rapidly but transiently blocks regeneration and that the immunosuppressive drug FK506 modestly enhances regeneration . Moreover, FK506 nearly restores normal regenerative ability in animals treated with submaximal doses of vincristine . Because neuropathy is the major dose-limiting side effect of vincristine, we propose that its efficacy could be enhanced by coadministration of FK506 analogs that are neuroactive but not immunosuppressive. Vet Res Commun, 2003 Dec, 27(8), 643 - 52 Influence of dexamethasone on some cellular aspects of the immune system in cats; Hoffmann-Jagielska M et al.; In view of the frequent use of glucocorticoids in the treatment of cats, we studied the effect of dexamethasone on their immunological system . The phagocytic activity and oxidative burst of neutrophils and monocytes were evaluated by cytometric analysis using commercial kits and the subpopulations of lymphocytes were assessed . Neutrophilia and monocytosis reduced phagocytic activity, as shown from the number of phagocytized bacteria, and variations in the intensity of the oxidative burst in activated neutrophils and monocytes were observed . Dexamethasone also caused an increase in the number of B lymphocytes. Inflamm Bowel Dis, 2003 Nov, 9(6), 363 - 71 The intestinal anti-inflammatory activity of UR-12746S on reactivated experimental colitis is mediated through downregulation of cytokine production; Galvez J et al.; BACKGROUND: UR-12746S (dersalazine sodium) is cleaved by colonic bacteria delivering the PAF antagonist UR-12715 and 5-ASA . This study describes the anti-inflammatory activity of UR-12746S in an experimental model of reactivated colitis and its effects on cytokine production . METHODS: Rats were initially rendered colitic by a colonic instillation of 10 mg of trinitrobenzenesulphonic acid (TNBS) dissolved in 0.25 ml of 50 % ethanol, and colitis was reactivated two weeks after by a second administration of the same dose of TNBS . Two groups of colitic rats received UR-12746S (25 and 50 mg/kg daily, p.o.) and colonic damage was evaluated every week for 4 weeks . Different biochemical markers of colonic inflammation were assayed: MPO activity and cytokine (IL-1beta and TNFalpha) levels . Also, the in vitro effects of UR-12715 and 5-ASA on cytokine production were assayed . RESULTS: UR-12746S showed anti-inflammatory effect in reactivated colitis in rats, as evidenced by a significant reduction in MPO activity . Both doses of UR-12746S decreased IL-1beta production, while only the highest dose assayed inhibited TNFalpha production . In vitro studies revealed that UR-12715 or 5-ASA (from 10(-6) to 10(-4) M) inhibited IL-8 production (30-40%) in HT-29 cells when incubated with LPS . This inhibitory effect was enhanced when both compounds were administered simultaneously at 10(-4) M . In addition, UR-12715 inhibited IL-1beta or TNFalpha production in THP-1 or U937 cells, respectively, when these cells were stimulated by PMA and LPS; whereas 5-ASA only showed a weak effect in inhibiting IL-1beta production . CONCLUSION: UR-12746S was able to prevent relapse in experimental colitis and inhibition of proinflammatory cytokine production participates in the intestinal anti-inflammatory activity exerted by this compound. J Virol, 2004 Jan, 78(1), 389 - 98 Spatial and temporal organization of adeno-associated virus DNA replication in live cells; Fraefel C et al.; Upon cell entry, the genomes of herpes simplex virus type 1 (HSV-1) and adenovirus (Ad) associate with distinct nuclear structures termed ND10 or promyelocytic leukemia (PML) nuclear bodies (NBs) . PML NB morphology is altered or disrupted by specific viral proteins as replication proceeds . We examined whether adeno-associated virus (AAV) replication compartments also associate with PML NBs, and whether modification or disruption of these by HSV-1 or Ad, both of which are helper viruses for AAV, is necessary at all . Furthermore, to add a fourth dimension to our present view of AAV replication, we established an assay that allows visualization of AAV replication in live cells . A recombinant AAV containing 40 lac repressor binding sites between the AAV inverted terminal repeats was constructed . AAV Rep protein and helper virus-mediated replication of this recombinant AAV genome was visualized by binding of enhanced yellow fluorescent protein-lac repressor fusion protein to double-stranded AAV replication intermediates . We demonstrate in live cells that AAV DNA replication occurs in compartments which colocalize with AAV Rep . Early after infection, the replication compartments were small and varied in numbers from 2 to more than 40 per cell nucleus . Within 4 to 8 h, individual small replication compartments expanded and fused to larger structures which filled out much of the cell nucleus . We also show that AAV replication compartments can associate with modified PML NBs in Ad-infected cells . In wild-type HSV-1-infected cells, AAV replication compartments and PML NBs did not coexist, presumably because PML was completely disrupted by the HSV-1 ICP0 protein . However, alteration or disruption of PML appears not to be a prerequisite for AAV replication, as the formation of replication compartments was normal when the ICP0 mutants HSV-1 dl1403 and HSV-1 FXE, which do not affect PML NBs, were used as the helper viruses; under these conditions, AAV replication compartments did not associate with PML NBs. Plant Physiol, 2004 Jan, 134(1), 286 - 95 Epub 2003 Dec 11. RHM2 is involved in mucilage pectin synthesis and is required for the development of the seed coat in Arabidopsis; Usadel B et al.; Pectins are major components of primary plant cell walls and the seed mucilage of Arabidopsis . Despite progress in the structural elucidation of pectins, only very few enzymes participating in or regulating their synthesis have been identified . A first candidate gene involved in the synthesis of pectinaceous rhamnogalacturonan I is RHM2, a putative plant ortholog to NDP-rhamnose biosynthetic enzymes in bacteria . Expression studies with a promoter beta-glucuronidase construct and reverse transcription PCR data show that RHM2 is expressed ubiquitously . Rhm2 T-DNA insertion mutant lines were identified using a reverse genetics approach . Analysis of the rhm2 seeds by various staining methods and chemical analysis of the mucilage revealed a strong reduction of rhamnogalacturonan I in the mucilage and a decrease of its molecular weight . In addition, scanning electron microscopy of the seed surface indicated a distorted testa morphology, illustrating not only a structural but also a developmental role for RGI or rhamnose metabolism in proper testa formation. Biochim Biophys Acta, 2003 Dec 8, 1607(2-3), 131 - 40 Dissecting a cyanobacterial proteolytic system: efficiency in inducing degradation of the D1 protein of photosystem II in cyanobacteria and plants; Kanervo E et al.; A chromatography fraction, prepared from isolated thylakoids of a fatty acid desaturation mutant (Fad6/desA Colon, two colons Km(r)) of the cyanobacterium Synechocystis 6803, could induce an initial cleavage of the D1 protein in Photosystem II (PSII) particles of Synechocystis 6803 mutant and Synechococcus 7002 wild type as well as in supercomplexes of PSII-light harvesting complex II of spinach . Proteolysis was demonstrated both in darkness and in light as a reduction in the amount of full-length D1 protein or as a production of C-terminal initial degradation fragments . In the Synechocystis mutant, the main degradation fragment was a 10-kDa C-terminal one, indicating an initial cleavage occurring in the cytoplasmic DE-loop of the D1 protein . A protein component of 70-90 kDa isolated from the chromatographic fraction was found to be involved in the production of this 10-kDa fragment . In spinach, only traces of the corresponding fragment were detected, whereas a 24-kDa C-terminal fragment accumulated, indicating an initial cleavage in the lumenal AB-loop of the D1 protein . Also in Synechocystis the 24-kDa fragment was detected as a faint band . An antibody raised against the Arabidopsis DegP2 protease recognized a 35-kDa band in the proteolytically active chromatographic fraction, suggesting the existence of a lumenal protease that may be the homologue DegP of Synechocystis . The identity of the other protease cleaving the D1 protein in the DE-loop exposed on the stromal (cytoplasmic) side of the membrane is discussed. Biochim Biophys Acta, 2003 Dec 8, 1607(2-3), 121 - 30 Kinetic analyses of state transitions of the cyanobacterium Synechococcus sp . PCC 7002 and its mutant strains impaired in electron transport; Huang C et al.; The state transitions of the cyanobacterium Synechococcus sp . PCC 7002 and of three mutant strains, which were impaired in PsaE-dependent cyclic electron transport (psaE(-)), respiratory electron transport (ndhF(-)) and both activities (psaE(-)ndhF(-)), were analyzed . Dark incubation of the wild type and psaE(-) cells led to a transition to state 2, while the ndhF(-) strains remained in state 1 after dark incubation . The ndhF(-) cells adapted to state 2 when the cells were incubated under anaerobic conditions or in the presence of potassium cyanide; these results suggest that the ndhF(-) cells were inefficient in performing state 1 to state 2 transitions in the dark unless cytochrome oxidase activity was inhibited . In the state 2 to state 1 transition of wild-type cells induced by light in the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), there was still a significant reduction of the interphotosystem electron carriers by both respiration and cyclic electron flow around PSI . Kinetic analysis of the state 2 to state 1 transition shows that, in the absence of PSII activity, the relative contribution to the reduced state of the interphotosystem electron carriers by respiratory and cyclic electron transfer is about 72% and 28%, respectively . The state 2 to state 1 transition was prevented by the cytochrome b(6)f inhibitor 2,5-dibromo-3-methyl-6-isopropylbenzoquinone (DBMIB) . On the other hand, the state 1 to state 2 transition was induced by DBMIB with half times of approximately 8 s in all strains . The externally added electron acceptor 2,5-dimethyl-benzoquinone (DMBQ) induced a state 2 to state 1 transition in the dark and this transition could be prevented by DBMIB . The light-induced oxidation of P700 showed that approximately 50% of PSI could be excited by 630-nm light absorbed by phycobilisomes (PBS) under state 2 conditions . P700 oxidation measurements with light absorbed by PBS also showed that the dark-induced state 1 to state 2 transition occurred in wild-type cells but not in the ndhF(-) cells . The possible mechanism for sensing an imbalanced light regime in cyanobacterial state transitions is discussed. Tuberculosis (Edinb), 2004, 84(1-2), 110 - 30 Iron, mycobacteria and tuberculosis; Ratledge C; The role of iron in the growth and metabolism of M . tuberculosis and other mycobacteria is discussed in relation to the acquisiton of iron from host sources, such as transferrin, lactoferrin and ferritin, and its subsequent assimilation and utilization by the bacteria . Key components involved in the acquisition of iron (as ferric ion) and its initial transport into the mycobacterial cell are extracellular iron binding agents (siderophores) which, in pathogenic mycobacteria, are the carboxymycobactins and, in saprophytic mycobacteria, are the exochelins . In both cases, iron may be transferred to an intra-envelope, short-term storage molecule, mycobactin . For transport across the cell membrane, a reductase is used which converts FeIII-mycobactin to the FeII form . The ferrous ion, possibly complexed with salicylic acid, is then shuttled across the membrane either for direct incorporation into various porphyrins and apoproteins or, for storage of iron within the bacterial cytoplasm, bacterioferritin . The overall process of iron acquisition and its utilization is under very genetic tight control . The importance of iron in the virulence of mycobacteria is discussed in relationship to the development of tuberculosis . The management of dietary iron can therefore be influential in aiding the outcome of this disease . The role of the old anti-TB compound, p-aminosalicylate (PAS), is discussed in its action as an inhibitor of iron assimilation, together with the prospects of being able to synthesize further selective inhibitors of iron metabolism that may be useful as future chemotherapeutic agents. Biol Chem, 2003 Oct-Nov, 384(10-11), 1411 - 9 Ribosomal tolerance and peptide bond formation; Yonath A; In the ribosome, the decoding and peptide bond formation sites are composed entirely of ribosomal RNA, thus confirming that the ribosome is a ribozyme . Precise alignment of the aminoacylated and peptidyl tRNA 3'-ends, which is the major enzymatic contribution of the ribosome, is dominated by remote interactions of the tRNA double helical acceptor stem with the distant rims of the peptidyl transferase center . An elaborate architecture and a sizable symmetry-related region within the otherwise asymmetric ribosome guide the A --> P passage of the tRNA 3'-end by a spiral rotatory motion, and ensures its outcome: stereochemistry suitable for peptide bond formation and geometry facilitating the entrance of newly formed proteins into their exit tunnel. Lipids, 2003 Oct, 38(10), 1085 - 92 On the origin of cis-vaccenic acid photodegradation products in the marine environment; Rontani JF et al.; The origin of 11-hydroxyoctadec-trans-12-enoic and 12-hydroxyoctadec-trans-10-enoic acids (photodegradation products of cis-vaccenic acid) in the marine environment was investigated . cis-Vaccenic acid is commonly used as a bacterial biomarker; however, in heterotrophic bacteria the observed rates of cis-vaccenic acid photodegradation are negligible . Here, two hypotheses explaining the source of the photoproducts were tested . According to the first hypothesis, the photoproducts originate from aerobic anoxygenic bacteria, i.e., photoheterotrophic organisms using bacteriochlorophyll-containing reaction centers . Alternatively, the photoproducts come from a heterotrophic bacterial community closely associated with senescent phytoplanktonic cells . cis-Vaccenic acid photodegradation was detected in both experimental setups . However, a detailed comparison of the cis-vaccenic acid photodegradation patterns with those observed in particulate matter samples of the DYFAMED station (Mediterranean Sea) suggests that photodegradation of heterotrophic bacteria attached to senescent phytoplanktonic cells constitutes the more likely source of cis-vaccenic acid oxidation products detected in situ. Environ Technol, 2003 Oct, 24(10), 1315 - 21 Effects of temperature on post-methanation of digested dairy cow manure in a farm-scale biogas production system; Kaparaju PL et al.; A post-methanation process that could be adopted at farm-scale, operating at temperatures prevailing in farm manure digester post-storage tanks, was evaluated . Digested manure samples from a farm digester (35 degrees C) and post-storage tank (5-10 degrees C) were incubated in parallel batches at 5-20 degrees C and as reference at 35 and 55 degrees C . Specific methane yields (kg(-1) volatile solids (VS)(added waste)) were 0.20-0.26 m3 at 35-55 degrees C and 0.085-0.09 m3 at 10-20 degrees C for digester material (345 days of incubation) and 0.16-0.21 m3 at 35-55 degrees C, 0.053-0.087 kg(-1) VS(added waste) m3 at 15-20 degrees C and 0.026 m3 at 10 degrees C for post-storage tank material (250 days) . Both materials produced less than 0.005 m3 at 5 degrees C . However, an increase in temperature to 35 degrees C (40 days) improved methane production in assays pre-incubated at 5-20 degrees C (9 months) . These results suggest that the untapped methane potential of the digested manure cannot effectively be recovered at temperatures prevailing in farm digested manure storage tanks during the winter in Northern latitudes . Nevertheless, as ambient temperatures increase during the late spring, an increase in methanogenesis can be expected. Arch Microbiol, 2004 Jan, 181(1), 1 - 7 Epub 2003 Dec 11. Molecular analysis of a subcellular compartment: the magnetosome membrane in Magnetospirillum gryphiswaldense; Schuler D; The ability of magnetotactic bacteria (MTB) to orient and migrate along magnetic field lines is based on magnetosomes, which are membrane-enclosed intracellular crystals of a magnetic iron mineral . Magnetosome biomineralization is achieved by a process involving control over the accumulation of iron and deposition of the magnetic particle, which has a specific morphology, within a vesicle provided by the magnetosome membrane . In Magnetospirillum gryphiswaldense, the magnetosome membrane has a distinct biochemical composition and comprises a complex and specific subset of magnetosome membrane proteins (MMPs) . Classes of MMPs include those with presumed function in magnetosome-directed uptake and binding of iron, nucleation of crystal growth, and the assembly of magnetosome membrane multiprotein complexes . Other MMPs comprise protein families of so far unknown function, which apparently are conserved between all other MTB . The mam and mms genes encode most of the MMPs and are clustered within several operons, which are part of a large, unstable genomic region constituting a putative magnetosome island . Current research is directed towards the biochemical and genetic analysis of MMP functions in magnetite biomineralization as well as their expression and localization during growth. J Biol Chem, 2004 Mar 5, 279(10), 8694 - 700 Epub 2003 Dec 10. Structural requirements of synthetic muropeptides to synergize with lipopolysaccharide in cytokine induction; Traub S et al.; Muropeptides contribute to the recognition of bacteria by modulating immune responses: the structural requirements for adjuvant activity were described in the seventies . During the last years, our knowledge of bacterial pattern recognition has increased dramatically and the importance of the absence of contaminations in both muropeptide preparations and other bacterial stimuli has become clear . We investigated a panel of 15 synthetic Limulus-negative muropeptides, four of them synthesized for the first time, as to their potency to synergize with lipopolysaccharide (LPS) in cytokine induction in human whole blood . No muropeptide was capable of stimulating cytokine release from human blood . However, as little as 20 nM of the muropeptides N-acetyl-muramyl-l-alanyl-d-isoglutamine (muramyl dipeptide, M(AdiQ)), N-acetyl-glucosamine-muramyl dipeptide GM(AdiQ), or C(18)M(AdiQ), which carries a non-natural additional fatty acid, sufficed to induce an up to 3 log-order shift in tumor necrosis factor alpha-release in response to 100 pg/ml LPS . The release of interleukin-1beta, interleukin-6, and interleukin-10 was also significantly enhanced although to a lesser extent . The synergistic effect was stereoselective with M(AdiQ) being the minimal active principle . Synergy was also observed on the transcriptional level by means of real-time PCR . Smaller molecules like N-acetylmuramic acid (M), aM, carrying a naturally occurring 1,6-anhydro-bound in M or M(A), containing only the amino acid l-alanine neither synergized with LPS nor influenced the synergy of other muropeptides with LPS . In conclusion, these data show that nanomolar quantities of muropeptides dramatically potentiate LPS-induced monocyte activation . This has implications for pyrogenicity testing and endotoxemia in patients. Food Chem Toxicol, 2004 Feb, 42(2), 221 - 35 Oral (gavage), in utero and post-natal exposure of Sprague-Dawley rats to low doses of tributyltin chloride . Part II: effects on the immune system; Tryphonas H et al.; The immunotoxic effects of tributyltin chloride (TBTC) were examined in the offspring of Sprague-Dawley rats exposed in utero from day 8 of gestation, through lactation and post-weaning until pups reached the age of 30 days (male and female), 60 days (female) and 90 days (male) . Daily oral (gavage) doses of 0.025, 0.25 and 2.5 mg/kg body weight/day were administered in olive oil 7 days/week . Immunologic endpoints were investigated at the termination of each study . Statistically significant results (P<0.05) included the following: At 30 days, the mean percent and absolute natural killer (NK) cell numbers were increased in male and female rats treated with the high TBTC dose . At 60 days, female rats had increased mean serum IgM levels at the low and high TBTC doses, increased mean percentage CD4(+)8(+) (immature) T lymphocytes at the middle and high doses, a non-linear dose-response increase in NK cell activity at the 50:1 and 100:1 effector:target cell ratios (pairwise comparisons significant at the low dose compared with control), and increased mean numbers of L . monocytogenes colony-forming bacteria on Day 2 post-infection (significant for trend) and Day 3 post infection (pairwise comparisons significant only in the middle dose) . The 90-day male rats had decreased mean serum IgA levels at the middle dose group; increased IgM levels at the high dose group, increased IgG levels at the middle and high doses; decreased IgG2(a) in the high dose compared to the control; a dose-related increase in the mean percentage NK cell numbers (pairwise comparisons significant at the high dose compared with the control) and increased mean NK cell activity (pairwise comparisons significant at all dose groups compared with the control) . The delayed-type hypersensitivity response to oxazolone was increased in the low and middle doses and decreased in the high dose . Thymus atrophy was observed in the high TBTC dose across all ages . Thus, in utero and post-natal treatment of F1 rats with low levels of TBTC affected some aspects of humoral and cell mediated immunity as well as the number and function of cells which are involved in the host's immunosurveillance mechanisms against tumours and viral infections. Proc R Soc Lond B Biol Sci, 2003 Nov 7, 270 Suppl 2, S202 - 5 Characterization of methanogenic and methanotrophic assemblages in landfill samples; Uz I et al.; A greater understanding of the tightly linked trophic groups of anaerobic and aerobic bacteria residing in municipal solid waste landfills will increase our ability to control methane emissions and pollutant fate in these environments . To this end, we characterized the composition of methanogenic and methanotrophic bacteria in samples taken from two regions of a municipal solid waste landfill that varied in age . A method combining polymerase chain reaction amplification, restriction fragment length polymorphism analysis and phylogenetic analysis was used for this purpose . 16S rDNA sequence analysis revealed a rich assemblage of methanogens in both samples, including acetoclasts, H2/CO2-users and formate-users in the newer samples and H2/CO2-users and formate-users in the older samples, with closely related genera including Methanoculleus, Methanofollis, Methanosaeta and Methanosarcina . Fewer phylotypes of type 1 methanotrophs were observed relative to type 2 methanotrophs . Most type 1 sequences clustered within a clade related to Methylobacter, whereas type 2 sequences were broadly distributed among clades associated with Methylocystis and Methylosinus species . This genetic characterization tool promises rapid screening of landfill samples for genotypes and, therefore, degradation potentials. Analyst, 2003 Oct, 128(10), 1286 - 90 Epub 2003 Jul 28. Gas phase electrochemical detection of single latex particles; Caruana DJ et al.; In this study we describe zero current potentiometric measurements in a gaseous flame electrolyte, for the detection of single latex particles . Combustion of polystyrene latex particles when added to a premixed hydrogen/oxygen/nitrogen flame, results in an increase in charged species relative to the surrounding hydrogen flame . As a consequence of this increase in ionic concentration over background, short-lived potential difference transients were measured between two platinum indicator electrodes placed in a two-compartment flame electrochemical cell (described in Electrochem . Commun., 2001, 3, 675-681) . The frequency of the transient events was dependent on the number density of latex particles in solution . It is proposed that each short-lived transient event corresponds to the combustion of single latex particles in a flame . A potential difference maximum of 0.56 V when 3.0 microm diameter particles were added to the flame was measured . Also it was shown that it is possible to detect 0.3 microm diameter latex particles using the same technique . It is postulated that the physical basis of the potential difference is due to the establishment of diffusion/junction potential due to the increase in ionisation from polystyrene combustion at the surface of one indicator electrode . This methodology may be applied to the detection of particulates composed of ionisable species (organic or inorganic) in gaseous environment such as bacteria, viruses, pollen grains and dust. J Vet Diagn Invest, 2003 Nov, 15(6), 570 - 4 Molecular and antigenic characterization of Bordetella bronchiseptica isolated from a wild southern sea otter (Enhydra lutris nereis) with severe suppurative bronchopneumonia; Staveley CM et al.; Bordetella bronchiseptica was isolated in pure culture from the lung, abdomen, and intestine of a wild free-ranging southern sea otter (Enhydra lutris nereis) with severe, suppurative bronchopneumonia . Immunohistochemistry, using antiserum raised to B . bronchiseptica, revealed strong positive staining of bacteria attached to bronchial ciliated epithelia as well as scattered positive staining in affected alveoli . Western blot analysis demonstrated that virulence factors, filamentous hemagglutinin, pertactin, and adenylate cyclase toxin are produced by the sea otter B . bronchiseptica isolate . Ribotype analysis using Pvu II restriction digests indicated that this isolate is most similar to strains commonly obtained in domestic dogs and cats. Arch Inst Pasteur Tunis, 1999 Jan-Apr, 76(1-4), 19 - 22 {Oral-dental health status in patients with infectious endocarditis}; Ayadi R et al.; Mouth and dental examination is a systematic act in the etiologic follow up of an infectious endocarditis . Our study concerned 42 patients collected during 5 years period, starting july 1995 until July 2000, in the dental medical service of Hedi Chaker university hospital of Sfax oriented by the cardiovascular diseases service looking for a buccodental entry of bacteria . Our patients group is divided into 25 men and 17 women of 36.1 years mean age . Dental or parodontal lesions were observed in 25 patients . Panoramic X-rays showed periapical lesions of granuloma or cystic type in 15 patients . Among the etiological factors encountered we noticed dental acts accomplished without antibioprophylaxis and dental bacterial collection medically treated without extraction . Buccodental lesions were a frequent cause of the infectious endocarditis in 59.5% of the patients studied in this report, and were due more to defectious hygienic conditions than to a disabled dental act. Genome, 2003 Dec, 46(6), 1059 - 69 SNP-based codominant markers for a recessive gene conferring resistance to corky root rot (Rhizomonas suberifaciens) in lettuce (Lactuca sativa); Moreno-Vazquez S et al.; The analysis of F2 progeny and derived F3 families of Lactuca sativa segregating for resistance to corky root rot caused by Rhizomonas suberifaciens permitted the identification of restriction fragment length polymorphism (RFLP) and single nucleotide polymorphism (SNP) markers linked to the recessive resistance gene cor . PCR-based markers were identified by bulked segregant analysis (BSA) . Allele-specific primers were generally designed with the 3 terminal base coinciding with an SNP, matching one of the alleles and mismatching the other, and with an additional subterminal 3 base mismatching both alleles . Codominant, robust, and inexpensive molecular markers were obtained that used standardized PCR conditions . Some of the markers could be analyzed in multiple Lactuca mapping populations that did not segregate for disease resistance allowing the cor locus to be located on several maps . The consistent low density of markers around cor in these maps suggests that cor may be in an area with an elevated rate of recombination . Evaluation of these markers in a large sample of cultivars and landraces identified pairs of flanking polymorphic markers that can be used for marker-assisted selection of corky root resistance. Can J Microbiol, 2003 Oct, 49(10), 625 - 32 A metalloproteinase extracellularly released by Crithidia deanei; d'Avila-Levy CM et al.; Actively motile cells from a cured strain of Crithidia deanei released proteins in phosphate buffer (pH 7.4) . The molecular mass of the released polypeptides, which included some proteinases, ranged from 19 to 116 kDa . One of the major protein bands was purified to homogeneity by a combination of anion-exchange and gel filtration chromatographs . The apparent molecular mass of this protein was estimated to be 62 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) . The incorporation of gelatin into SDS-PAGE showed that the purified protein presented proteolytic activity in a position corresponding to a molecular mass of 60 kDa . The enzyme was optimally active at 37 degrees C and pH 6.0 and showed 25% of residual activity at 28 degrees C for 30 min . The proteinase was inhibited by 1,10-phenanthroline and EDTA, showing that it belonged to the metalloproteinase class . A polyclonal antibody to the leishmanial gp63 reacted strongly with the released C . deanei protease . After Triton X-114 extraction, an enzyme similar to the purified metalloproteinase was detected in aqueous and detergent-rich phases . The detection of an extracellular metalloproteinase produced by C . deanei and some other Crithidia species suggests a potential role of this released enzyme in substrate degradation that may be relevant to the survival of trypanosomatids in the host. Can J Microbiol, 2003 Oct, 49(10), 602 - 12 Methanotrophic diversity in high arctic wetlands on the islands of Svalbard (Norway)--denaturing gradient gel electrophoresis analysis of soil DNA and enrichment cultures; Wartiainen I et al.; The methanotrophic community in arctic soil from the islands of Svalbard, Norway (78 degrees N) was analysed by combining group-specific PCR with PCR of the highly variable V3 region of the 16S rRNA gene and then by denaturing gradient gel electrophoresis (DGGE) . Selected bands were sequenced for identification . The analyses were performed with DNA extracted directly from soil and from enrichment cultures at 10 and 20 degrees C . The two genera Methylobacter and Methylosinus were found in all localities studied . The DGGE band patterns were simple, and DNA fragments with single base differences were separated . The arctic tundra is a potential source of extensive methane emission due to climatic warming because of its large reservoirs of stored organic carbon . Higher temperatures due to climatic warming can cause increased methane production, and the abundance and activity of methane-oxidizing bacteria in the arctic soil may be important regulators for methane emission to the atmosphere. J Clin Microbiol, 2003 Dec, 41(12), 5434 - 41 Culture and phenotypic characterization of a Wolbachia pipientis isolate; Fenollar F et al.; The recent isolation of Wolbachia pipientis in the continuous cell line Aa23, established from eggs of a strain of the Asian tiger mosquito Aedes albopictus, allowed us to perform extensive characterization of the isolate . Bacterial growth could be obtained in C6/36, another A . albopictus cell line, at 28 degrees C and in a human embryonic lung fibroblast monolayer at 28 and 37 degrees C, confirming that its host cell range is broader than was initially thought . The bacteria were best visualized by Diff-Quik and May-Grunwald-Giemsa staining . Proteins from 213 to 18 kDa with two major protein bands of 65 and 25 kDa were observed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis . By Western blotting with specific polyclonal mouse and rabbit antisera, dominant immunoreactive antigens were found at approximately 100, 80, and 30 kDa . The genome size was calculated to be 1,790 +/- 17 kb by pulsed-field gel electrophoresis . The sequence of the citrate synthase gene (gltA) of W . pipientis was determined by gene walking . Its position in the phylogenetic tree constructed with gltA confirmed that found in a phylogenetic tree constructed with 16S rRNA genes and that it belongs in the alpha subgroup of the class Proteobacteria and that it is closely related to but independent from the genera Ehrlichia, Anaplasma, and Neorickettsia. Curr Opin Biotechnol, 2003 Dec, 14(6), 627 - 33 Novel biologically active natural and unnatural products; Myles DC; Natural products have been used as medicinal agents for many years . In addition, these compounds have served as the starting points for semisynthetic analogs with improved properties . This review highlights work on several classes of natural products and their derivatives, including both well established and emerging structural classes that are in, or nearing, clinical use for a variety of important indications. Curr Opin Biotechnol, 2003 Dec, 14(6), 577 - 82 New substrates for reliable enzymes: enzymatic modification of polymers; Gubitz GM et al.; Recent studies clearly indicate that the modification of synthetic and natural polymers with enzymes is an environmentally friendly alternative to chemical methods using harsh conditions . New processes using lipases, proteases, nitrilases and glycosidases have been developed for the specific non-destructive functionalization of polymer surfaces . The specificity of enzymes has also been exploited in polymer synthesis; for example, lipases have been used for the production of optically active polyesters . Oxidoreductases have been used for the cross-linking and grafting of lignaceous materials and for the production of polymers from phenolics . Recent successes in this area are mainly attributable to advances in the design of reaction systems (e.g . biphasic systems and micellar solutions), while the enzymes are mainly from commercial sources. Comp Biochem Physiol B Biochem Mol Biol, 2003 Dec, 136(4), 943 - 55 Cloning of bovine peroxiredoxins-gene expression in bovine tissues and amino acid sequence comparison with rat, mouse and primate peroxiredoxins; Leyens G et al.; The peroxiredoxin (PRDX) family is a recently identified family of peroxidases found in organisms ranging from bacteria to mammals . In mammals, six PRDX isoforms have been characterized in human (Homo sapiens), rat (Rattus norvegicus) and mouse (Mus musculus) . PRDXs are cytosolic, secreted or targeted to organelles such as peroxisomes, mitochondria and the nucleus . Some PRDXs are synthesized as larger precursor proteins with a presequence that is cleaved to produce the mature form . To study the expression of the six PRDXs in bovine (Bos taurus), we first cloned cDNAs coding for PRDX1, PRDX2, PRDX4 and PRDX5 . PRDX3 and PRDX6 had previously been cloned and characterized in bovine . The comparison of bovine PRDXs with their rat, mouse and primate orthologues reveals a minimum of 95% similarity of mature proteins . Even though mitochondrial or export signal presequences are normally less conserved, the unprocessed proteins still present a minimum of 84% similarity . Nevertheless, a major divergence lies at the N-terminus of bovine PRDX2, where a Cys-Val-Cys motif was identified . The expression of the six PRDXs in 22 bovine tissues has been studied by RT-PCR . Our results point out the ubiquity of the different PRDX transcripts in bovine tissues . The important conservation of the different PRDXs, the multiple processes they have been associated with, as well as the ubiquity of all the members of the family analyzed in this study for the first time altogether, suggest that they play a major role in the basal metabolism of mammalian cells. Comp Biochem Physiol B Biochem Mol Biol, 2003 Dec, 136(4), 723 - 30 Molecular diversity of skin mucus lectins in fish; Suzuki Y et al.; Among lectins in the skin mucus of fish, primary structures of four different types of lectin have been determined . Congerin from the conger eel Conger myriaster and AJL-1 from the Japanese eel Anguilla japonica were identified as galectin, characterized by its specific binding to beta-galactoside . Eel has additionally a unique lectin, AJL-2, which has a highly conserved sequence of C-type lectins but displays Ca(2+)-independent activity . This is rational because the lectin exerts its function on the cutaneous surface, which is exposed to a Ca(2+) scarce environment when the eel is in fresh water . The third type lectin is pufflectin, a mannose specific lectin in the skin mucus of pufferfish Takifugu rubripes . This lectin showed no sequence similarity with any known animal lectins but, surprisingly, shares sequence homology with mannose-binding lectins of monocotyledonous plants . The fourth lectin was found in the ponyfish Leiognathus nuchalis and exhibits homology with rhamnose-binding lectins known in eggs of some fish species . These lectins, except ponyfish lectin, showed agglutination of certain bacteria . In addition, pufflectin was found to bind to a parasitic trematode, Heterobothrium okamotoi . Taken together, these results demonstrate that skin mucus lectins in fish have wide molecular diversity. Biochemistry, 2003 Dec 16, 42(49), 14501 - 6 Lack of negative charge in the E46Q mutant of photoactive yellow protein prevents partial unfolding of the blue-shifted intermediate; Derix NM et al.; The long-lived light-induced intermediate (pB) of the E46Q mutant (glutamic acid is replaced by glutamine at position 46) of photoactive yellow protein (PYP) has been investigated by NMR spectroscopy . The ground state of this mutant is very similar to that of wild-type PYP (WT), whereas the pB state, formed upon illumination, appears to be much more structured in E46Q than in WT . The differences are most striking in the N-terminal domain of the protein . In WT, the side-chain carboxylic group of E46 is known to donate its proton to the chromophore upon illumination . The absence of the carboxylic group near the chromophore in the E46Q mutant prohibits the formation of a negative charge at this position upon formation of pB . This prevents the partial unfolding of the mutant, as evidenced from NMR chemical shift comparison and proton/deuterium (H/D) exchange studies. J Biomater Sci Polym Ed, 2003, 14(10), 1029 - 42 Production of purified polyhydroxyalkanoates (PHAs) for applications in contact with blood; Sevastianov VI et al.; Samples of olyhydroxyalkanoates (PHAs), polyhydroxybutyrate (PHB) and copolymers poly(hydroxybutyrate-co-hydroxyvalerate) (PHBV) with 4 and 18 mol% hydroxyvalerate, synthesized by the bacteria Ralstonia eutropha B5786, were investigated . PHA films in contact with blood did not activate the hemostasis system at the level of cell response, but they did activate the coagulation system and the complement reaction . To detect biologically-active components in the PHAs, a detailed analysis of the composition of the polymers was conducted . Gas chromatography-mass spectrometry revealed long-chain fatty acids (FAs) in the tested PHAs . Their total concentration in the polymer ranged from tenths of mol% to 2-3 mol%, depending on the purification method . C16:0 constituted the largest proportion, up to 70% . Of the long-chain hydroxy acids, only beta-OH-C14:0 was detected and it did not exceed 0.06 mol% . The analysis of the hemocompatibility properties of the PHAs purified by a specialized procedure, including the quantitative and morphological estimation of platelets adherent to the surface of polymer films, the plasma recalcification time and complement activation studies, indicated that PHB and PHBV can be used in contact with blood . It has been found out that the lipopolysaccharides of bacteria producing PHAs, which contain mostly long-chain hydroxy acids, can be the factor activating the hemostasis systems . Thus, the technology of PHA purification must satisfy rather stringent specific requirements. Shanghai Kou Qiang Yi Xue, 2003 Apr, 12(2), 109 - 11 {Clinical studies of calcium hydroxide disinfecting infectious root canal of deciduous tooth}; Zhao J et al.; OBJECTIVE: To search for a more ideal way to disinfect infectious root canal of deciduous tooth . METHODS: According to bacterial occurrence and clinical effect, 40 cases of infectious root canal of deciduous teeth disinfected with Ca(OH)2 were investigated, the other 40 cases with traditional way of using FC and CP respectively, were used as the control . RESULTS: Fist of all, the bacteria of deciduous tooth infectious root canal were same as the bacteria of permanent tooth infectious root canal . Secondly, Ca(OH)2 was stronger in disinfecting deciduous tooth infectious root canal . Thirdly, so far as sterilization was concerned, Ca(OH)2 had the same disinfectant as FC, and was better than CP, but FC had some irritation and poisonous side-effects to periodical tissue . So Ca(OH)2 was safe and effective for deciduous tooth infectious root canal . CONCLUSION: It was a more ideal way to disinfect deciduous tooth infectious root canal by Ca(OH)2. Appl Environ Microbiol, 2003 Dec, 69(12), 7430 - 4 Real-time PCR assay for detection and enumeration of Dekkera bruxellensis in wine; Phister TG et al.; Traditional methods to detect the spoilage yeast Dekkera bruxellensis from wine involve lengthy enrichments . To overcome this difficulty, we developed a quantitative real-time PCR method to directly detect and enumerate D . bruxellensis in wine . Specific PCR primers to D . bruxellensis were designed to the 26S rRNA gene, and nontarget yeast and bacteria common to the winery environment were not amplified . The assay was linear over a range of cell concentrations (6 log units) and could detect as little as 1 cell per ml in wine . The addition of large amounts of nontarget yeasts did not impact the efficiency of the assay . This method will be helpful to identify possible routes of D . bruxellensis infection in winery environments . Moreover, the time involved in performing the assay (3 h) should enable winemakers to more quickly make wine processing decisions in order to reduce the threat of spoilage by D . bruxellensis. Res Vet Sci, 2004 Feb, 76(1), 1 - 18 Molecular differentiation of Mycobacterium bovis isolates . Review of main techniques and applications; Haddad N et al.; Until recently, none of the Mycobacterium bovis typing techniques permitted a satisfactory differentiation of isolates . During the last 10 years, the genome of pathogenic mycobacteria has been extensively studied, and phylogenetic analyses have shown that all (except Mycobacterium avium) belong to a single genetic species: the Mycobacterium tuberculosis complex . This increase in knowledge about the genome of these bacteria has lead to the discovery of molecular markers that allow us to differentiate isolates . Because of the phylogenetic proximity of the strains, even if most of these markers have been discovered in M . tuberculosis, they could be successfully adapted to the other bacteria of the M . tuberculosis complex, especially M . bovis . The most common markers in use today are the IS6110 insertion sequence, the direct repeat (DR) region, the poly(GC) rich (PGRS) sequences and the variable number tandem repeats (VNTR) sequences . The corresponding typing techniques are briefly described, and current knowledge of polymorphism and marker stability is detailed . If molecular markers are to offer wide perspectives for field studies, these two characteristics (polymorphism and stability) must be taken into account when choosing the marker(s) used in a study . In this context, examples of the application of molecular typing techniques for M . bovis are reviewed, on the one hand with epidemiological studies for which the major problem is the comparison between isolates and, on the other, with more general studies about the population genetics of M . bovis in a given country, and about its history and its phylogeny. Proc Natl Acad Sci U S A, 2003 Dec 9, 100(25), 15271 - 5 Epub 2003 Dec 01. The population structure of Mycobacterium bovis in Great Britain: clonal expansion; Smith NH et al.; We have analyzed 11,500 isolates of Mycobacterium bovis (the cause of tuberculosis in cattle and other mammals) isolated in Great Britain (England, Wales and Scotland)} and characterized by spoligotype . Genetic exchange between cells is rare or absent in strains of the Mycobacterium tuberculosis complex so that, by using spoligotypes, it is possible to recognize "clones" with a recent common ancestor . The distribution of variable numbers of tandem repeats types in the most common clone in the data set is incompatible with random mutation and drift . The most plausible explanation is a series of "clonal expansions," and this interpretation is supported by the geographical distribution of different genotypes . We suggest that the clonal expansion of a genotype is caused either by the spread of a favorable mutation, together with all other genes present in the ancestral cell in which the mutation occurred, or by the invasion of a novel geographical region by a limited number of genotypes . A similar pattern is observed in M . tuberculosis (the main cause of tuberculosis in humans) . The significance of clonal expansion in other bacteria that have recombination is discussed. Int J Syst Evol Microbiol, 2003 Nov, 53(Pt 6), 1833 - 42 Molecular signatures in protein sequences that are characteristic of cyanobacteria and plastid homologues; Gupta RS et al.; Fourteen conserved indels (i.e . inserts or deletions) have been identified in 10 widely distributed proteins that appear to be characteristic of cyanobacterial species and are not found in any other group of bacteria . These signatures include three inserts of 6, 7 and 28 aa in the DNA helicase II (UvrD) protein, an 18-21 aa insert in DNA polymerase I, a 14 aa insert in the enzyme ADP-glucose pyrophosphorylase, a 3 aa insert in the FtsH protein, an 11-13 aa insert in phytoene synthase, a 5 aa insert in elongation factor-Tu, two deletions of 2 and 7 aa in ribosomal S1 protein, a 2 aa insert in the SecA protein, a 1 aa deletion and a 6 aa insert in the enzyme inosine-5'-monophosphate dehydrogenase and a 1 aa deletion in the major sigma factor . These signatures, which are flanked by conserved regions, provide molecular markers for distinguishing cyanobacterial taxa from all other bacteria and they should prove helpful in the identification of cyanobacterial species, simply on the basis of the presence or absence of these markers in the corresponding proteins . The signatures in six of these proteins (SecA, elongation factor-Tu, ADP-glucose pyrophosphorylase, phytoene synthase, FtsH and ribosomal S1 protein) are also commonly present in plastid homologues from plants and algae (chlorophytes, chromophytes and rhodophytes), indicating their specific relationship to cyanobacteria and supporting their endosymbiotic origin from these bacteria . In phylogenetic trees based on a number of these proteins (SecA, UvrD, DNA polymerase I, elongation factor-Tu) that were investigated, the available cyanobacterial homologues grouped together with high affinity (>95 % bootstrap value), supporting the view that the cyanobacterial phylum is monophyletic and that the identified signatures were introduced in a common ancestor of this group. Environ Sci Technol, 2003 Nov 15, 37(22), 5175 - 80 Virus inactivation in aluminum and polyaluminum coagulation; Matsui Y et al.; Inorganic aluminum salts, such as aluminum sulfate, are coagulants that cause small particles, such as bacteria and viruses as well as inorganic particles, to destabilize and combine into larger aggregates . In this investigation, batch coagulation treatments of water samples spiked with Qbeta, MS2, T4, and P1 viruses were conducted with four different aluminum coagulants . The total infectious virus concentration in the suspension of floc particles that eventually formed by dosing with coagulant was measured after the floc particles were dissolved by raising the pH with an alkaline beef extract solution . The virus concentrations were extremely reduced after the water samples were dosed with aluminum coagulants . Viruses mixed with and adsorbed onto preformed aluminum hydroxide floc were, however, completely recovered after the floc dissolution . These results indicated that the aluminum coagulation process inactivates viruses . Virucidal activity was most prominent with the prehydrolyzed aluminum salt coagulant, polyaluminum chloride (PACl) . Virucidal activity was lower in river water than in ultrapure water--natural organic matter in the river water depressed the virucidal activity . Mechanisms and kinetics of the virus inactivation were discussed . Our results suggest that intermediate polymers formed during hydrolysis of the aluminum coagulants sorbed strongly to viruses, either rendering them inactive or preventing infectivity. Berl Munch Tierarztl Wochenschr, 2003 Nov-Dec, 116(11-12), 447 - 53 Molecular typing of pathogens; Wassenaar TM; Molecular typing and fingerprinting of bacterial pathogens has become a major part of epidemiology, disease monitoring, intervention and food safety research . This treatise will briefly address the aims of molecular typing and the criteria that are important to choose the optimal method of typing . However, since the method of choice will depend on a number of factors, including available facilities and research goals, no particular methods are recommended; instead, theoretical considerations are presented as a guide line for the best decision . Since molecular typing is examining the nature of the population genetics of a particular organism, it is important to understand how the degree of clonality of that particular organism will influence outcome and interpretation of results . The mechanisms that lead to non-clonality are briefly outlined . The problems with typing of clonal, non-clonal, and weakly clonal populations are briefly treated . The merits and myths of multilocus sequence typing (MLST) are discussed. Turk J Gastroenterol, 2003 Sep, 14(3), 168 - 72 Expression of class I and II MHC receptors in Helicobacter pylori-positive patients with active gastritis and duodenal ulcer; Suleymanov Z; BACKGROUND/AIMS: Helicobacter pylori colonizes on the epithelial surface below the mucous membrane in the gastric antrum, causing chronic active gastritis and duodenal ulcer . However, we know little about the response of the immune system, which is responsible for protecting the organism, to this bacteria and the duodenal tissue damage . The aims of our study were to examine the expression of class I and II MHC receptors in the immune cells in the peripheral venous blood of patients with chronic active gastritis and duodenal ulcer . METHODS: The study included a total of 124 cases (Helicobacter pylori-positive patients without prior treatment, 47 of whom had small-sized and 56 medium-sized duodenal ulcer, and 21 healthy individuals) . Immune cells carrying receptors CD3, CD4, CD3/4, CD8, CD3/8, CD14, CD45, CD14/45, HLA-DR, CD3/HLA-DR, CD16/56, and CD3/16/56 by applying DAKO Dual Color Reagent, and non-specific indicators of reactivity, were investigated in the peripheral venous blood samples . RESULTS: In both study groups, nonspecific indicators of reactivity in peripheral venous blood were not different from those in the healthy group irrespective of the ulcer size . It was detected that NK cells which express only CD3/16/56 receptor are more aggressive than class I MHC carriers, which were increased in both patient groups more markedly than in the control group (p<0.05) . The number of CD14 cells in patient groups with small- and medium-sized duodenal ulcers was found to be lower than in the control group . This difference was more marked in the small-sized ulcer group than in the medium-sized ulcer group . While there was a similarity in the number of CD45 cells in all three groups, the number of CD14/45 cells was reduced in the study group . This reduction was found statistically insignificant in the medium-sized ulcer group, but significant in the small-sized ulcer group (p<0.05) . As compared to the control group, the number of HLA-DR cells was found to be increased in both study groups, and CD3/HLA-DR was found to be increased in the medium-sized ulcer group (p<0.05) . CONCLUSIONS: The reduced number of CD14 cells may have been among the factors predisposing to the development of Helicobacter pylori infection . Such a deficit in cellular defense may be compensated through the upregulation of cells with HLA-DR and CD3/HLA-DR markers by the organism . The increase in the number of cells expressing CD3/16/56 in chronic antral gastritis and duodenal ulcer patients positive for Helicobacter pylori suggests a role for autoimmune events in these diseases. Mol Genet Metab, 2003 Dec, 80(4), 389 - 97 PCR methods in clinical investigations of human ureaplasmas: a minireview; Colaizy TT et al.; Human ureaplasmas are small, cell-wall-deficient organisms that are implicated in many human infections . Due to their small size and fastidious growth requirements, ureaplasmal infections are hard to diagnose clinically, and ureaplasmal disease is difficult to study in clinical samples . Standard culture methods for ureaplasmas are technically challenging, and 3 to 5 days are required to identify this pathogen . PCR methods have been increasingly used in the diagnosis of these infections and in the study of this pathogen in human specimens from multiple sites . These methods have theoretical advantages over traditional culture methods . Organism identification can occur in the presence of low numbers of bacteria, and viability is not necessary . Rapid identification of organisms within 24 h is also possible . In addition, subtyping of isolates can be performed faster with PCR methods than with culture methods . The use of PCR methods in translational research in multiple human ureaplasmal diseases will be reviewed in this paper, and their usefulness will be compared to culture methods. Eur J Biochem, 2003 Dec, 270(24), 4909 - 20 The astacin protein family in Caenorhabditis elegans; Mohrlen F et al.; In the nematode Caenorhabditis elegans, 40 genes code for astacin-like proteins (nematode astacins, NAS) . The astacins are metalloproteases present in bacteria, invertebrates and vertebrates and serve a variety of physiological functions like digestion, hatching, peptide processing, morphogenesis and pattern formation . With the exception of one distorted pseudogene, all the other C . elegans astacins are expressed and are evidently functional . For 13 genes we found splicing patterns differing from the Genefinder predictions in WormBase, sometimes markedly . The GFP expression pattern for NAS-4 shows a specific localization in anterior pharynx cells and in the whole digestive tract (as the secreted form) . In contrast, NAS-7 is found in the head of adult hermaphrodites, but not in pharynx cells or in the lumen of the digestive tract . In embryos, NAS-7 fluorescence becomes detectable just before hatching . In C . elegans astacins, three basic structural and functional moieties can be discerned: a prepro portion, the central catalytic chain and long C-terminal extensions with presumably regulatory functions . Within the regulatory moiety, EFG-like, CUB, SXC, and TSP-1 domains can be distinguished . Based on structural differences of the regulatory unit we established six NAS subgroups, which seemingly represented different functional and evolutionary clusters . This pattern deduced exclusively from the domain arrangement in the regulatory moiety is perfectly reflected in an evolutionary tree constructed solely from amino acid sequence information of the catalytic chain . Related catalytic chains tend to have related regulatory extensions . The notable gene, NAS-39 shows a striking resemblance to human BMP-1 and the tolloids. Respir Care, 2003 Dec, 48(12), 1204 - 13; discussion 1213-5 Exacerbations of chronic obstructive pulmonary disease; Wedzicha JA et al.; Exacerbations of chronic obstructive pulmonary disease (COPD) cause morbidity, hospital admissions, and mortality, and strongly influence health-related quality of life . Some patients are prone to frequent exacerbations, which are associated with considerable physiologic deterioration and increased airway inflammation . About half of COPD exacerbations are caused or triggered primarily by bacterial and viral infections (colds, especially from rhinovirus), but air pollution can contribute to the beginning of an exacerbation . Type 1 exacerbations involve increased dyspnea, sputum volume, and sputum purulence; Type 2 exacerbations involve any two of the latter symptoms, and Type 3 exacerbations involve one of those symptoms combined with cough, wheeze, or symptoms of an upper respiratory tract infection . Exacerbations are more common than previously believed (2.5-3 exacerbations per year); many exacerbations are treated in the community and not associated with hospital admission . We found that about half of exacerbations were unreported by the patients, despite considerable encouragement to do so, and, instead, were only diagnosed from patients' diary cards . COPD patients are accustomed to frequent symptom changes, and this may explain their tendency to underreport exacerbations . COPD patients tend to be anxious and depressed about the disease and some might not seek treatment . At the beginning of an exacerbation physiologic changes such as decreases in peak flow and forced expiratory volume in the first second (FEV(1)) are usually small and therefore are not useful in predicting exacerbations, but larger decreases in peak flow are associated with dyspnea and the presence of symptomatic upper-respiratory viral infection . More pronounced physiologic changes during exacerbation are related to longer exacerbation recovery time . Dyspnea, common colds, sore throat, and cough increase significantly during prodrome, indicating that respiratory viruses are important exacerbation triggers . However, the prodrome is relatively short and not useful in predicting onset . As colds are associated with longer and more severe exacerbations, a COPD patient who develops a cold should be considered for early therapy . Physiologic recovery after an exacerbation is often incomplete, which decreases health-related quality of life and resistance to future exacerbations, so it is important to identify COPD patients who suffer frequent exacerbations and to convince them to take precautions to minimize the risk of colds and other exacerbation triggers . Exacerbation frequency may vary with the severity of the COPD . Exacerbation frequency may or may not increase with the severity of the COPD . As the COPD progresses, exacerbations tend to have more symptoms and take longer to recover from . Twenty-five to fifty percent of COPD patients suffer lower airway bacteria colonization, which is related to the severity of COPD and cigarette smoking and which begins a cycle of epithelial cell damage, impaired mucociliary clearance, mucus hypersecretion, increased submucosal vascular leakage, and inflammatory cell infiltration . Elevated sputum interleukin-8 levels are associated with higher bacterial load and faster FEV(1) decline; the bacteria increase airway inflammation in the stable patient, which may accelerate disease progression . A 2-week course of oral corticosteroids is as beneficial as an 8-week course, with fewer adverse effects, and might extend the time until the next exacerbation . Antibiotics have some efficacy in treating exacerbations . Exacerbation frequency increases with progressive airflow obstruction; so patients with chronic respiratory failure are particularly susceptible to exacerbation. Reprod Biol Endocrinol . 2003 Dec 02;1(1):122. Immunology of term and preterm labor; Peltier MR; During pregnancy there is an alteration in maternal immunity within the uterus where innate, proinflammatory immune responses are tightly regulated to prevent immunological rejection of the fetal allograft . Disruption of the delicate balance of cytokines by bacteria or other factors increases the production of proinflammatory cytokines at the maternal-fetal interface and activates the parturition mechanism prematurely . Despite years of searching, there is still no broadly effective strategy for preventing preterm labor and most therapies are directed at inhibiting myometrial contractions and improving neonatal outcome . Recent studies with progestins and interleukin-10 (IL-10), however, are showing promise in randomized clinical trials and animal studies . Furthermore, the identification of the Toll-like receptors as upstream mediators of inflammation may offer alternative therapeutic targets for preventing this common pregnancy complication. J Endod, 2003 Nov, 29(11), 729 - 34 Direct capping with four different materials in humans: histological analysis of odontoblast activity; Scarano A et al.; Pulp inflammation in restored teeth is mainly due to the presence of bacteria or bacterial products introduced by microleakage around the restoration or to the material toxicity . Recent knowledge has permitted a precise identification of the risks for pulpal irritation associated with adhesive materials and procedures . The purpose of this work was to evaluate the cellular events that occur in direct pulp exposure capped using different materials . Twenty-four vital teeth without caries, scheduled for extraction for orthodontic reasons, were selected . After a control of the hemostasis, each pulp was directly capped with a different material . The samples were randomly divided into four groups of six specimens each: group I: dental-bonding agent (Solist) followed by resin composite (Ecusit); group II: dental adhesive (Prompt) and resin composite (Pertac II); group III: traditional calcium hydroxide (Dycal) plus resin composite (Ecusit); group IV: light-curing calcium hydroxide (Ultrablend Plus) and amalgam (Dentsply) . After 15 days the teeth were extracted, immediately fixed in 10% buffered formalin, embedded in resin (7200 Technovit), and prepared for thin ground sections with Precise 1 System . In the specimens of all groups, there were active odontoblasts near the composite resins and no newly formed dentin . Small quantities of inflammatory cells were present . A 1- to 3-microm layer zone of necrosis was present . In conclusion, all materials tested in this study induced similar tissue responses. Chang Gung Med J, 2003 Sep, 26(9), 621 - 36 Possible application of milk oligosaccharides for drug development; Kobata A; By applying a finger-printing method to the analysis of human milk oligosaccharides, several oligosacchartides were found to be deleted in the milk of non-secretor or Lewis negative individual . This finding afforded a clue to elucidate the enzymatic basis of blood types in humans . Furthermore, disappearance of some major oligosaccharides led to the finding of five novel minor oligosaccharides, which were hidden under the major oligosaccharides . Later on, structures of more than seventy oligosaccharides were elucidated . These oligosaccharides are derived from eleven core oligosaccharides by sialylation and/or fucosylation . All these oligosaccharides contain lactose at their reducing termini . This evidence, together with the deletion phenomena found in the milk of two blood type individuals, suggested that the oligosaccharides are formed by the concerted action of glycosyltransferases, which are responsible for formation of the sugar chains of glycoproteins on the surface of epithelial cells constructing the mucous membrane . The elongation may start by the action of iGnT . This enzyme is responsible for the addition of a beta-N-acetylglucosamine residue to the C-3 position of the galactose moiety constructing the N-acetyllactosamine group of the sugar chains of glycoconjugates . Therefore, oligosaccharides in human milk may include many structures, starting from the N-acetyllactosamine residues in the sugar chains of various glycoproteins . Many evidences, which indicate that virulent enteric bacteria and viruses start their infection by binding to particular sugar chains of glycoconjugates on the surface of their target cells, were presented recently . Therefore, milk oligosaccharides are expected to be useful to inhibit the infection of these bacteria and viruses. Acta Crystallogr D Biol Crystallogr, 2003 Dec, 59(Pt 12), 2065 - 71 Epub 2003 Nov 27. Structure of the hybrid cluster protein (HCP) from Desulfovibrio desulfuricans ATCC 27774 containing molecules in the oxidized and reduced states; Macedo S et al.; The hybrid cluster protein (HCP) from the sulfate-reducing bacteria Desulfovibrio desulfuricans ATCC 27774 has been isolated and crystallized anaerobically . The protein sample used in the crystallization studies was several months old, having been stored at 193 K, and initial crystal structure studies were unable to fully resolve details of the hybrid cluster despite the use of high-resolution data to 1.25 A collected at the ESRF, Grenoble, France . Full elucidation of the structure has only become possible with the complete knowledge of the as-isolated and fully reduced crystal structures . The analysis clarifies the significant movements in the position of the Fe atom linked to the persulfide moiety in the oxidized as-isolated protein and the S atom of the persulfide itself as the protein is reduced . The structures of the as-isolated and reduced states are discussed in terms of the putative function of the HCP proteins. Biol Trace Elem Res, 2003 Nov, 95(2), 97 - 106 Serum levels of vitamins A, C, and E, beta-carotene, selenium, and zinc in patients with Behçet's disease: a controlled study; Erel A et al.; Behcet's disease is a multisystemic disease characterized by activation and remission periods . The etiopathogenesis is not exactly known; a genetic defect in the immunoregulatory system induced by infectious agents, like viruses and bacteria, is thought to cause the disease . In this study, we examine the serum levels of vitamins A, C, and E, beta-carotene, selenium, and zinc in Behcet's disease patients and investigate the relationship between these serum levels and the activation of the disease . We conclude that adding vitamin E to the treatment of Behcet's disease patients and its effects on the prognosis of the disease need to be further investigated by controlled studies. Biochim Biophys Acta, 2003 Dec 3, 1618(1), 59 - 66 Characterisation of subunit III and its oligomer from spinach chloroplast ATP synthase; Poetsch A et al.; Proton ATP synthases carry out energy conversion in mitochondria, chloroplasts, and bacteria . A key element of the membrane integral motor CFO in chloroplasts is the oligomer of subunit III: it converts the energy of a transmembrane electrochemical proton gradient into rotational movement . To enlighten prominent features of the structure-function relationship of subunit III from spinach chloroplasts, new isolation methods were established to obtain highly pure monomeric and oligomeric subunit III in milligram quantities . By Fourier-transform infrared (FTIR) and CD spectroscopy, the predominantly alpha-helical secondary structure of subunit III was demonstrated . For monomeric subunit III, a conformational change was observed when diluting the SDS-solubilized protein . Under the same conditions the conformation of the oligomer III did not change . A mass of 8003 Da for the monomeric subunit III was determined by MALDI mass spectrometry (MALDI-MS), showing that no posttranslational modifications occurred . By ionisation during MALDI-MS, the noncovalent homooligomer III14 disaggregated into its III monomers. J Theor Biol, 2004 Feb 7, 226(3), 341 - 8 Chaos game representation of protein sequences based on the detailed HP model and their multifractal and correlation analyses; Yu ZG et al.; Similar to the chaos game representation (CGR) of DNA sequences proposed by Jeffrey (Nucleic Acid Res . 18 (1990) 2163), a new CGR of protein sequences based on the detailed HP model is proposed . Multifractal and correlation analyses of the measures based on the CGR of protein sequences from complete genomes are performed . The Dq spectra of all organisms studied are multifractal-like and sufficiently smooth for the Cq curves to be meaningful . The Cq curves of bacteria resemble a classical phase transition at a critical point . The correlation distance of the difference between the measure based on the CGR of protein sequences and its fractal background is also proposed to construct a more precise phylogenetic tree of bacteria. Mutat Res, 2003 Dec 10, 533(1-2), 211 - 26 Signaling events for metallothionein induction; Haq F et al.; Metallothioneins (MTs) are low molecular weight, cysteine-rich metal-binding proteins found in a wide variety of organisms including bacteria, fungi and all eukaryotic plant and animal species . They are the single most abundant group of intracellular zinc-binding proteins in eukaryotic cells {Prog . Food Nutr . Sci . 14 (1990) 193}: 5-10% of zinc in human hepatocytes is bound to MTs {Methods Enzymol . 205 (1991) 613; FEBS Lett . 39 (1974) 229} . A critical physiological role for MTs has been suggested to encompass control of zinc availability to proteins requiring zinc for activity, but has not been definitively described . Nevertheless, a hallmark of MT gene regulation is their pattern of expression in different cell types and tissues, and their inducibility by a host of chemical and physical agents acting directly or indirectly on multiple cis-acting motifs in the regulatory regions of MT genes {Prog . Nucleic Acid . Res . Mol . Biol., 66 (2001) 357} . The pattern of physical and chemical events regulating basal MT gene transcription, and induction or repression of MT gene activity, provides valuable insight into the potential functions of MTs . In this review, we describe the transcriptional regulatory processes involved in MT gene expression. Neurobiol Aging, 2003 Dec, 24(8), 1071 - 7 Use of YFP to study amyloid-beta associated neurite alterations in live brain slices; Brendza RP et al.; Neuritic plaques are one of the defining neuropathological features of Alzheimer's disease (AD) . These structures are composed of a buildup of fibrils of the amyloid-beta (Abeta) peptide (amyloid) surrounded by activated glial cells and degenerating nerve processes (dystrophic neurites) . To study neuritic plaques and possible abnormalities associated with dendrites, axons, and synaptic structures, we have developed an acute slice preparation model using PDAPP, yellow fluorescent protein (YFP) double transgenic mice (a mouse model with AD-like pathology that stably expresses YFP in a subset of neurons in the brain) . With laser scanning confocal microscopy, we have imaged living brain slices from PDAPP, YFP double transgenic mice as old as 20 months and have been able to visualize axons, dendrites, dendritic spines, and dystrophic neurites for many hours . Our initial studies suggest that dystrophic axons and dendrites within neuritic plaques are fairly stable structures in the absence of exogenous perturbations . This acute slice preparation model should prove to be a useful tool to explore the pathophysiology of Abeta-related axonal, dendritic, and synaptic dysfunction. J Struct Biol, 2003 Oct-Nov, 144(1-2), 172 - 83 Windex: a toolset for indexing helices; Ward A et al.; We describe here a set of procedures and algorithms that may be used as an aid in determining the indexing rule of a helical specimen . Crystallizing macromolecules into helical arrays has the potential to speed up and simplify the process of three-dimensional reconstruction of the macromolecular structure . The process of helical reconstruction has been largely automated except for the critical first step of indexing the helical diffraction pattern . This is quite often the rate-limiting step in the overall process, particularly in the case of large helical tubes, which have complicated helical diffraction patterns that may vary from tube to tube . We have developed a set of procedures, supported by a graphical user interface, that provide a straightforward and semi-automated approach to indexing a helical structure . The new procedures have been tested using a number of helical specimens, including TMV, acto-myosin, decorated microtubules, and a variety of helical tubes of a bacterial membrane protein. J Struct Biol, 2003 Oct-Nov, 144(1-2), 144 - 51 Low-resolution structure refinement in electron microscopy; Chen JZ et al.; A real-space structure refinement method, originally developed for macromolecular X-ray crystallography, has been applied to protein structure analysis by electron microscopy (EM) . This method simultaneously optimizes the fit of an atomic model to a density map and the stereo-chemical properties of the model by minimizing an energy function . The performance of this method is characterized at different resolution and signal-to-noise ratio conditions typical for EM electron density maps . A multi-resolution scheme is devised to improve the convergence of the refinement on the global energy minimum . Applications of the method to various model systems are demonstrated here . The first case is the arrangement of FlgE molecules in the helical filament of flagellar hook, in which refinement with segmented rigid bodies improves the density correlation and reduces severe van der Waals contacts among the symmetry-related subunits . The second case is a conformational analysis of the NSF AAA ATPase in which a multi-conformer model is used in the refinement to investigate the arrangement of the two ATPase domains in the molecule . The third case is a docking simulation in which the crystal structure of actin and the NOE data from NMR experiments on the dematin headpiece are combined with a low-resolution EM density map to generate an atomic model of the F-actin-dematin headpiece structure. Br J Nutr, 2003 Dec, 90(6), 1071 - 80 The effect of feeding structured triacylglycerols enriched in eicosapentaenoic or docosahexaenoic acids on murine splenocyte fatty acid composition and leucocyte phagocytosis; Kew S et al.; The effects of altering the type of n-3 polyunsaturated fatty acid (PUFA) in the mouse diet on the ability of monocytes and neutrophils to perform phagocytosis were investigated . Male weanling mice were fed for 7 d on one of nine diets which contained 178 g lipid/kg and which differed in the type of n-3 PUFA and in the position of these in dietary triacylglycerol (TAG) . The control diet contained 4.4 g alpha-linolenic acid/100 g total fatty acids . In the other diets, eicosapentaenoic acid (EPA) or docosahexaenoic acid (DHA) replaced a proportion (50 or 100 %) of the alpha-linolenic acid, and were in the sn-2 or the sn-1(3) position of dietary TAG . There were significant increases in the content of n-3 PUFA in spleen-cell phospholipids when EPA or DHA was fed . These increases were largely independent of the position of EPA or DHA in dietary TAG except when EPA was fed at the highest level, when the incorporation was greater when it was fed in the sn-2 than in the sn-1(3) position . There was no significant effect of dietary DHA on monocyte or neutrophil phagocytic activity . Dietary EPA dose-dependently decreased the number of monocytes and neutrophils performing phagocytosis . However, when EPA was fed in the sn-2 position, the ability of active monocytes or neutrophils to engulf bacteria was increased in a dose-dependent fashion . This did not occur when EPA was fed in the sn-1(3) position . Thus, there appears to be an influence of the position of EPA, but not of DHA, in dietary TAG on its incorporation into cell phospholipids and on the activity of phagocytic cells. J Oral Rehabil, 2003 Dec, 30(12), 1177 - 82 In vitro comparison of the efficacy of Carisolv and conventional rotary instrument in caries removal; Yazici AR et al.; The purpose of this in vitro study was to compare the efficacy of a new chemomechanical caries removal agent, Carisolv (MediTeam AB, Savedalen, Sweden), with conventional slow-speed rotary instrument (bur) . Fourteen extracted human molar teeth with deep dentine caries and no enamel coverage were selected for the study . Their laser fluorescence values were over 30 (DIAGNOdent; KaVo, Biberach, Germany) . After the teeth were sectioned through the centre of the carious lesion, one half was removed with conventional drilling (bur); the other half was removed with Carisolv gel . Removal of carious dentine was continued until the lesion was deemed caries-free by visual and tactile criteria . The preparation time for each caries removal technique was also noted . The two halves of each tooth were fixed in 10% buffered-formaldehyde for 1 week . They were then decalcified, dehydrated and embedded in paraffin blocks for histological studies . After taking serial sections of 5 microm thickness, sections were mounted on glass slides, deparaffinized, dehydrated and stained with toluidine blue for observation under a light microscope . Each section was examined for the presence of bacteria . Complete removal of caries was achieved in 13 (93%) of 14 conventionally prepared teeth, and 5 (36%) of 14 chemomechanically prepared teeth (P < 0.05) . Mean (+/-SD) time for caries removal was 272 s (+/-53.3) with Carisolv, and 116 s (+/-49.4) with drilling . The results of this study suggest that conventional rotary instrument (bur) was more effective than Carisolv in removal of carious tissue and also takes shorter time. Environ Microbiol, 2003 Dec, 5(12), 1226 - 41 Integrated regulation in response to aromatic compounds: from signal sensing to attractive behaviour; Shingler V; Deciphering the complex interconnecting bacterial responses to the presence of aromatic compounds is required to gain an integrated understanding of how aromatic catabolic processes function in relation to their genome and environmental context . In addition to the properties of the catabolic enzymes themselves, regulatory responses on at least three different levels are important . At a primary level, aromatic compounds control the activity of specific members of many families of transcriptional regulators to direct the expression of the specialized enzymes for their own catabolism . At a second level, dominant global regulation in response to environmental and physiological cues is incorporated to subvert and couple transcription levels to the energy status of the bacteria . Mediators of these global regulatory responses include the alarmone (p)ppGpp, the DNA-bending protein IHF and less well-defined systems that probably sense the energy status through the activity of the electron transport chain . At a third level, aromatic compounds can also impact on catabolic performance by provoking behavioural responses that allow the bacteria to seek out aromatic growth substrates in their environment. Cell Microbiol, 2003 Dec, 5(12), 861 - 73 Genome sequencing and comparative genomics of tropical disease pathogens; Carlton JM; The sequencing of eukaryotic genomes has lagged behind sequencing of organisms in the other domains of life, archae and bacteria, primarily due to their greater size and complexity . With recent advances in high-throughput technologies such as robotics and improved computational resources, the number of eukaryotic genome sequencing projects has increased significantly . Among these are a number of sequencing projects of tropical pathogens of medical and veterinary importance, many of which are responsible for causing widespread morbidity and mortality in peoples of developing countries . Uncovering the complete gene complement of these organisms is proving to be of immense value in the development of novel methods of parasite control, such as antiparasitic drugs and vaccines, as well as the development of new diagnostic tools . Combining pathogen genome sequences with the host and vector genome sequences is promising to be a robust method for the identification of host-pathogen interactions . Finally, comparative sequencing of related species, especially of organisms used as model systems in the study of the disease, is beginning to realize its potential in the identification of genes, and the evolutionary forces that shape the genes, that are involved in evasion of the host immune response. Biofouling, 2003 Oct, 19(5), 327 - 34 A new antifouling bioassay monitoring brown algal spore swimming behaviour in the presence of echinoderm extracts; Iken K et al.; Epibiosis, the colonization of biogenic surfaces by epibiotic organisms such as bacteria, filamentous algae, and sessile invertebrates, poses a major threat to the fitness and survival of macroorganisms which could potentially be fouled . Fouling of artificial submerged structures can also cause severe economic problems, making the need for refined bioassays to determine the efficacy of potential antifouling compounds even more important . The aim of this study was to use the distinct swimming behaviour of zoospores of the fouling brown alga Hincksia irregularis to develop a new laboratory antifouling bioassay to test the effect of marine natural products . Spores were exposed to different concentrations of aqueous and organic extracts from body walls of sympatric echinoderms (Asteroidea: Luidia clathrata, Astropecten articulatus; Ophiuroidea: Astrocyclus caecilia) . Computer-assisted motion analysis was used to distinguish between the straight and fast swimming movements of undisturbed spores (controls) and the helical and erratic swimming patterns of chemically irritated spores, using the quantitative parameters rate of direction change (RCD) and swimming speed (SPD) . The ratio RCD/SPD of spore swimming paths at extract treatments compared to controls can be used to quantify the detrimental effect of echinoderm extracts . Echinoderm extracts had significant effects on spore swimming behaviour at concentrations three orders of magnitude lower than that present naturally in the echinoderm body walls (mg extract/dry weight echinoderm body wall) . Comparative studies on spore settlement and germination under similar treatment conditions show that changes in spore swimming behaviour reflect decreased fitness and survivourship of algal spores . It is suggested that this bioassay can be used to screen potential antifouling extracts and compounds at very low concentrations, making this assay particularly suitable for detection of concentration dependent effects and for bioassay-guided fractionation of extracts to identify active compounds. Zhong Yao Cai, 2003 Jul, 26(7), 471 - 4 {Diseases and its control on Dendrobium}; Zeng S et al.; The diseases on the Dendrobium plants and their occurrence and damage as well as control methods have been investigated and studied . 11 kinds of fungi, 4 kinds of bacteria, 3 kinds of virus and one root-knot nematode were recorded . To control them effectively, cultural methods such as selecting cultivable field, keeping the field sanitation, enhancing cultural operations are mostly recommended . The application of chemical germicides is also stressed. Ground Water, 2003 Nov-Dec, 41(6), 816 - 27 A modular injection system, multilevel sampler, and manifold for tracer tests; Mailloux BJ et al.; Ground water injection and sampling systems were developed for bacterial transport experiments in both homogenous and heterogeneous unconsolidated, surficial aquifers . Two types of injection systems, a large single tank and a dynamic mixing tank, were designed to deliver more than 800 L of amended ground water to the aquifer over 12 hours, without altering the ground water temperature, pH, Eh, or dissolved gas composition . Two types of multilevel samplers (MLSs) were designed and installed . Permanent MLSs performed well for the homogenous surficial aquifer, but their installation procedure promoted vertical mixing, which could obfuscate experimental data obtained from vertically stratified, heterogeneous aquifers . A novel, removable MLS was designed to fit in 2- and 4-inch wells . Expandable O-rings between each sampling port hydraulically isolated each port for sample collection when a nut was tightened at the land surface . A low-cost vacuum manifold system designed to work with both MLS designs used 50 mL centrifuge tubes to efficiently sample 12 MLS ports with one peristaltic pump head . The integrated system was developed and used during four field campaigns over a period of three years . During each campaign, more than 3000 ground water samples were collected in less than one week . This system should prove particularly useful for ground water tracer, injection, and push-pull experiments that require high-frequency and/or high-density sampling. Rapid Commun Mass Spectrom, 2003, 17(23), 2655 - 60 Analysis of ketones by selected ion flow tube mass spectrometry; Smith D et al.; A selected ion flow tube mass spectrometry (SIFT-MS) study of the reactions of H3O+, NO+ and O2+* ions with the ketones (M) 2-heptanone, 2-octanone, 2-nonanone, 2-undecanone and 2-aminoacetophenone has been conducted in preparation for studies of volatile emissions from bacteria . The H3O+ reactions all proceed rapidly via exothermic proton transfer, producing only MH+ ions that form their monohydrates when water vapour is present in the helium carrier gas . The O2+* reactions proceed rapidly via dissociative charge transfer producing parent cations M+* and some fragment ions . The NO+ reactions form the NO+M adduct ions at rates which are dependent on the pressure of the helium carrier gas . Combining the present NO+ kinetic data with those available from previous SIFT studies, the phenomenon of charge transfer complexing is clearly demonstrated . This results in adduct formation in these NO+/ketone reactions at or near the collisional rate . SIFT-MS spectra are presented to illustrate the simplicity of SIFT-MS analysis of ketones using both H3O+ and NO+ precursor ions . J Pathol, 2003 Dec, 201(4), 596 - 602 Long-term infection with Helicobacter felis and inactivation of the tumour suppressor gene p53 cumulatively enhance the gastric mutation frequency in Big Blue transgenic mice; Jenks PJ et al.; The aims of this study were to determine whether colonization with Helicobacter felis resulted in the accumulation of mutations within murine gastric tissue and whether the degree of genetic damage was increased by p53 deficiency . Female C57BL/6 mice carrying either the lambda/lacI transgene (Big Blue transgenic mice) or the lambda/lacI transgene and deficient in one allele of the p53 tumour suppressor gene (TSG-p53/Big Blue) were inoculated with H felis . Seven months after inoculation, mutations in the target lacI gene were assessed using the Big Blue transgenic mutagenesis assay system in these animals and in controls . There was an approximately two-fold increase in lacI mutations in gastric mucosa harvested from mice infected with H felis and also from non-infected mice heterozygous for the p53 allele relative to wild-type mice . The mutation frequency in mice infected with H felis and deficient in one allele of p53 was increased approximately three-fold . Active gastric inflammation was significantly greater in H felis-infected p53 hemizygous mice compared with H felis p53 wild-type mice . Gastric epithelial proliferation was similarly increased with infection in both of these latter groups of mice . In infected mice, there was a significant correlation between the mutation frequency and the degree of active gastric inflammation . These data suggest a synergistic action between infection with H felis and p53 deficiency in the accumulation of mutations within gastric tissue . Active neutrophil infiltration in gastric Helicobacter infection may contribute to the increased levels of mutation observed . Water Sci Technol, 2003, 48(6), 263 - 9 Effect of natural and modified zeolite addition on anaerobic digestion of piggery waste; Milan Z et al.; The effect of natural and modified zeolites on the anaerobic degradation of acetate and methanol was evaluated by the determination of specific methane productivity (SMP) in batch minidigesters of 50 mL at doses of 0.01, 0.05 and 0.1 g of zeolite/g of VSS . The effects of the different zeolite concentrations were determined by the results of the SMP . A kinetic characterization with data of accumulated methane gas volume was also carried out . In the second phase of the study, the effects of natural and nickel zeolite concentrations were tested with piggery waste in laboratory scale digesters of 2.5 L operating at semi continuous mode, by increasing the organic load applied from 0.2 to 22.0 g TCOD/d corresponding to organic loading rates (OLR) of 0.1-8.8 g TCOD/l x d . A greater effect of modified zeolite on SMP was observed, with an increase of 8.5 times with magnesium zeolite, 4.4 times with cobalt zeolite and 2.8 times with nickel zeolite . Two phases were defined in the kinetic study and an increase of more than 2 times the apparent constant of digesters with modified zeolites was observed in the second phase when compared to unmodified natural zeolite . Modified natural zeolite addition to digesters can allow an increase in the potential biodegradability of piggery waste solid fraction and/or a considerable reduction of digestion volume. Water Sci Technol, 2003, 48(6), 249 - 54 The influence of pH in the hydrolytic stage of anaerobic digestion of the organic fraction of urban solid waste; Dinamarca S et al.; The influence of the pH in the first stage, the hydrolytic stage, of the anaerobic digestion of the organic fraction of urban solid waste in a two phase anaerobic reactor was studied . The reactor was fed with a solution of the organic fraction of urban solid residues containing 5 to 7% solids . Four reactors with a working volume of 3 L were used, the experiments were done at three controlled pHs; 6, 7, and 8, and one with free pH, the temperature was keep at 37 degrees C in all the experiments . The higher degradation of TSS and VSS was obtained in the reactors operated at pH 7 and 8; 75% degradation of TSS and 85% degradation of VSS . The volatile fatty acids were determined at the different pH conditions, no significant differences were found, and as was expected, the acetic acid was found at the higher value among them (from 25 to 29 g/L) . According to the results obtained it is possible to conclude that in the case of the hydrolytic stage of the anaerobic digestion of the organic fraction of urban solid waste it is not necessary to control the pH, the pH is kept stable by the buffer effect of the protein residues and other macromolecules present in the residue. Water Sci Technol, 2003, 48(6), 227 - 34 Performance evaluation of an UASB reactor used for combined treatment of domestic sewage and excess aerobic sludge from a trickling filter; Pontes PP et al.; This work aimed at evaluating the influence of the excess sludge produced in a trickling filter (TF) on the performance of a UASB reactor used for the combined treatment of domestic sewage and aerobic sludge . During phase 1 of the research, the UASB reactor/TF system was fed with domestic sewage pumped directly from the sewer collector of Arrudas stream, in Belo Horizonte-Brazil . During phase 2, besides feeding the reactor with domestic sewage, the UASB reactor was also fed with the aerobic sludge from the trickling filter . The UASB reactor, with a volume of 420 litres, was operated at a mean hydraulic detention time of 5.6 hours in both operational phases . After 133 days of continuous monitoring, no detrimental effect was noticed on the performance of the UASB reactor regarding the return of the aerobic sludge produced in the TF . On the contrary, the COD results indicated a higher percentage of compliance with the discharge standards set forth by the Brazilian environmental legislation . During phase 2 of the research, when the UASB reactor was used for combined treatment of domestic sewage and excess aerobic sludge from the TF, the anaerobic effluent presented mean concentrations of 108 mgCOD x L(-1), 57 mgBOD x L(-1) and 18 mgTSS x L(-1). Water Sci Technol, 2003, 48(6), 219 - 26 Decentralised treatment of concentrated sewage at low temperature in a two-step anaerobic system: two upflow-hybrid septic tanks; Elmitwalli TA et al.; The decentralised treatment of concentrated sewage (about 3,600 mgCOD/l) at low temperature was investigated in a two-step anaerobic system: two-anaerobic hybrid (AH) septic tanks (each 0.575 m3) . The two reactors were placed in a temperature controlled-room and the HRT was 2.5 days for each reactor . The system was fed with concentrated domestic sewage, mainly black water from about 40 toilets flushed with only 4 litre of water and a limited amount of grey water . The system showed high removal efficiency for the different COD fractions . Mean removal efficiencies in the two-step AH-septic tank at 5 days HRT and 13 degrees C were 94, 98, 74 and 78% for total COD, suspended COD, colloidal COD and dissolved COD respectively . The results of short run experiments indicated that the presence of reticulated polyurethane foam (RPF) media in the AH-septic tank improved the removal of suspended COD by 22% . The first AH-septic tank was full of sludge after 4 months of operation due to the high removal of particulate COD and the limited hydrolysis at low temperature conditions . Therefore, a simple mathematical model was developed based on ADM1 (the IWA model in 2002) . Based on the experimental results and the mathematical model, only a one-step AH septic tank is required . An HRT of 5.5-7.5 days is needed for that one-step AH septic tank to treat concentrated sewage at a low temperature of 13 degrees C . Such a system can provide a total COD removal as high as 87% and will be full of sludge after a period of more than a year. Water Sci Technol, 2003, 48(6), 179 - 86 Operating feasibility of anaerobic whey treatment in a stirred sequencing batch reactor containing immobilized biomass; Ratusznei SM et al.; The scope of this work was to evaluate the operating feasibility of anaerobic whey treatment in a stirred sequencing batch reactor (ASBR) containing biomass immobilized on inert support . Assays were performed using 8-hour cycles and agitation rate of 200 rpm at 30 +/- 1 degrees C, for treating cheese whey containing 500 to 4,000 mgCOD/L, which corresponded to a volumetric organic load (VOL) of 0.81 to 5.7 gCOD/L x d . Stability and high organic matter removal of about 96% were achieved at effluent concentration below 160 mgCOD/L for non filtered samples . Operating stability of the reactor was shown to be strongly dependent on the alkalinity supplementing strategy during the assay, especially during the startup period, where NaHCO3 supplementation was approximately 20-30% of the chemical oxygen demand (mgNaHCO3/mgCOD) . After startup, alkalinity supplementation could be reduced down to 10% maintaining efficiency and stability . Moreover, proper homogenization of the system through mechanical agitation was also shown to be indispensable, especially with increasing organic load. Water Sci Technol, 2003, 48(6), 141 - 7 Anaerobic degradation kinetics of a cholesteryl ester; Gutierrez S et al.; The most important components of wool scouring effluent grease are esters of sterols . Cholesteryl palmitate (CP) is the main ester in this grease . In this paper, the influence of the ester concentration in the anaerobic digestion and the relative rate of the different degradation steps, are studied . The experiment was carried out to measure methane production in the anaerobic degradation of acetate, palmitic acid (PA) and CP . A first-order kinetic model was assumed for hydrolysis and Monod models were assumed for both the methanogenic and acetogenic steps . Maximum hydrolysis rate was found to be around 20 times faster than the maximum methanogenic reaction rate during the experience . The lanolin emulsion drop size effect was also evaluated employing fine and coarse stock lanolin emulsions and no adapted sludge . Concentrations of 13.7 to 4.6 gCOD x l(-1) were employed . In a previous study, the effect of palmitic acid emulsion size was found important when similar sludge was tested . When esters are degraded, a significant effect of drop size on the degradation rate was not found . The difference between CP and PA emulsions behavior could be due to the fact that cholesterol produced during the ester degradation has a protective effect on the sludge. Water Sci Technol, 2003, 48(6), 33 - 40 Accumulation of long chain fatty acids onto anaerobic sludge under steady state and shock loading conditions: effect on acetogenic and methanogenic activity; Pereira MA et al.; Accumulation of substrate onto the biomass was quantified under steady-state and shock conditions in a fixed bed reactor fed with an oleic acid-based synthetic effluent . The accumulation of substrate onto the sludge was more dependent on oleic acid concentration than on oleic acid loading rate and decreased the acetogenic, acetoclastic and hydrogenophilic activity . However, even when the methanogenic activity measurements indicate a severe inhibition, the anaerobic sludge was able to methanise efficiently the accumulated substrate that was mainly adsorbed LCFA . Methanogenic activity measurements for a sludge loaded with 2,861 mg COD/gVSS as LCFA, revealed that only hydrogenophilic activity was detected, whereas the methanogenic activities with acetate, propionate and butyrate as substrates were null . However the methanogenic activity of the same sludge after allowing the depletion of the adsorbed LCFA were significantly enhanced in the presence of all substrates, except in propionate . A discussion about the relative importance of metabolic inhibition and transport limitations for the anaerobic degradation of LCFA is launched. Acta Med Croatica, 2003, 57(4), 295 - 301 {Detection of human papillomaviruses and other agents causing sexually transmitted diseases with molecular diagnosis methods}; Grce M et al.; Causative agents of sexually transmitted diseases (STD) are different types of bacteria, viruses, fungi and protozoa . The last two decades of the twentieth century were marked with a sudden rise in the number of cases of STDs . Human immunodeficiency virus (HIV), which emerged in the 1980s, is the most prominent STD agent because of its fast spread and severity of the disease it causes, acquired immunodeficiency syndrome (AIDS) . Beside HIV, human papillomaviruses (HPVs), herpes simplex viruses (HSVs) and Chlamydia trachomatis are nowadays among most health-threatening STD pathogens . In order to stop the spread of infection, apart from education about precautions, early detection of the disease is essential . Although most STD pathogens can be detected by classical methods of cultivation, biochemical and/or serologic methods, molecular diagnosis of infectious diseases has largely simplified and accelerated their detection . For instance, HPVs that cause benign and malignant tumors of genital skin and mucosa cannot be routinely detected on cell culture, whereas serologic analysis is not sensitive and informative enough . Moreover, cytologic (Pap smear) and histologic analyses can indicate changes associated with HPV infection, but neither of these methods can prove the presence of HPV . That is why the molecular methods are essential to demonstrate the presence of the infection and, even more important, to determine the type of the virus, which is associated either with low-grade or high-grade genital lesions . There are numerous methods based on hybridization with DNA or RNA probes, some of them are suitable for detecting wide range of types and screening of large collection of samples . However, the most sensitive and informative methods are based on polymerase chain reaction (PCR), and they have the advantage of being able to determine the type of the virus and distinguishing between multiple infections . Herein, we present when and why molecular analysis is useful and necessary for the detection of STD agents. Acta Med Croatica, 2003, 57(4), 255 - 9 {MHC tetramers: tracking specific immunity}; Kosor E et al.; In an adaptive immune response, antigen is recognized by two distinct sets of highly variable receptor molecules: (1) immunoglobulins, that serve as antigen receptors on B cells and (2) the antigen-specific receptors on T cells . T cells play important role in the control of infection and in the development of protective immunity . These cells can also mediate anti-tumor effects and, in case of autoimmune syndromes, contribute to the development and pathology of disease . The specificity of T cells is determined by T cell receptors (TCR) . Understanding of the success of immune responses requires the direct measurement of antigen-specific T lymphocytes . Cell with major histocompatibility complex (MHC) class I molecules are able to present antigens to antigen-specific CD8+ cytotoxic T lymphocytes . MHC class I molecules present small peptides (epitopes) processed from intracellular antigens such as viruses and intracellular bacteria . MHC class I molecules in humans are designated as human leukocyte antigen (HLA) class I and divided into HLA-A, -B and -C . CD8+ T cells recognize MHC class I molecules and after activation produce proteins that destroy infected cells . MHC class II molecules receive their peptides mainly from extracellular and soluble antigens and present them to the CD4+ T helper cells . A recently described technique that can be used in flow cytometry enables us to quantify ex vivo antigen-specific T cells by binding of soluble tetramer MHC-peptide complexes attached to fluorochrome . Quantitative analyses of antigen-specific T cell populations provide important information on the natural course of immune responses . The interaction of T cell receptors on T lymphocytes with tetrameric MHC-peptide complexes mimics the situation on the cell surface, and allows for reliable binding . Tetramers consist of four biotinylated HLA-peptide epitope complexes bound to streptavidin conjugated with fluorescent dye . Tetramer technology has sensitivity of detection as little as 0.02% of total cytotoxic T cell pool or T helper cell pool (i.e . approximately 1 in 50.000 lymphocytes) . The combination of this technology with intracellular cytokine staining methods opens up significantly better ways of studying these cells than previously possible, allowing immunologists to look at their life cycle (activation and proliferation), manner of death (aging and apoptosis) and effector function (cytotoxic potential and cytokine production) . MHC tetramers class I have yielded useful insights into in vivo dynamic and function of antigen-specific CD8+ T cells in viral infections, parasitic infections, cancer, autoimmune disease and transplantation . This knowledge is of special interest for immunotherapy, diagnostic monitoring of T cell mediated immunity, and the development of new vaccination strategies . There is some possibility for cell therapy with antigen-specific CD8+ T cells for various diseases including cancer and viral infections . Targeted immunotherapy of selective deletion of auto--or alloreactive T cells with MHC tetramers may be important for the treatment of autoimmune disease, or to prevent the rejection of transplanted organs . The utility of this technique for the immunotherapy in vivo needs to be confirmed and modified in further research . Understanding how antigen-specific cells develop and function in different circumstances and pathologies will be the key to unravelling the secrets of cellular immune system. J Am Acad Dermatol, 2003 Dec, 49(6), 979 - 1000; quiz 1000-2 Tropical dermatology: viral tropical diseases; Lupi O et al.; Viruses are important pathogens in tropical areas; most of them, especially the tropical hemorrhagic fevers, produce mucocutaneous manifestations . More than any other kind of pathogen, viruses have the possibility for being widespread, since they have a greater probability of mutation than do bacteria, can cross species barriers easily, and infect both human beings and animals in habitats with a great biodiversity . Tropical habitats also have been subject to major ecologic changes in the last few decades, exposing humans to direct contact with these viruses and allowing hemorrhagic fevers due to new emergent viruses such as flaviviruses, filoviruses, arenaviruses, and hantaviruses to become major threats to public health . The collapse of eradication programs in many countries, as well as population increases and ecologic modifications, have led to the spread of dengue and yellow fever to large portions of the world owing to the dissemination of vectors, especially mosquitoes, with broad ecologic ranges . Viruses previously restricted to some geographic areas, such as Rift Valley fever, Crimean-Congo hemorrhagic fever, West Nile fever, and monkeypox are now affecting new countries and populations . Other viruses such as herpes B infection often affect travelers and animal handlers in most parts of the world . Dermatologic lesions occur in all these diseases and can facilitate a rapid diagnosis, leading to control of the virus and helping prevent possible outbreaks. J Cell Biol, 2003 Nov 24, 163(4), 715 - 21 Dynamics and calcium sensitivity of the Ca2+/myristoyl switch protein hippocalcin in living cells; O'Callaghan DW et al.; Hippocalcin is a neuronal calcium sensor protein that possesses a Ca2+/myristoyl switch allowing it to translocate to membranes . Translocation of hippocalcin in response to increased cytosolic {Ca2+} was examined in HeLa cells expressing hippocalcin-enhanced yellow fluorescent protein (EYFP) to determine the dynamics and Ca2+ affinity of the Ca2+/myristoyl switch in living cells . Ca2+-free hippocalcin was freely diffusible, as shown by photobleaching and use of a photoactivable GFP construct . The translocation was dependent on binding of Ca2+ by EF-hands 2 and 3 . Using photolysis of NP-EGTA, the maximal kinetics of translocation was determined (t1/2 = 0.9 s), and this was consistent with a diffusion driven process . Low intensity photolysis of NP-EGTA produced a slow {Ca2+} ramp and revealed that translocation of hippocalcin-EYFP initiated at around 180 nM and was half maximal at 290 nM . Histamine induced a reversible translocation of hippocalcin-EYFP . The data show that hippocalcin is a sensitive Ca2+ sensor capable of responding to increases in intracellular Ca2+ concentration over the narrow dynamic range of 200-800 nM free Ca2+. Infect Immun, 2003 Dec, 71(12), 7219 - 22 Abortive potency of Chlamydophila abortus in pregnant mice is not directly correlated with placental and fetal colonization levels; Bouakane A et al.; Abortion, placental and fetal colonization, and levels of gamma interferon were analyzed for four Chlamydophila abortus strains presenting antigenic variations in a mouse model . Expression of virulence of these strains varied and indicated that abortion was not directly related to the number of bacteria in the placenta, and thus, other factors may have an important role in activating the abortion process. Infect Immun, 2003 Dec, 71(12), 7208 - 10 Functional BvgAS virulence control system in Bordetella bronchiseptica is necessary for induction of Ca2+ transients in ciliated tracheal epithelial cells; Groathouse NA et al.; To study initial Bordetella bronchiseptica-tracheal epithelial cell interactions, we coincubated B . bronchiseptica with rabbit tracheal explant cultures and assayed bacterial adherence and host cell Ca(2+) signaling . Wild-type B . bronchiseptica (RB50) preferentially adhered to cilia and induced ciliated host cell Ca(2+) transients within 2 min of coincubation, whereas coincubation with an avirulent strain (RB57) resulted in limited binding and Ca(2+) signaling . The described cell system allows for assessment of initial B . bronchiseptica-host cell interactions that can contribute to pathogenicity or to host cell defense