Biochemistry, 2002 Jun 11, 41(23), 7253 - 66 Organization of the membrane domain of the human liver sodium/bile acid cotransporter; Hallen S et al.; Mammalian sodium/bile acid cotransporters (SBATs) are glycoproteins with an exoplasmic N-terminus, an odd number of transmembrane regions, and a cytoplasmic C-terminus . Various algorithms predict eight or nine membrane-embedded regions derived from nine hydrophobic stretches of the protein (H1-H9) . Three methods were used to define which of these were transmembrane or membrane-associated segments in the liver bile acid transporter . The first was in vitro translation/insertion scanning using either single hydrophobic sequences between the N-terminal domain of the alpha-subunit of the gastric H,K-ATPase and the C-terminal domain of the beta-subunit that contains five N-linked glycosylation exoplasmic flags or using constructs beginning with the N-terminus of the transporter of various lengths and again ending in the C-terminus of the H,K-ATPase beta-subunit . Seven of the predicted segments, but not the amphipathic H3 and H8 sequences, insert as both individual signal anchor and stop transfer sequences in the reporter constructs . These sequences, H3 and H8, are contained within two postulated long exoplasmic loops in the classical seven-transmembrane segment model . The H3 segment acts as a partial stop transfer signal when expressed downstream of the endogenous H2 . In a similar manner, the other amphipathic segment, H8, inserts as a signal anchor sequence when translated in the context with the upstream transporter sequence in two different glycosylation constructs . Alanine insertion scanning identified regions of the transporter requiring precise alignment of sequence to form competent secondary structures . The transport activity of these mutants was evaluated either in native protein or in a yellow fluorescent protein (YFP) fusion protein construct . All alanine insertions in H3 and H8 abolished taurocholate uptake, suggesting that both these regions have structures with critical intramolecular interactions . Moreover, these insertions also prevented trafficking to the plasma membrane as assessed by confocal microscopy with a polyclonal antibody against either the C-terminus of the transporter or the YFP signal of the YFP-transporter fusion protein . Two glycosylation signals inserted in the first postulated loop region and four of five such signals in the second postulated loop region were not recognized by the oligosaccharide transferase, and the L256N mutation exhibited 10% glycosylation and was inactive . These findings support a topography with nine membrane-spanning or membrane-associated segments. Lupus, 2002, 11(4), 234 - 9 The nature and outcome of infection in systemic lupus erythematosus; Gladman DD et al.; Infection remains a major cause of morbidity and mortality in systemic lupus erythematosus (SLE) . To describe the nature and outcomes of infection and determine their associated risk factors in patients with SLE, we performed a nested case-control study at the University of Toronto Lupus Clinic, with prospective follow-up according to a standard protocol since 1970 . Cases were SLE patients seen between January 1987 and January 1992 who had documented infections and controls were patients without infection from the same cohort matched for age, gender and time of visit . The type, site and outcome of infection were recorded for each case . A conditional logistic regression analysis was performed to compare factors associated with infection in cases and their controls . Ninety-three patients had 148 infection episodes; the majority were bacterial, but viral, fungal and protozoan organisms were also identified (multiple organisms in seven) . Forty-eight patients required hospital admission and three patients died . Steroids at time of infection, as well as use ever, duration and dose, immunosuppressives at time of infection and use ever, active renal disease, CNS damage, SLEDAI at the time of infection, adjusted mean SLEDAI and variability measure were significantly associated with infection by univariate analysis . By multivariate analysis one factor remained statistically significant: use of steroids ever (P = 0.029) . Infection carries a large burden for SLE patients . Until new medications which will control disease activity without predisposing to infection are developed, careful titration of steroids and cytotoxic drugs to control disease activity will remain crucial. J Endod, 2002 Apr, 28(4), 287 - 90 Effect of methotrexate-induced neutropenia on pulpal inflammation in rats; Nakamura K et al.; The purpose of this study was to determine the role of neutropenia in pulpal inflammation . We investigated the effect of methotrexate-induced neutropenia on pulpal inflammation in rats . Pulpal inflammation was produced by pulpal exposure . Thirty-six rats were divided equally into control and experimental groups . The control animals received no injection, whereas the experimental animals were injected with 7.5 mg/kg of methotrexate once a day for 3 days before the pulpal exposure . The pulp was exposed in the mandibular first molar of all animals, and the exposed areas were left open . Animals were killed at 2, 4, and 7 days thereafter . Before they were killed, peripheral blood was taken . The number of total leukocytes and neutrophils in the peripheral blood of experimental animals was significantly decreased compared with those of control animals . The methotrexate-induced neutropenia resulted in the initiation of a bacterial invasion into the pulpal tissue and an increase in pulpal necrosis, as well as lessened abscess formation . Histometrically, the area of pulpal necrosis in experimental animals was significantly greater than that in the control animals . Immunohistochemically, the neutropenia resulted in inhibition of the infiltration by neutrophils . These results suggest that the neutrophil plays an important role in the defense against bacteria in pulpal tissue. Zh Mikrobiol Epidemiol Immunobiol, 2002 Mar-Apr, (2), 89 - 94 {Some mechanisms of Helicobacter pylori persistence}; Bukharin OV et al.; The mechanisms of the pathogenesis of Helicobacter pylori infection, ensuring the prolonged survival of these bacteria in the aggressive medium (gastric mucosa), are considered . A new approach to the systematization of the mechanisms of H . pylori persistence is proposed: the mechanisms ensuring the stability of H . pylori in the presence of aggressive physical and chemical factors, the mechanisms ensuring antagonistic effects in biocenosis and the mechanisms ensuring resistance to the protective factors of the host . Data on the persistence potential of H . pylori in accordance with the proposed classification are presented. Microb Ecol, 2002 May, 43(4), 408 - 15 Epub 2002 Apr 08. Endogenous methanogenesis stimulates oxidation of atmospheric CH(4) in alpine tundra soil; West AE et al.; Experiments were done to test the hypothesis that atmospheric CH(4) oxidizers in a well-drained alpine tundra soil are supported by CH(4) production from anaerobic microsites in the soil . Soil was subjected to 22 days of anaerobic conditions with elevated H(2) and CO(2) in order to stimulate methanogenesis . This treatment stimulated subsequent atmospheric CH(4) consumption, probably by increasing soil methanogenesis . After removal from anaerobic conditions, soils emitted CH(4) for up to 6 h, then oxidized atmospheric CH(4) at 111 (+/- 5.7) pmol (g dry weight)(-1) h(-1), which was more than 3 times the rate of control soils . Further supporting our hypothesis, additions of lumazine, a highly specific inhibitor of methanogenesis, prevented the stimulation of atmospheric CH(4) oxidation by the anaerobic treatment . The method used to create anaerobic conditions with elevated H(2) and CO(2) also elevated headspace CH(4) concentrations . However, elevated CH(4) concentrations under aerobic conditions did not stimulate CH(4) oxidation as much as preexposure to H(2) and CO(2) under anaerobic conditions . Anaerobic conditions created by N(2) flushing did not stimulate atmospheric CH4 oxidation, probably because N2 flushing inhibited methanogenesis by removing necessary precursors for methane production . We conclude that anaerobic conditions with elevated H(2) and CO(2) stimulate atmospheric CH(4) oxidation in this dry alpine tundra soil by increasing endogenous CH(4) production . This effect was prevented by inhibiting methanogenesis, indicating the importance of endogenous CH(4) production in a CH(4-) consuming soil. Nat Rev Genet, 2002 Jun, 3(6), 475 - 81 The curious history of yeast mitochondrial DNA; Williamson D; Forty years ago, soon after yeast mitochondrial DNA (mtDNA) was recognized, some animal versions of mtDNA were shown to comprise circular molecules . Supporting an idea that mitochondria had evolved from bacteria, this finding generated a dogmatic belief that yeast mtDNA was also circular, and the endless linear molecules actually observed in yeast were regarded as broken circles . This concept persisted for 30 years and has distorted our understanding of the true nature of the molecule. J Chemother, 1991 Jan, 3 Suppl 1, 93 - 7 The phagocytic process and the role of complement in host defense; Verhoef J; Three lines of defense play an integral role in host defense . The mechanical barrier (skin and mucous membrane: first line), non-specific defense (phagocytic cells non-specific humoral factors) and the specific line of defense . Phagocytic cells act in phases: chemotaxis, attachment of the bacteria to the membrane of the phagocytic cells, ingestion, killing and digestion . Attachment of the particle to receptors is only optimal when the bacteria are loaded with antibodies (IgG) and/or activated complement factors (C3b, C3Bbi), because the phagocyte has receptors for these opsonins (Fc, and C receptors) . The late complement factors are also able to kill and lyse certain bacteria without phagocytes . The killing mechanism of the phagocyte is complex . It is oxygen dependent and oxygen independent . Presumably toxic oxygen species are most important to kill bacteria by phagocytes. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai), 2001, 33(4), 365 - 367 In Memory of Professor WANG Ying-Lai; Lin QS et al.; Professor WANG Ying-Lai, world-renowned biochemist and a member of the Chinese Academy of Sciences, passed away at 19:10, May 5, 2001 resulting from an incurable disease . Since then, the Chinese Communist Party has lost an outstanding member struggling all his life for the development of science in China . The scientific communities in China have lost an outstanding scientist enjoying world prestige . His colleagues and students have lost a valuable friend and good teacher . Today, although he has left us, his scientific achievement and noble morality will be engraved on our mind forever . Born in an overseas Chinese family in Jinmen county, Fujian Province in 1907, Professor Wang lost his father when he was 2 years old and lost his mother when he was 6 . His hard childhood contributed, to some extent, to the forming of his strong and hard working personality . In 1925, he enrolled in Fujian Union College and Nanjing Jinling University successively to study chemistry and graduated in 1929 with excellent grade and a "Golden Key" Award . In 1938, Professor Wang continued his study in the Cambridge University in Britain and got his Ph.D . in 1941 . Later, he worked in the Cambridge University and carried on the research on he moglobin in the laboratory led by the famous scientist Keilin . After World War II, he declined the kind offering of Professor Keilin and returned to his motherland in 1945 . Thereafter, he worked in the former Medical College of Central University and the preparatory department of the Institute of Medical Science, Academia Sinica in Shanghai . Undoubtedly, Professor Wang was a great patriot . In 1950, Professor Wang was appointed the Deputy Director of the newly established Institute of Physiology and Biochemistry, the Chinese Academy of Sciences (CAS) . He joined the Jiu San Society in 1953 and became a member in its Central Committee and Vice Chairman in its Shanghai Branch . He was elected as a member of the Council of Biology in CAS in 1955 . Professor Wang had served as the Director of the Institute of Biochemistry, CAS since its establishment in 1958 and joined the Communist Party of China in the same year . He had served as Honorary Director of Institute of Biochemistry, CAS since 1984 and President of the Shanghai Branch of CAS from 1978 to 1983 . He was Honorary President and former President of Chinese Biochemical Society, Honorary Chief Editor and former Chief Editor of Acta Biochimica et Biophysica Sinica . Professor Wang was also elected the Delegate of the 3rd, 5th and 6th People's Congress . With the effort of Professor Wang, the International Meeting on Biochemistry was held successfully in China in 1987.Professor Wang, as chairperson of this conference, had made extremely important contribution to the meeting . As a world-renowned scientist, Professor Wang was Foreign Member of Belgian Royal Academy of Science, Literature and Fine Arts, Foreign Member of Hungarian Academy of Sciences, Foreign Member of Czech Academy of Sciences and Honorary Member of American Society of Biochemistry and Molecular Biology . Professor Wang was an outstanding scientist with great creativity, one of the founders of biochemical sciences in China, a distinguished organizer and leader, and a model of scientists and scientific research leaders in our country . He was honored as pioneer of biochemistry in China at a commendatory meeting for scientists working for 50 years held by the Shanghai Branch of CAS in the Spring Festival of 1985 . Professor Wang then cited the maxim "The future is yet for oneself to shape" to express his persistent sincerity in the development of biochemical research in China . Dr . Joseph Needham, the famous expert of history of science, appraised that Professor Wang was one of the persons who started and founded the biochemical research in China . The successful total synthesis of bovine insulin and yeast alanine transfer ribonucleic acid (tRNA) was the embodiment of decades of Professor Wang's devotion to initiating and developing the biochemical research in China . For these, he won the Special Achievement Award in the winter Biotechnology Symposium in Miami, U.S.A . in 1988 and the He Liang He Li Scientific and Technological Achievement Award of Hong Kong in 1996 . He contributed also in the initiative studies carried out by himself . When he was in Cambridge University, he first found the toxicity of excessive vitamin A and the defect of tissues as a result of vitamin E deficiency . He set up methods for the micro-determination of four water soluble vitamins, and demonstrated for the first time the existence of hemoglobin in the nodule bacteria of legume . He studied on the succinic dehydrogenase in the membrane after coming back to China and purified first in the world the membrane protein succinic dehydrogenase which could be reconstituted . He further revealed the linkage of coenzyme and enzyme . His work reached the leading level of the world and won the important achievement awards of CAS and National Scientific Meeting . In 1984, Professor Wang initiated a new research field of interaction of nucleic acids and proteins . He led a research group to study the interaction of the aminoacyl-tRNA synthetase and related tRNA, and published more than 60 papers in domestic and international journals . Professor Wang was not only a remarkable scientist, but also a strategic policymaker and leader of scientific research . His great contribution was due to his acute foresight and broad mind which directed the biochemical research in our country at an advanced starting point and catch up the trend of the world according to the international development of biological sciences . It was Professor Wang who made correct judgement and directed the research in the world frontiers, resolutely decided, organized and implemented the projects of total synthesis of bovine insulin and yeast alanine tRNA . These two great achievements of life sciences in the world frontiers have become milestones of biochemical sciences . In particular, the total synthesis of bovine insulin is the first success of total synthesis of protein in the world, which made a brilliant record for our country in the history of life science research . He also led the implementation of genetic engineering research in China in the 70's, which not only adjusted the direction of scientific research of the Institute of Biochemistry, but also accelerated the research of molecular biology in our country . Starting from the foundation of the nation, Professor Wang participated in and took charge of making the biochemistry and molecular biology parts of the planning program for science and technology development in China in 1956, 1962, 1964 and 1977 . He also took up some of the important tasks in the program with experts in the institute . As a deserving talent-finder, Professor Wang attracted, trained and brought up many leading talents of life science research in China, who contributed greatly to the development of biochemical research . On the initial stage of setting up the Institute of Biochemistry, he step by step invited Dr . ZOU Cheng-Lu(Chen-Lu TSOU), Dr . CAO Tian-Qin, Dr . ZHANG You-Duan, Dr . WANG De-Bao, Dr . NIU Jing-Yi, Dr . ZHOU Guang-Yu and other biochemical experts from abroad to work in the Institute, according to the needs of the research development . As a result, many important achievements were obtained and the Institute became well known at home and abroad . In training scientists, Professor Wang paid much of his attention to the development of biochemical research in China and educated many scientific researchers and academic leaders in biochemistry by setting up the national advanced biochemistry training classes with lectures given by the best experts in the Institute of Biochemistry . Professor Wang was also the person who founded the biochemical reagent industry in our country . The Dongfeng Biochemical Reagent Factory was established in 1958 under his leadership and produced amino acids for the synthesis of insulin and various biochemical reagents for the whole country . Long before our advocating of knowledge innovation and accelerating the industrialization of the scientific findings, Professor Wang had put it into practice 40 years ago . Professor Wang paid much attention to the cultivation of scientific morality and advocated the academic atmosphere of "dedication, realism, consolidation, courage" . In spite of his contribution, he did not put his name on the list of authors and the prize winners in the total synthesis of bovine insulin and yeast alanine tRNA . Affected by Professor Wang and scientists of the elder generation, an atmosphere of pursuing reality and refusing the undeserved reputation has been formed in the Institute of Biochemistry . Professor Wang had devoted his lifetime energy to the development of biochemistry in China . He deserved to be a pioneer in biochemistry of our country because of his scientific achievements and contributions . He had made basic, strategic and perspective contribution for the development of life sciences in our country . To be a man strict with himself and kind to others, cautious and unselfish, he had become a model in the scientific circle . He will be engraved on our heart forever . Although Professor Wang has passed away, it is consolable that along his footprint, his colleagues and students all over the country and abroad will continue to climb the new peaks in science . May you rest in peace, Professor Wang! Plant Cell Physiol, 2002 May, 43(5), 532 - 9 Isolation and characterization of a putative transducer of endoplasmic reticulum stress in Oryza sativa; Okushima Y et al.; Following endoplasmic reticulum (ER) stress that prevents correct folding or assembly of ER proteins, at least three responses occur to maintain cell homeostasis: induction of chaperones, attenuation of protein synthesis, and enhancement of lipid synthesis . Transducers that transmit ER stress to the nucleus have already been identified in yeast and mammals . We report here isolation of a cDNA, OsIre1, from rice encoding a putative homolog of Ire1p, a yeast transducer of ER stress . OsIre1 encodes a polypeptide consisting of 893 amino acids, in which two hydrophobic stretches are present in the amino-terminal (N-terminal) and middle regions, possibly serving as a signal peptide and a transmembrane domain, respectively . The carboxyl-terminal (C-terminal) domain was found to possess serine/threonine protein kinase and ribonuclease-like domains showing high similarities with regions in Ire1 homologs from other organisms . A fusion protein of OsIre1 and green fluorescent protein (GFP) expressed in tobacco BY2 cells could be demonstrated to localize to the ER and the N-terminal domain of OsIre1 could substitute for yeast Ire1p in yeast cells . When produced in bacteria as a fusion protein, the C-terminal region of OsIre1 showed autophosphorylation activity . These results thus indicate that OsIre1 encodes a putative plant transducer of ER stress. Plant Cell Physiol, 2002 May, 43(5), 513 - 21 pilG Gene cluster and split pilL genes involved in pilus biogenesis, motility and genetic transformation in the cyanobacterium Synechocystis sp . PCC 6803; Yoshihara S et al.; The unicellular motile cyanobacterium Synechocystis sp . PCC 6803 exhibits phototactic motility that depends on the type IV-like thick pilus structure . By gene disruption analysis, we showed that a gene cluster of slr1041, slr1042, slr1043 and slr1044, whose predicted products are homologous to PatA, CheY, CheW and MCP, respectively, was more or less required for pilus assembly, motility and natural transformation competency with extraneous DNA . By sequence homology, the missing cheA-like gene in this cluster was identified as novel split genes, slr0073 and slr0322, at separate loci on the genome . This was confirmed by non-motile phenotype of their disruptants . Unique hyperpiliation was observed in the slr1042 and slr0073 disruptants, suggestive of their specific interaction with pilT1 . The genes, thus identified as pil genes in this study, were designated pilG (slr1041), pilH (slr1042), pilI (slr1043), pilJ (slr1044), pilL-N (slr0073) and pilL-C (slr0322). Appl Environ Microbiol, 2002 Jun, 68(6), 3121 - 5 Use of the Verrucomicrobia-specific probe EUB338-III and fluorescent in situ hybridization for detection of "Candidatus Xiphinematobacter" cells in nematode hosts; Vandekerckhove TT et al.; Fluorescent in situ hybridization with a 16S rRNA probe specific for Verrucomicrobia was used to (i) confirm the division-level identity of and (ii) study the behavior of the obligate intracellular verrucomicrobium "Candidatus Xiphinematobacter" in its nematode hosts . Endosymbionts in the egg move to the pole where the gut primordium arises; hence, they populate the intestinal epithelia of juvenile worms . During the host's molt to adult female, the endosymbionts concentrate around the developing ovaries to occupy the ovarian wall . Some bacteria are enclosed in the ripening oocytes for vertical transmission . Verrucomicrobia in males stay outside the testes because the tiny spermatozoids are not suitable for transmission of cytoplasmic bacteria. Appl Environ Microbiol, 2002 Jun, 68(6), 3076 - 84 Crescent bodies of Parachlamydia acanthamoeba and its life cycle within Acanthamoeba polyphaga: an electron micrograph study; Greub G et al.; Parachlamydiaceae are endosymbionts of free-living amoeba first identified in 1997 . Two developmental stages, elementary and reticulate bodies, were observed; however, their localization and proportions according to culture condition and duration remain unknown . The life cycle of Parachlamydia acanthamoeba within Acanthamoeba polyphaga was studied by transmission electron microscopy of 8-, 36-, and 144-h coculture . Morphometry and quantification were performed using SAMBA software . The elementary body, the predominant stage within the amoebae, was located mainly within their vacuoles . The multiplication of Parachlamydia bacteria by binary fission of reticulate bodies was independently associated with culture in PYG broth (odds ratio {OR} = 4.4; 95% confidence interval {CI}, 1.55 to 12.46) and with the presence of reticulate bodies within the amoebae (OR = 2.10; 95% CI, 1.53 to 2.89) . A third developmental stage was observed, the crescent body . Its presence outside and inside the amoebae was associated mainly with prolonged incubation time (OR = 3.98; 95% CI, 1.49 to 10.68, and OR = 5.98; 95% CI, 1.75 to 20.4, respectively) . Elementary and crescent bodies were released into the extracellular medium within vesicles or after amoebal lysis . For both, phagocytosis was their mode of entry . This electron micrograph study revealed another infective developmental stage, the crescent body, and provided quantitative analysis of the life cycle of P . acanthamoeba within A . polyphaga. Appl Environ Microbiol, 2002 Jun, 68(6), 2965 - 71 Elemental composition (C, N, P) and cell volume of exponentially growing and nutrient-limited bacterioplankton; Vrede K et al.; Marine bacterioplankton were isolated and grown in batch cultures until their growth became limited by organic carbon (C), nitrogen (N), or phosphorus (P) . Samples were taken from the cultures at both the exponential and stationary phases . The elemental composition of individual bacterial cells was analyzed by X-ray microanalysis with an electron microscope . The cell size was also measured . The elemental content was highest in exponentially growing cells (149 +/- 8 fg of C cell(-1), 35 +/- 2 fg of N cell(-1), and 12 +/- 1 fg of P cell(-1); average of all isolates +/- standard error) . The lowest C content was found in C-limited cells (39 +/- 3 fg of C cell(-1)), the lowest N content in C- and P-limited cells (12 +/- 1 and 12 +/- 2 fg of N cell(-1), respectively), and the lowest P content in P-limited cells (2.3 +/- 0.6 fg of P cell(-1)) . The atomic C:N ratios varied among treatments between 3.8 +/- 0.1 and 9.5 +/- 1.0 (average +/- standard error), the C:P ratios between 35 +/- 2 and 178 +/- 28, and the N:P ratios between 6.7 +/- 0.3 and 18 +/- 3 . The carbon-volume ratios showed large variation among isolates due to different types of nutrient limitation (from 51+/- 4 to 241 +/- 38 fg of C microm(-1); average of individual isolates and treatments +/- standard error) . The results show that different growth conditions and differences in the bacterial community may explain some of the variability of previously reported elemental and carbon-volume ratios. Gene, 2002 Feb 20, 285(1-2), 169 - 73 Evolution of DNA binding motifs and operators; Roy S et al.; A gene regulatory protein with helix-turn-helix (HTH) DNA-binding motif, GalS contains a functional operator within the DNA sequences encoding the HTH region (Nature 369 (1994) 314) . We searched for operator-like sequences within the DNA sequences encoding the DNA binding motifs of other regulatory proteins . Five such proteins, DeoR, CytR, LRP, LuxR and PurR, were found to have actual operator or operator-like sequences in the DNA sequences encoding the DNA-binding motif . Except DeoR, all of them including GalS, are known to be auto-regulated . Auto-regulation in case of DeoR has not been investigated . Seven other proteins containing a HTH motif, do not have operator-like sequences in the DNA sequences encoding the HTH motif; none of them, except MerR, are known to be auto-regulated . The DNA binding proteins may have evolved from a common ancestor containing a DNA binding site within its gene segment that encodes the DNA-binding motif to facilitate auto-regulation . We have discussed current evidence for monophyletic or polyphyletic origin of such sequences. Med Trop (Mars), 2002, 62(1), 73 - 6 {Pelvic actinomycosis simulating adnexal malignant tumor}; Benkiran L et al.; The purpose of this report is to describe the case of a 35-year-old patient admitted to the National Oncology Institute in Rabat, Morocco for pelvic pain and deteriorating general status ongoing for 8 months . Clinical and ultrasonographic examination showed a heterogenous mass measuring 7 cm in maximum width located inferior and lateral to the inferior aspect of the right side of the uterus . These findings were suggestive of a malignant tumor of the right ovary . Ovariectomy and omentectomy were performed . Histological examination of surgical specimens demonstrated right tubo-ovarian actinomycosis associated with peritonitis . Genital tract actinomycosis is an uncommon finding in women of childbearing age . It is due to colonization by a pyogenic bacteria (Actinomyces) usually secondary to a gastrointestinal infection, e.g . ileocecum, and sometimes in association with the presence of an intrauterine device or foreign body . Based on this case report, the authors discuss abdominopelvic actinomyocosis with emphasis on tumor-like findings that can lead to misdiagnosis by clinicians and radiologists. Am J Ophthalmol, 2002 Jun, 133(6), 773 - 9 Presumed trematode-induced granulomatous anterior uveitis: a newly recognized cause of intraocular inflammation in children from south India; Rathinam SR et al.; PURPOSE: To describe the epidemiologic, clinical, and histopathologic features of a presumed trematode granulomatous anterior uveitis, primarily in children from south India . DESIGN: Prospective, noncomparative, case series . METHODS: Children with clinical evidence of granulomatous anterior uveitis were selected for the study . Those who presented with distinct anterior chamber nodules were evaluated . Demographic details, such as clinical findings and course of illness, were noted . Patients underwent either medical treatment or surgical aspiration of the lesion based on the size of the lesion . Aspirated materials were subjected to histopathologic analysis and cultures for bacteria and fungi . Response to treatment and final visual status were evaluated . RESULTS: One hundred thirteen patients with anterior chamber nodules were seen between 1998 and 2000 . Ninety-three (82.4%) were males and 20 (17.7%) were females . The median age was 11.0 years . All patients were from south India and all gave a history of bathing or swimming in the local pond or river . All had normal systemic work ups . Of the 113 patients, 110 had anterior chamber nodules and three had both anterior chamber and subconjunctival nodules . Aspirates of the anterior chamber lesions revealed lymphocytes, intact and necrotic neutrophils, and eosinophils admixed with histiocytes . One subconjunctival nodule showed necrotizing granuloma, displaying the tegument of a trematode . Those patients who were followed had good visual recovery after medical or surgical intervention or both . CONCLUSION: The present study shows a newly recognized granulomatous anterior uveitis caused by a presumed water-borne trematode infection . This infection appears to be a common cause of pediatric granulomatous anterior uveitis in south India. Virology, 2002 Apr 25, 296(1), 125 - 35 Leporipoxvirus Cu-Zn superoxide dismutase homologs inhibit cellular superoxide dismutase, but are not essential for virus replication or virulence; Cao JX et al.; Vertebrate poxviruses encode homologs of cellular cupro-zinc superoxide dismutases (Cu-Zn SOD) . In this study we have examined the molecular genetic properties of two Cu-Zn SOD homologs encoded by the Shope fibroma virus (SFV) and myxoma virus . These Leporipoxvirus proteins should be catalytically inactive as judged by the point mutations which alter a key catalytic arginine and restructure the predicted Cu-binding domain . This prediction was confirmed using in situ gel assays and recombinant proteins produced both in bacteria and in mammalian cells . Western blot analysis showed that these proteins are produced in abundance late in infection and can, upon exposure to oxidizing conditions, form disulfide cross-linked dimers . They are also virion components and not essential for growth in culture or virulence . Leporipoxvirus Cu-Zn SOD homologs affected two phenotypes . First, deletion of the myxoma M131R gene caused the mutant virus to grow better ( approximately 10-fold) in culture than does the wild-type parent . Second, expression of either native or recombinant Leporipoxvirus proteins is accompanied by a decline in cellular Cu-Zn SOD activity . We concluded that these gene products can somehow modulate the activity of host Cu-Zn SODs, but what advantage is thus gained by the virus remains to be established. Indian J Pathol Microbiol, 2001 Oct, 44(4), 439 - 40 Malakoplakia of the kidney--a case report; Shah AN et al.; Malakoplakia is a rare disease expressed as a special type of inflammatory reaction to infection with various bacteria and fungi . We present a case of renal malakoplakia in a 30-year-old female patient . The symptoms were not characteristic enough for making the ture diagnosis preoperatively . A preoperative diagnosis of renal cell carcinoma was made in this case. Microb Ecol, 2000 Dec, 40(4), 330 - 335 The Toxic Symbiont Caedibacter caryophila in the Cytoplasm of Paramecium novaurelia; Kusch J et al.; Endosymbiotic bacteria were observed to inhabit the cytoplasm of the freshwater ciliate Paramecium novaurelia . Transmission electron microscopy and toxicity tests with sensitive paramecia showed that the endosymbionts belong to the genus Caedibacter . The bacteria conferred a killer trait to their host paramecia . The production of a proteinaceous inclusion body ("R-body") in the bacterial cell makes them toxic to other paramecia after they become enclosed in food vacuoles . R-bodies of Caedibacter sp were associated with phages, which are known in most other Caedibacter species to code for the R-body proteins . The killer-effect of P . novaurelia on sensitive P . caudatum strains was of the "paralysis" type, which is a characteristic of the symbiont species Caedibacter caryophila . Until now C . caryophila was known to inhabit the macronucleus of Paramecium caudatum only . Sequencing of the 16S rRNA-gene proved that Caedibacter sp from the cytoplasm of P . novaurelia belongs to the species C . caryophila as well . The rDNA-sequence of 1695 bp length differed in a total of only 1 bp from the corresponding gene in C . caryophila from the macronucleus of P . caudatum . The results indicate that the infection of specific host cell compartments may depend on host genes, but not on different traits of the infecting symbiont species . The occurrence of killer and sensitive paramecia strains together in one pond is discussed with respect to the competitive advantage of the killer trait. Plant Cell, 2002 May, 14(5), 1005 - 15 RAR1 and NDR1 contribute quantitatively to disease resistance in Arabidopsis, and their relative contributions are dependent on the R gene assayed; Tornero P et al.; Plant disease resistance (R) genes mediate specific pathogen recognition, leading to a successful immune response . Downstream responses include ion fluxes, an oxidative burst, transcriptional reprogramming, and, in many cases, hypersensitive cell death at the infection site . We used a transgenic Arabidopsis line carrying the bacterial avirulence gene avrRpm1 under the control of a steroid-inducible promoter to select for mutations in genes required for RPM1-mediated recognition and signal transduction . We identified an allelic series of eight mutants that also were allelic to the previously identified pbs2 mutation . Positional cloning revealed this gene to be AtRAR1, the Arabidopsis ortholog of barley RAR1, a known mediator of R function . AtRAR1 is required for both full hypersensitive cell death and complete disease resistance mediated by many, but not all, tested R genes . Double mutant analysis of Atrar1 in combination with the R signal intermediate ndr1 suggests that AtRAR1 and NDR1 can operate in both linear and parallel signaling events, depending on the R gene function triggered . In Atrar1 null plants, the levels of RPM1-myc are reduced severely, suggesting that AtRAR1 may regulate R protein stability or accumulation. Plant Cell, 2002 May, 14(5), 979 - 92 Arabidopsis RAR1 exerts rate-limiting control of R gene-mediated defenses against multiple pathogens; Muskett PR et al.; We have identified the Arabidopsis ortholog of barley RAR1 as a component of resistance specified by multiple nucleotide binding/Leu-rich repeat resistance (R) genes recognizing different bacterial and oomycete pathogen isolates . Characterization of partially and fully defective rar1 mutations revealed that wild-type RAR1 acts as a rate-limiting regulator of early R gene-triggered defenses, determining the extent of pathogen containment, hypersensitive plant cell death, and an oxidative burst at primary infection sites . We conclude that RAR1 defense signaling function is conserved between plant species that are separated evolutionarily by 150 million years . RAR1 encodes a protein with two zinc binding (CHORD) domains that are highly conserved across eukaryotic phyla, and the single nematode CHORD-containing homolog, Chp, was found previously to be essential for embryo viability . An absence of obvious developmental defects in null Arabidopsis rar1 mutants favors the notion that, in contrast, RAR1 does not play a fundamental role in plant development. Nucleic Acids Res, 2002 Jun 1, 30(11), 2501 - 7 Evidence for strong selective constraint acting on the nucleotide composition of 16S ribosomal RNA genes; Wang HC et al.; Previous studies have shown that the guanine plus cytosine (G+C) content of ribosomal RNAs (rRNAs) is highly correlated with bacterial growth temperatures . This correlation is strongest in the double-stranded stem regions of the rRNA, a fact that can be explained by selection for increased structural stability at high growth temperatures . In this study, we examined the single-stranded regions of 16S rRNAs . We reasoned that, since these regions of the molecule are subject to less structural constraint than the stem regions, their nucleotide content might simply reflect the overall nucleotide content of the genome . Contrary to this expectation, however, we found that all of the single-stranded regions are characterized by very high adenine (A) and relatively low cytosine (C) contents . Moreover, the nucleotide content of these single-stranded regions is surprisingly constant between species, despite dramatic differences in optimal growth temperatures, and despite large differences in the overall genomic G+C content . This provides compelling evidence for strong stabilizing selection acting on 16S rRNA single-stranded regions . We found that selection favors purines (A+G), and especially adenine (A), in the single-stranded regions of these rRNAs. Gene, 2002 Apr 17, 288(1-2), 195 - 201 Identification of six major outer membrane proteins from Actinobacillus actinomycetemcomitans; Komatsuzawa H et al.; We have identified six major sarcosyl-insoluble outer membrane proteins (Omp) of Actinobacillus actinomycetemcomitans Y4, and designated them as Omp100, Omp64, Omp39, Omp29, Omp18 and Omp16 according to the molecular mass . A similar N-terminal sequence was found in the first 15 amino acid residues of Omp16 and Omp18 . The N-terminal sequence of Omp29 matched perfectly with the sequence previously identified . We cloned and determined the DNA sequences of three complete genes encoding Omp100, Omp64 and Omp18/16, and one incomplete gene encoding Omp39 . Each Omp revealed homologies with some bacterial virulence factors responsible for adhesion, invasion, serum resistance, or protein antigenicity . Serum from patients with periodontitis suspected to be related to A . actinomycetemcomintans infection strongly reacted with Omp100, Omp29 and Omp16 as did serum from mice immunized with A . actinomycetemcomitans Y4 whole bacteria . These findings suggest that Omps of A . actinomycetemcomitans can be associated with periodontal disease. Biol Chem, 2002 Mar-Apr, 383(3-4), 347 - 64 Peroxiredoxins; Hofmann B et al.; Present knowledge on peroxiredoxins is reviewed with special emphasis on catalytic principles, specificities and biological function . Peroxiredoxins are low efficiency peroxidases using thiols as reductants . They appear to be fairly promiscuous with respect to the hydroperoxide substrate; the specificities for the donor substrate vary considerably between the subfamilies, comprising GSH, thioredoxin, tryparedoxin and the analogous CXXC motifs in bacterial AhpF proteins . Peroxiredoxins are definitely responsible for antioxidant defense in bacteria (AhpC), yeast (thioredoxin peroxidase) and trypanosomatids (tryparedoxin peroxidase) . They are considered to determine virulence of mycobacteria and trypanosomatids . In higher plants they are involved in balancing hydroperoxide production during photosynthesis . In higher animals peroxiredoxins appear to be involved in the redox-regulation of cellular signaling and differentiation, displaying in part opposite effects. Appl Environ Microbiol, 1998 Jan, 64(1), 74 - 81 13C and 1H nuclear magnetic resonance study of glycogen futile cycling in strains of the genus Fibrobacter; Matheron C et al.; We investigated the carbon metabolism of three strains of Fibrobacter succinogenes and one strain of Fibrobacter intestinalis . The four strains produced the same amounts of the metabolites succinate, acetate, and formate in approximately the same ratio (3.7/1/0.3) . The four strains similarly stored glycogen during all growth phases, and the glycogen-to-protein ratio was close to 0.6 during the exponential growth phase . 13C nuclear magnetic resonance (NMR) analysis of {1-13C}glucose utilization by resting cells of the four strains revealed a reversal of glycolysis at the triose phosphate level and the same metabolic pathways . Glycogen futile cycling was demonstrated by 13C NMR by following the simultaneous metabolism of labeled {13C}glycogen and exogenous unlabeled glucose . The isotopic dilutions of the CH2 of succinate and the CH3 of acetate when the resting cells were metabolizing {1-13C}glucose and unlabeled glycogen were precisely quantified by using 13C-filtered spin-echo difference 1H NMR spectroscopy . The measured isotopic dilutions were not the same for succinate and acetate; in the case of succinate, the dilutions reflected only the contribution of glycogen futile cycling, while in the case of acetate, another mechanism was also involved . Results obtained in complementary experiments are consistent with reversal of the succinate synthesis pathway . Our results indicated that for all of the strains, from 12 to 16% of the glucose entering the metabolic pathway originated from prestored glycogen . Although genetically diverse, the four Fibrobacter strains studied had very similar carbon metabolism characteristics. J Endod, 2002 May, 28(5), 386 - 90 The sealing ability and retention characteristics of mineral trioxide aggregate in a model of apexification; Hachmeister DR et al.; Treatment of the immature pulpless tooth presents both an endodontic and restorative challenge . A more favorable long-term prognosis may be achieved with a mineral trioxide aggregate (MTA) apexification procedure followed by an internal bonding technique . We investigated the efficacy of this treatment option by testing the sealing ability and retention characteristics of MTA when placed as an apical barrier in a standardized in vitro open apex model . MTA was placed as an apical barrier at a thickness of 1 mm or 4 mm, with and without prior calcium hydroxide medication . The barriers were challenged with bacteria exposure within a leakage model and displacement forces on an Instron machine . In the leakage study, 100% of the MTA apical barriers showed bacterial penetration by day 70, compared with 20% of MTA root-end fillings used as controls . The displacement study demonstrated a statistically significant greater resistance to force with a 4-mm thickness of MTA, regardless of calcium hydroxide use . We concluded that it was the intracanal delivery technique and not the MTA that contributed to the leakage observed . MTA shows promise in our proposed treatment option of immature pulpless teeth if the sealing ability can be enhanced by improving the delivery technique. J Ind Microbiol Biotechnol, 2002 Jun, 28(6), 311 - 5 Comparison of the effects of temperature and water activity on growth rate of food spoilage moulds; Sautour M et al.; The influence of temperature (T) and water activity (aw) on the growth rate (mu) of seven moulds (Alternaria alternata, Aspergillus flavus, Cladosporium cladosporioides, Mucor racemosus, Penicillium chrysogenum, Rhizopus oryzae and Trichoderma harzianum) was assessed in suboptimal conditions . Firstly, the dependence of fungal growth on temperature, at aw 0.99, was modelled through an approach described previously for bacteria . A dimensionless growth rate variable: mu(dimalpha)=mu/mu (optalpha) depended on the following normalised temperature: T(dim)=(T-T(min))/(T(opt)- T(min)) according to a power function: mu(dimalpha)={T(dim)}alpha, where alpha was an exponent to be estimated . Secondly, the same approach was used to describe the influence of aw on fungal growth, at the respective optimum temperatures for each mould . Similarly, mu(dimbeta)=mu/mu(optbeta) depended on the following normalised water activity: a(wdim)=(aw-a(wmin))/(a(wopt)-a(wmin)) according to a power function: mu(dimbeta)={a(wdim)}(beta) . Results show: (i) for each mould, the alpha-value is significantly less than the beta-value, confirming that water activity has a greater influence than temperature on fungal development; (ii) the alpha-values and the beta-values depend on the mould; (iii) the alpha-value is less than 1 for the mesophilic mould A . flavus, whereas the other moulds are characterised by higher alpha-values ranging from 1.10 to 1.54; (iv) the mesophilic A . flavus exhibits a low beta-value, 1.50, compared to the hydrophilic T . harzianum, beta=2.44, while beta-values are within the range (1.71-2.37) for the other moulds. Proc Natl Acad Sci U S A, 2002 May 28, 99(11), 7786 - 91 An Arabidopsis mutation in translation elongation factor 2 causes superinduction of CBF/DREB1 transcription factor genes but blocks the induction of their downstream targets under low temperatures; Guo Y et al.; Low temperature regulates gene expression in bacteria, yeast, and animals as well as in plants . However, the signal transduction cascades mediating the low temperature responses are not well understood in any organism . To identify components in low temperature signaling genetically, we isolated Arabidopsis thaliana mutants in which cold-responsive genes are no longer induced by low temperatures . One of these mutations, los1-1, specifically blocks low temperature-induced transcription of cold-responsive genes . Surprisingly, cold-induced expression of the early response transcriptional activators, C-repeat/dehydration responsive element binding factors (CBF/DREB1s), is enhanced by the los1-1 mutation . The los1-1 mutation also reduces the capacity of plants to develop freezing tolerance but does not impair the vernalization response . Genetic analysis indicated that los1-1 is a recessive mutation in a single nuclear gene . The LOS1 gene encodes a translation elongation factor 2-like protein . Protein labeling studies show that new protein synthesis is blocked in los1-1 mutant plants specifically in the cold . These results reveal a critical role of new protein synthesis in the proper transduction of low temperature signals . Our results also suggest that cold-induced transcription of CBF/DREB1s is feedback inhibited by their gene products or by products of their downstream target genes. EMBO J, 2002 Jun 3, 21(11), 2769 - 77 Assigning a function to a conserved group of proteins: the tRNA 3'-processing enzymes; Schiffer S et al.; Accurate tRNA 3' end maturation is essential for aminoacylation and thus for protein synthesis in all organisms . Here we report the first identification of protein and DNA sequences for tRNA 3'-processing endonucleases (RNase Z) . Purification of RNase Z from wheat identified a 43 kDa protein correlated with the activity . Peptide sequences obtained from the purified protein were used to identify the corresponding gene . In vitro expression of the homologous proteins from Arabidopsis thaliana and Methano coccus janaschii confirmed their tRNA 3'-processing activities . These RNase Z proteins belong to the ELAC1/2 family of proteins and to the cluster of orthologous proteins COG 1234 . The RNase Z enzymes from A.thaliana and M.janaschii are the first members of these families to which a function can now be assigned . Proteins with high sequence similarity to the RNase Z enzymes from A.thaliana and M.janaschii are present in all three kingdoms. EMBO J, 2002 Jun 3, 21(11), 2646 - 54 Paradoxical redox properties of DsbB and DsbA in the protein disulfide-introducing reaction cascade; Inaba K et al.; Protein disulfide bond formation in the bacterial periplasm is catalyzed by the Dsb enzymes in conjunction with the respiratory quinone components . Here we characterized redox properties of the redox active sites in DsbB to gain further insights into the catalytic mechanisms of DsbA oxidation . The standard redox potential of DsbB was determined to be -0.21 V for Cys41/Cys44 in the N-terminal periplasmic region (P1) and -0.25 V for Cys104/Cys130 in the C-terminal periplasmic region (P2), while that of Cys30/Cys33 in DsbA was -0.12 V . To our surprise, DsbB, an oxidant for DsbA, is intrinsically more reducing than DsbA . Ubiquinone anomalously affected the apparent redox property of the P1 domain, and mutational alterations of the P1 region significantly lowered the catalytic turnover . It is inferred that ubiquinone, a high redox potential compound, drives the electron flow by interacting with the P1 region with the Cys41/Cys44 active site . Thus, DsbB can mediate electron flow from DsbA to ubiquinone irrespective of the intrinsic redox potential of the Cys residues involved. Clin Chim Acta, 2002 Jul, 321(1-2), 35 - 41 Flow cytometry as a new method to quantify the cellular content of human saliva and its relation to gingivitis; Aps JK et al.; BACKGROUND: Determining the cellular content of saliva by means of conventional microscopy chamber counting is a very time-consuming and operator-sensitive procedure . This study concentrated on the use of flow cytometry to examine the cellular content of saliva . Erythrocytes, leukocytes, epithelial cells and bacteria were quantified and the results were compared with caries experience and the presence of gingivitis . METHODS: 258 uncentrifuged vortexed paraffin-stimulated saliva samples (112 males and 146 females) were analyzed with the UF-100 flow cytometer . Salivary reference values were established for erythrocyte, leukocyte, epithelial cell and bacterial count . Caries experience (DMF) and the presence of gingivitis were recorded . RESULTS: Caries experience or caries risk could not be assessed with flow cytometry . However, salivary flow cytometry may be useful in determining an individual's risk for gingivitis: a significant increase in salivary leukocytes was observed in individuals with gingivitis . At a cut-off level of 10(3) leukocytes micro l(-1) saliva, a sensitivity of 76% and a specificity of 45% was obtained . Other analytes were not significantly different between individuals with and without gingivitis . CONCLUSION: Flow cytometry of paraffin-stimulated human saliva seems a promising diagnostic or predictive tool and further investigations of diseases of the oro-pharyngeal loge, such as tonsillitis and periodontitis, should be carried out in the future. Comp Biochem Physiol B Biochem Mol Biol, 2002 Jun, 132(2), 309 - 13 Rhodanese distribution in porcine (Sus scrofa) tissues; Aminlari M et al.; The enzyme rhodanese (thiosulfate/cyanide sulfurtransferase) is an ubiquitous enzyme and its activity is present in all living organisms from bacteria to man . Evidence has been accumulated to indicate that this enzyme plays a central role in cyanide detoxification . A comparison was made of rhodanese activity in different tissues of young male and adult male and female pig (Sus scrofa) . The highest activity of rhodanese was in liver and kidney cortex of all animals . Among the remaining tissues examined, the kidney medulla and the stomach epithelium tended to have higher levels than other tissues, although this was not significant (P>0.05) . The rhodanese activity of heart ventricle tissue of 6-month-old male animals was higher than 7-week-old male animals (P<0.05), and 6-month-old male animals had higher rhodanese activity in lung tissue, compared to 6-month-old female pigs (P<0.05) . Medulla and spleen of younger male animals exhibited higher levels of activity (P<0.10) compared to older male pigs . The results of this study may indicate the involvement of rhodanese in cyanide detoxification in pig tissues, which have greater potential to be exposed to higher levels of cyanide. Phytochemistry, 2002 Jun, 60(4), 375 - 9 Flavonoids from Tephrosia aequilata; Tarus PK et al.; From the roots of the plant Tephrosia aequilata Baker, five flavonoids were isolated of which, 3,4:8,9-dimethylenedioxypterocarpan is reported for the first time . Its structure and those of the already known flavonoids were established by physical and spectroscopic analysis . Application of 2D NMR techniques was useful for complete characterization of the new pterocarpan as well as the other known flavonoids. Oral Microbiol Immunol, 2002 Jun, 17(3), 157 - 62 Characterization of binding and utilization of hemoglobin by Prevotella nigrescens; Guan S et al.; The ability of Prevotella nigrescens to utilize and bind to hemoglobin was investigated . Growth studies showed that P . nigrescens was able to utilize hemoglobin efficiently as an iron source . Binding of P . nigrescens to hemoglobin was demonstrated by dot blot assay . Heat and trypsin treatments of the bacteria led to a decrease in activity . Globin gave nearly complete inhibition of activity . Additionally, lactoferrin partially inhibited activity . In contrast, transferrin, cytochrome C and catalase exerted little or no inhibitory effect . Although the sugars tested did not affect activity, several of the amino acids tested, including arginine, cysteine, histidine and lysine, inhibited activity . In a solid phase assay, 41-, 56- and 59-kDa proteins of P . nigrescens reacted with hemoglobin . These results suggest that P . nigrescens utilizes hemoglobin for growth and 41-, 56- and 59-kDa proteins may be involved in hemoglobin binding. Aliment Pharmacol Ther, 2002 Jun, 16(6), 1163 - 70 Amoxicillin and ampicillin are not transferred to gastric juice irrespective of Helicobacter pylori status or acid blockade by omeprazole; Ortiz RA et al.; BACKGROUND: The effects of proton pump inhibitors and Helicobacter pylori infection on the distribution of drugs used for the eradication of the bacteria are poorly understood . AIM: The aim of this study was to investigate the effects of a 7-day administration of 20 mg of omeprazole on the pharmacokinetics of amoxicillin and ampicillin in the plasma, saliva and gastric juice of individuals with and without H . pylori infection . METHODS: Fifty-four healthy volunteers without endoscopic lesions were enrolled . Twenty-six volunteers were included in the amoxicillin study and 28 individuals in the ampicillin study . Each study had an open randomized two-period crossover design and a 21-day washout period between phases . Plasma, saliva and gastric juice concentrations of amoxicillin and ampicillin in subjects with and without omeprazole pre-treatment were measured by reversed-phase HPLC using UV detection . RESULTS: Neither pre-treatment with omeprazole nor H . pylori infection interfered with the plasma bioavailability of amoxicillin or ampicillin, as assessed by the AUC0-2 h . Neither ampicillin nor amoxicillin were detected in saliva or gastric juice in any study phase . CONCLUSION: Short-term treatment with omeprazole does not interfere with the pharmacokinetics of amoxicillin or ampicillin . Our results also exclude the presence of a transfer mechanism for amoxicillin or ampicillin from the plasma to the gastric lumen. Environ Microbiol, 2002 May, 4(5), 287 - 95 Seasonal dynamics of particle-associated and free-living marine Proteobacteria in a salt marsh tidal creek as determined using fluorescence in situ hybridization; Dang H et al.; The seasonal distributions of salt marsh free-living and particle-associated bacteria belonging to three subdivisions of the Proteobacteria were determined by fluorescence in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM) . More than 66% (median = 78%) of total bacterial cells that were stainable with the fluorescent DNA stain Yo-Pro-1 were also detected using the bacterial probe EUB338 . The alpha-Proteobacteria, especially those from the marine Rhodobacter group, were abundant on suspended particles and as free-living cells all year round . The marine Rhodobacter group constituted more than 25% of the particle-associated bacteria and more than 18% of the free-living bacteria . Probes specific for three subgroups within the marine Rhodobacter group detected more than 49% of the total marine Rhodobacter group cells . These subgroups displayed different seasonal dynamics . The marine Rhodobacter group is clearly a widespread, diverse and important bacterial lineage in bacterioplankton and particle-associated assemblages in south-eastern United States salt marshes at all times of the year. Prof Nurse, 2000 Oct, 16(1), 830 - 3 Scissors: are they an infection control risk? Kelly J, Trundle C. Increasing bacterial resistance means that nurses must re-examine infection control procedures . Bacteria were cultured from 59% of scissors swabbed . Some were still contaminated after cleaning . Some nurses do not appear to recognise the risk of infection from using their scissors for a variety of purposes. Arch Dermatol Res, 2002 May, 294(3), 131 - 4 Epub 2002 Apr 05. Pityriacitrin -- an ultraviolet-absorbing indole alkaloid from the yeast Malassezia furfur; Mayser P et al.; As the main nitrogen source in Malassezia furfur, tryptophan induces the formation of fluorochromes and pigments, which make the yeast less sensitive to UV light . To detect a chemical UV filter, M . furfur (CBS 1878) was incubated at 30 degrees C for 14 days on a pigment-inducing medium and agar extracts were purified by column chromatography, preparative TLC and HPLC . Structural analysis of the pure metabolites was performed by mass spectroscopy and NMR . A yellow compound eluting from the column with 64% acetonitrile was found to be a potential UV filter because of its broad UV absorption (lambda(max) 389, 315, 289, 212 nm) . It was an indole derivative (C(20)H(13)N(3)O; pityriacitrin) which had recently been shown to be a potent UV filter in bacteria . Its UV protective properties were confirmed in a yeast model and also in humans . Pityriasis versicolor induced by Malassezia yeasts is characterized by depigmented skin areas showing reduced melanin synthesis but no increased UV sensitivity . This UV protection might be explained by the presence of pityriacitrin which is produced by M . furfur. J Mol Evol, 2002 Jun, 54(6), 763 - 73 Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins; Filee J et al.; A phylogenetic analysis of the five major families of DNA polymerase is presented . Viral and plasmid sequences are included in this compilation along with cellular enzymes . The classification by Ito and Braithwaite (Ito and Braithwaite 1991) of the A, B, C, D, and X families has been extended to accommodate the "Y family" of DNA polymerases that are related to the eukaryotic RAD30 and the bacterial UmuC gene products . After analysis, our data suggest that no DNA polymerase family was universally conserved among the three biological domains and no simple evolutionary scenario could explain that observation . Furthermore, viruses and plasmids carry a remarkably diverse set of DNA polymerase genes, suggesting that lateral gene transfer is frequent and includes non-orthologous gene displacements between cells and viruses . The relationships between viral and host genes appear very complex . We propose that the gamma DNA polymerase of the mitochondrion replication apparatus is of phage origin and that this gene replaced the one in the bacterial ancestor . Often there was no obvious relation between the viral and the host DNA polymerase, but an interesting exception concerned the family B enzymes: in which ancient gene exchange can be detected between the viruses and their hosts . Additional evidence for horizontal gene transfers between cells and viruses comes from an analysis of the small damage-inducible DNA polymerases . Taken together, these findings suggest a complex evolutionary history of the DNA replication apparatus that involved significant exchanges between viruses, plasmids, and their hosts. Oral Surg Oral Med Oral Pathol Oral Radiol Endod, 2002 Apr, 93(4), 461 - 8 A mouse model of inflammatory root resorption induced by pulpal infection; Balto K et al.; OBJECTIVE: The present study was undertaken to determine the frequency and extent of apical root resorption associated with induced periradicular lesions in mice . STUDY DESIGN: Bone and root resorption was quantified by using two- and three-dimensional micro-computed tomography (mu-CT) in the lower first molars of mice subjected to pulp exposure and infection . RESULTS: mu-CT measurements showed significant apical resorption in exposed and infected teeth, resulting in an average distal root shortening of 12.7% (P <.001 vs unexposed) . These findings were confirmed with three-dimensional reconstituted images that showed thinning and shortening of the distal root . Tartrate-resistant acid phosphatase clastic cells were associated with resorption lacunae on the cementum of root apices, as well as on bone at the periphery of the periradicular lesions . Brown and Brenn staining showed the presence of bacteria in dentinal tubules adjacent to resorbed cementum . CONCLUSIONS: Apical root resorption is a prominent and consistent finding associated with periradicular infection in the mouse . This species represents a convenient model for studying the pathogenesis of inflammatory root resorption in vivo. J Bacteriol, 2002 Jun, 184(12), 3287 - 95 Definition of the mycobacterial SOS box and use to identify LexA-regulated genes in Mycobacterium tuberculosis; Davis EO et al.; The bases of the mycobacterial SOS box important for LexA binding were determined by replacing each base with every other and examining the effect on the induction of a reporter gene following DNA damage . This analysis revealed that the SOS box was longer than originally thought by 2 bp in each half of the palindromic site . A search of the Mycobacterium tuberculosis genome sequence with the new consensus, TCGAAC(N)(4)GTTCGA, identified 4 sites which were perfect matches and 12 sites with a single mismatch which were predicted to bind LexA . Genes which could potentially be regulated by these SOS boxes were ascertained from their positions relative to the sites . Examination of expression data for these genes following DNA damage identified 12 new genes which are most likely regulated by LexA as well as the known M . tuberculosis DNA damage-inducible genes recA, lexA, and ruvC . Of these 12 genes, only 2 have a predicted function: dnaE2, a component of DNA polymerase III, and linB, which is similar to 1,3,4,6-tetrachloro-1,4-cylcohexadiene hydrolase . Curiously, of the remaining 10 genes predicted to be LexA regulated, 7 are members of the M . tuberculosis 13E12 repeat family, which has some of the characteristics of mobile elements. Syst Biol, 2002 Apr, 51(2), 199 - 216 Reconstruction of biogeographic and evolutionary networks using reticulograms; Legendre P et al.; A reticulogram is a general network capable of representing a reticulate evolutionary structure . It is particularly useful for portraying relationships among organisms that may be related in a nonunique way to their common ancestor - relationships that cannot be represented by a dendrogram or a phylogenetic tree . We propose a new method for constructing reticulograms that represent a given distance matrix . Reticulate evolution applies first to phylogenetic problems; it has been found in nature, for example, in the within-species microevolution of eukaryotes and in lateral gene transfer in bacteria . In this paper, we propose a new method for reconstructing reticulation networks and we develop applications of the reticulate evolution model to ecological biogeographic, population microevolutionary, and hybridization problems . The first example considers a spatially constrained reticulogram representing the postglacial dispersal of freshwater fishes in the Quebec peninsula; the reticulogram provides a better model of postglacial dispersal than does a tree model . The second example depicts the morphological similarities among local populations of muskrats in a river valley in Belgium; adding supplementary branches to a tree depicting the river network leads to a better representation of the morphological distances among local populations of muskrats than does a tree structure . A third example involves hybrids between plants of the genus Aphelandra. J Periodontol, 2002 May, 73(5), 511 - 6 Effects of Porphyromonas gingivalis on the central nervous system: activation of glial cells and exacerbation of experimental autoimmune encephalomyelitis; Shapira L et al.; BACKGROUND: Several studies have suggested that peripheral inflammation may be involved in the etiology of multiple sclerosis (MS), a demyelinating disease of the central nervous system (CNS) . T-cells activated in the periphery enter the CNS, leading to demyelination and axonal loss . We hypothesized that peripheral infection by Porphyromonas gingivalis can affect pathological processes in the CNS and aggravate MS . METHODS: Glial cells derived from rat brains were cultured and stimulated with P . gingivalis or P . gingivalis lipopolysaccharide (LPS) . Secretion of nitric oxide (NO) and prostaglandin E2 (PGE2) was determined . In addition, we examined the proliferation of lymphocytes harvested from P . gingivalis-immunized mice in response to stimulation by echephalitogenic proteins . The effect of peripheral inflammation induced by P . gingivalis on the clinical course of the disease was tested in experimental autoimmune encephalomyelitis (EAE), a mouse model used for the study of MS . RESULTS: P . gingivalis LPS and heat-killed bacteria induced secretion of the proinflammatory mediators NO and PGE2 by CNS glial cells . Lymphocytes derived from P . gingivalis-immunized mice proliferated in the presence of the echephalitogenic protein myelin basic protein . Injection of P . gingivalis into subcutaneous chambers in mice, followed by EAE induction led to aggravation of the disease . CONCLUSIONS: The present study provides evidence that infection with a periodontal pathogen, such as P . gingivalis, may play a role in the pathogenesis of CNS inflammatory disorders such as MS. Prof Nurse, 2001 Jul, 16(10), 1417 - 9 Handwashing; Bursey S et al.; Hands are easily contaminated by transient bacteria and nurses must be aware of when and how to wash them and whether social handwashing or hygienic hand disinfection is required . Regular updates on good practice are recommended. J Nutr Sci Vitaminol (Tokyo), 2002 Feb, 48(1), 18 - 23 Influence of dietary supplementation of herb extracts on volatile sulfur production in pig large intestine; Ushid K et al.; Volatile sulfur compounds (VS) are generated in the large intestine by the bacterial metabolism of sulfate and sulfur amino acids . VS are potentially harmful to the host . The effect of dietary supplementation of herb extracts on volatile sulfur production in the large intestine of pig was evaluated in this study . The extracts Perilla frutescens (Soyou), Mentha piperita (Peppermint), and Ajuga decumbens (Kiransou) were fed to pigs equipped with a permanent cannula at the cecum . Cecal digesta were sampled and analyzed for ammonia and short-chain fatty acids (SCFA) . Sampled digesta were incubated anaerobically either with or without L-methionine for 24 h to estimate volatile sulfur production in vivo . L-Methionine was supplemented to enhance methanethiol (MeSH) production . At the end of the incubation, head space concentrations of volatile sulfur compounds such as hydrogen sulfide (H2S), MeSH, and dimethyl sulfide (DMS) were determined by flame-photometric gaschromatography after the addition of 6 N HCl . Sampled digesta were also subjected to the most probable number estimations for sulfate-reducing bacteria (SRB), sulfide producer from L-methionine, and MeSH producers from L-methionine . All three herb extracts significantly decreased H2S (p<0.05), MeSH (p<0.05), and ammonia (p<0.05) production, but SCFA production was not affected (p>0.05) . The number of volatile sulfur-producing bacteria did not vary among groups by the dietary supplementation of these herb extracts . Serial solvent extraction was done on these herb extracts to specify the active fractions that reduce volatile sulfur production . n-Butanol fraction of all three extracts significantly reduced volatile sulfur production in vitro. Mol Plant Microbe Interact, 2002 Apr, 15(4), 376 - 9 Expressed sequence tags from roots and nodule primordia of Lotus japonicus infected with Mesorhizobium loti; Poulsen C et al.; Messenger RNA from young Lotus japonicus roots carrying root nodule primordia appearing after inoculation with Mesorhizobium loti bacteria were used to construct a cDNA expression library . Single-pass sequencing employing colony-polymerase chain reaction (PCR) and analysis of PCR products established a total of 2,397 new expressed sequence tags (ESTs) . We have putatively identified 1,236 known and 484 hypothetical proteins coded by the corresponding mRNAs . The remaining cDNAs are unknown (316) or redundant overlapping cDNAs (361) . We hope that this batch of ESTs will assist in the recognition of plant genes involved during development of nitrogen-fixing root nodules. Indian J Pathol Microbiol, 2001 Jul, 44(3), 283 - 8 Comparison of endoscopic brush cytology with biopsy for detection of Helicobacter pylori in patients with gastroduodenal diseases; Ahluwalia C et al.; Upper GI endoscopy was performed in 50 adult patients attending the gastroenterology OPD with gastroduodenal diseases . Gastric antral mucosal brushings were taken for cytological evaluation and urea broth test followed by antral biopsy . The slides prepared were stained with Wright Giemsa (WG), Hema toxylin & Eosin (H&E) and Papanicolaou (Pap) . Brush Cytology Smears were compared with biopsy sections for detection of Helicobacter pylori and the staining techniques were evaluated to see which stain was easiest to perform and interpret on routine basis . H&E stained sections were examined for histomorphological parameters associated with H . pylori infection . Brush cytology was rapid and simple with observed sensitivity of 90% and specificity of 100% . On evaluating the various stains, M.B . and W.G . were found to the rapid and easy to perform and the bacteria stood out very well against the background . Of the histomorphological parameters studied, presence of actively and lymphoid aggregates and absence of intestinal metaplasia correlated positively with the presence of the bacteria . Cytological brushing urea broth test was not very sensitive (55.2%) and specific (51%) for detection of the bacteria. Mikrobiologiia, 2002 Mar-Apr, 71(2), 264 - 71 {Methanotrophic communities in the soils of Russian northern taiga and subarctic tundra}; Kaliuzhnaia MG et al.; The PCR analysis of DNA extracted from soil samples taken in Russian northern taiga and subarctic tundra showed that the DNA extracts contain genes specific to methanotrophic bacteria, i.e., the mmoX gene encoding the conserved alpha-subunit of the hydroxylase component of soluble methane monooxygenase, the pmoA gene encoding the alpha-subunit of particulate methane monooxygenase, and the mxaF gene encoding the alpha-subunit of methanol dehydrogenase . PCR analysis with group-specific primers also showed that methanotrophic bacteria in the northern taiga and subarctic tundra soils are essentially represented by the type I genera Methylobacter, Methylomonas, Methylosphaera, and Methylomicrobium and that some soil samples contain type II methanotrophs close to members of the genera Methylosinus and Methylocystis . The electron microscopic examination of enrichment cultures obtained from the soil samples confirmed the presence of methanotrophic bacteria in the ecosystems studied and showed that the methanotrophs contain only small amounts of intracytoplasmic membranes. Mikrobiologiia, 2002 Mar-Apr, 71(2), 211 - 4 {Antigenic identity of the capsule lipopolysaccharides, exopolysaccharides, and O-specific polysaccharides in Azospirillum brasilense}; Matora LIu et al.; The antigenic identity (and close values of electrophoretic mobility) of capsular polysaccharides, exopolysaccharides, and O-specific polysaccharides was revealed in the Azospirillum brasilense strains Sp7 and Sp245 by the immunodiffusion and immunoelectrophoretic methods . Together with the literature data on the identity of the monosaccharides composition of these polymers, this gives evidence of the absence of a specific capsular antigen in the bacteria studied . Thus, extracellular Azospirillum brasilense polysaccharides are likely to represent O-antigenic lipopolysaccharide fragments excreted by the bacteria into the culture medium, and their identification as a capsule or as an exopolysaccharide depends on the strength of the attachment of these polysaccharides to the cell surface. Microb Ecol, 2001 Oct, 42(3), 372 - 382 Bacterioplankton Production in Lakes along an Altitude Gradient in the Subarctic North of Sweden; Karlsson J et al.; We examined changes in bacterioplankton standing stock and production in subarctic lakes in the north of Sweden to elucidate their coupling to lake physical, chemical, and biological characteristics . Sixteen lakes situated along an altitude gradient extending from the coniferous forest to the high-alpine belt were studied during 1998 and 1999 . The summer mean bacterial numbers and production varied substantially between the lakes, with a general trend toward decreasing values with increasing altitude . The results demonstrate that P probably restricted bacterial utilization of DOC in the coniferous forest lakes, while low DOC concentrations limited bacterial growth during the summer in the alpine lakes . The primary production of plankton was insufficient to support bacterial production in the lakes . High input of allochthonous DOC to the alpine lakes in spring was sufficient both to increase the bacterial production and to induce P-limitation . As a consequence, there was a tendency toward higher bacterial activity in the spring compared to the summer in the alpine lakes . The results indicate that most of the bacterial standing stock and production are supported by allochthonous DOC plus DOC from benthic production, and more or less limited by the phosphorus supply . We therefore suggest that bacteria populations in subarctic lakes may be indirectly affected by climate variations through its impact on the input of DOC and nutrients from the lake catchments. Microb Ecol, 2001 Dec, 42(4), 598 - 605 Investigating Influential Factors on Bacterioplankton Community Composition: Results from a Field Study of Five Mesotrophic Lakes; Lindstrom ES; In order to investigate which biotic and abiotic factors may have an impact on the community composition of bacterioplankton, five mesotrophic lakes were studied . The composition of the bacterioplankton communities was determined by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA . Multivariate statistical analyses of the gel patterns, in relation to each other and to the chemical, biological, and physical parameters of the lakes, were performed . The analyses showed that the import of allochthonous bacteria and the interaction with other plankton organisms (for example, grazing) in the lakes probably had an impact on the composition of the communities. Microb Ecol, 2001 Dec, 42(4), 513 - 523 Nutrient Acquisition and Population Growth of a Mixotrophic Alga in Axenic and Bacterized Cultures; Sanders RW et al.; Axenic growth of a mixotrophic alga, Ochromonas sp., was compared in several inorganic and organic media, and in the presence of live bacteria under nutrient-replete and low-nutrient conditions . Axenic growth in the light was negligible in inorganic media with or without the addition of glucose . Addition of vitamins increased growth rate, but average cell size declined, resulting in no net increase in biomass . Supplementing axenic cultures with a more complex organic substrate resulted in moderate growth and higher maximal abundance (and biomass) than in the inorganic media with added vitamins . The absence of light did not greatly affect population growth rate in the presence of complex dissolved organic compounds, although cell size was significantly greater in the light than in the dark . The highest growth rates for the alga (up to 2.6 d-1) were measured in treatments containing live bacteria . Increases in cell number of Ochromonas sp . in the presence of bacterial prey were similar in the light and dark, although chloroplast and cell sizes differed . Bacterial abundance was reduced and dissolved phosphorus and ammonia were rapidly released in bacterized cultures in the light and dark, indicating high rates of bacterial ingestion and suggesting an inability of the alga to store or utilize N and P in excess of the quantities required for heterotrophic growth . Low-nutrient conditions in the presence of bacteria were promoted by adding glucose to stimulate bacterial growth and the uptake of N and P released by algal phagotrophy . Subsequent decreases in dissolved N and P following the addition of glucose corresponded to a second period of rapid growth of the alga in both light and dark . This result, combined with evidence for slow axenic growth of this strain, indicated that nutrient acquisition for this species in the presence of bacteria was accomplished primarily via ingestion of bacteria. Mol Cell Biol, 2002 Jun, 22(12), 4033 - 42 Components of the SAGA histone acetyltransferase complex are required for repressed transcription of ARG1 in rich medium; Ricci AR et al.; Transcriptional regulation of the Saccharomyces cerevisiae ARG1 gene is controlled by positive and negative elements . The transactivator Gcn4p is required for activation in minimal medium, while arginine repression requires the ArgR/Mcm1 regulatory complex, which binds to two upstream arginine control elements . We have found that the coordinated regulation of ARG1 requires components of the SAGA chromatin-remodeling complex . Using gcn5 deletion strains and a Gcn5 protein carrying the E173Q mutation in the histone acetyltransferase (HAT) region, we show that the HAT activity of Gcn5p is required for repression of ARG1 in rich medium . Similar increases in expression were seen upon deletion of other SAGA components but not upon deletion of the ADA-specific component, Ahc1p . Chromatin immunoprecipitations using antibodies to acetylated H3 confirmed that a decrease in the level of acetylated histones at the ARG1 promoter correlated with increased ARG1 expression . Up-regulation of ARG1 in the absence of Gcn5p also correlated with increased binding of TATA-binding protein to the promoter . The analysis of promoter deletions showed that Gcn5/Ada repression of ARG1 was mediated through the action of the ArgR/Mcm1 regulatory complex . In addition, studies with minimal medium demonstrated a requirement for the Ada proteins in activation of ARG1 . This suggests that SAGA has a dual role at ARG1, acting to repress transcription in rich medium and activate transcription in minimal medium. Mol Cell Biol, 2002 Jun, 22(12), 3981 - 93 Protein kinase A operates a molecular switch that governs yeast pseudohyphal differentiation; Pan X et al.; The yeast Saccharomyces cerevisiae undergoes a dimorphic filamentous transition in response to nutrient cues that is affected by both mitogen-activated protein kinase and cyclic AMP-protein kinase A signaling cascades . Here two transcriptional regulators, Flo8 and Sfl1, are shown to be the direct molecular targets of protein kinase A . Flo8 and Sfl1 antagonistically control expression of the cell adhesin Flo11 via a common promoter element . Phosphorylation by the protein kinase A catalytic subunit Tpk2 promotes Flo8 binding and activation of the Flo11 promoter and relieves repression by prohibiting dimerization and DNA binding by Sfl1 . Our studies illustrate in molecular detail how protein kinase A combinatorially effects a key developmental switch . Similar mechanisms may operate in pathogenic fungi and more complex multicellular eukaryotic organisms. J Biol Chem, 2002 Aug 2, 277(31), 27887 - 95 Epub 2002 May 22. Identification of diacylated ureas as a novel family of fungus-specific leukocyte-activating pathogen-associated molecules; Schroder JM et al.; Polymorphonuclear leukocytes represent primary components of the host's innate immune defenses against fungal infection, suggesting involvement of fungal leukocyte attractants . We have found in various fungi, but not in bacteria or host cells, unstable lipid-like leukocyte chemoattractants, which also induced adherence and degranulation in human neutrophils . Purification from bakers' yeast and structural analyses by electrospray mass spectrometry, (1)H NMR spectroscopy, and chemical synthesis revealed these inflammatory mediators as diacylated ureas, a novel class of unstable lipoids . The N,N'-dipalmitoleyl urea appeared to be the most potent innate immune responses inducing compound eliciting half-maximum neutrophil chemotactic activity at 140 nm . The all-trans isomer, N,N'-dipalmitelaidyl urea, was found to be inactive with respect to stimulation of degranulation in neutrophils, which indicates a Delta(9) cis-double bond to be essential for bioactivity of these diacyl ureas . N,N'-Dipalmitoleyl urea elicited Ca(2+) mobilization in neutrophils, which was found to be pertussis toxin-sensitive and sensitive toward a carboxylmethyltransferase inhibitor, indicating that these diacyl ureas activate leukocytes via a putative Galpha(i)-protein-coupled receptor . Their isolation exclusively from fungi suggests that these lipoids are fungus-specific pathogen-associated molecules that may alert the human innate immunity system to the presence of a fungal infection. Emerg Infect Dis, 2002 Jun, 8(6), 625 - 30 Parachlamydiaceae: potential emerging pathogens; Greub G et al.; Parachlamydiaceae, which naturally infect amoebae, form a sister taxon to the Chlamydiaceae on the basis of the Chlamydia-like cycle of replication and 80% to 90% homology of ribosomal RNA genes . Because intra-amoebal growth could increase the virulence of some intracellular bacteria, Parachlamydiaceae may be pathogenic . Arguments supporting a pathogenic role are that Chlamydia pneumoniae, a well-recognized agent of pneumonia, was shown to infect free-living amoebae and that another member of the Chlamydiales, Simkania negevensis, which has 88% homology with Parachlamydia acanthamoebae, has caused pneumonia in adults and acute bronchiolitis in infants . The recent identification of a 16S rRNA gene sequence of a Parachlamydiaceae from bronchoalveolar lavage is additional evidence supporting potential for pathogenicity. FEBS Lett, 2002 May 22, 519(1-3), 87 - 92 Bifunctional phosphomannose isomerase/GDP-D-mannose pyrophosphorylase is the point of control for GDP-D-mannose biosynthesis in Helicobacter pylori; Wu B et al.; In this report a recombinant bifunctional phosphomannose isomerase/GDP-D-mannose pyrophosphorylase from Helicobacter pylori has been studied . The enzyme catalyzes the first and third steps of GDP-D-mannose biosynthesis from D-fructose-6-phosphate . The first step, isomerization from D-fructose-6-phosphate to D-mannose-6-phosphate, is found to be rate-limiting in GDP-D-mannose biosynthesis due to feedback inhibition . The inhibition is of non-competitive (mixed) type . As the enzyme is found only in bacteria probably participating in capsular polysaccharide biosynthesis, it could be a specific therapeutic target against bacterial infection. Biochemistry, 2002 May 28, 41(21), 6752 - 60 Kinetic basis for the stimulatory effect of phosphorylation on the methylesterase activity of CheB; Anand GS et al.; Response regulators are activated to elicit a specific cellular response to an extracellular stimulus via phosphotransfer from a cognate sensor histidine kinase to a specific aspartate residue . Phosphorylation at the conserved aspartate residue modulates the activity of the response regulator . Methylesterase CheB is a two-domain response regulator composed of a regulatory domain and an effector domain with enzymatic activity . CheB functions within the bacterial chemotaxis pathway to control the level of chemoreceptor methylation . In its unphosphorylated state, the regulatory domain inhibits methylesterase activity of the effector domain . Phosphorylation of the regulatory domain leads to an enhancement of methylesterase activity through a relief of inhibition and a stimulatory effect on catalysis . CheB is a useful model protein for understanding the effects of phosphorylation of the regulatory domain on interdomain interactions and stimulation of enzymatic activity of the effector domain . Kinetic analyses of CheB activation indicate that the basis for the nearly 100-fold methylesterase activation upon phosphorylation is due to a change in the catalytic rate constant for the methylesterase reaction . It is also shown that the P2 domain of histidine kinase CheA inhibits the methylesterase activity of CheB and that this inhibition is decreased upon phosphorylation of CheB . Finally, studies of methylesterase catalysis by the free catalytic domain in the presence and absence of the regulatory domain have enabled detection of an association between the two domains in the absence of the linker. J Am Chem Soc, 2002 May 29, 124(21), 6194 - 201 Gas-phase photochemistry of the photoactive yellow protein chromophore trans-p-coumaric acid; Ryan WL et al.; The photoisomerization of trans-p-coumaric acid (trans-CA) triggers a photocycle in photoactive yellow protein that ultimately mediates a phototactic response to blue light in certain purple bacteria . We have used fluorescence excitation and dispersed emission methods in a supersonic jet to investigate the nature of the electronic excited states involved in the initial photoexcitation and subsequent photoisomerization of trans-CA . We observed three distinct regions in the fluorescence excitation spectrum of trans-CA . Region I is characterized by sharp features that upon excitation exhibit trans-CA S(1) emission . In region II, features increase in width and decrease in intensity with increasing excitation energy . Upon excitation, we observed dual emission from the S(1) state of trans-CA and what may be the S(1) state of cis-CA . The onset of dual emission corresponds to an isomerization barrier of about 3.4 kcal/mol . Finally, the extremely broad absorption feature in region III is excitation to the S(2) electronic excited state and excitation results in trans-CA S(1) emission . Furthermore, we collected CA from the molecular beam after laser excitation in each of the three regions as further evidence of the photoisomerization process . The relative amounts of trans- and cis-CA in the collected molecules were measured with high-pressure liquid chromatography . Although trans-CA was excited in all three regions, a significant cis-CA peak appeared only in region II, though a small cis peak was observed in region III. Comp Med, 2002 Apr, 52(2), 160 - 6 Validation of an enzyme-linked immunosorbent assay for detection of mouse parvovirus infection in laboratory mice; Ball-Goodrich LJ et al.; PURPOSE: Parvoviruses are among the most prevalent infectious agents in mouse colonies . Infection in laboratory mice is confirmed by detection of serum antibodies to these agents, and most diagnostic tests cannot distinguish serogroup of the infecting agent . The principal objective of the research reported here was to develop and validate a sensitive, serogroup-specific diagnostic test that will distinguish between mouse parvovirus (MPV) and minute virus of mice (MVM) infection . METHODS: The MPV VP2 protein was expressed in bacteria, purified by use of metal-chelation chromatography, and used as antigen in an ELISA . More than 580 sera from uninfected mice and experimentally or naturally infected mice were screened by MPV indirect fluorescent antibody (IFA) test, then were re-tested using the MPV ELISA to define test sensitivity and specificity . An additional 3,700 sera were screened using a variety of tests, including the MPV ELISA and recombinant NS1 ELISA (rNS1 ELISA) . RESULTS: Using MPV IFA test results as a benchmark, the MPV ELISA had sensitivity of 92.3% and specificity of 99.8% . In addition, the MPV ELISA detected anti-viral antibodies at a higher dilution of serum than did the IFA test, and confirmed the infecting agent as MPV or MVM . When compared directly in a commercial laboratory, the MPV ELISA had higher sensitivity (90.3% versus 65%) than and similar specificity (98.3% versus 99.6%) to the rNS1 ELISA . CONCLUSION: The MPV VP2 ELISA provides a sensitive, serogroup-specific alternative for diagnosis and classification of parvovirus infection in laboratory mice. Microb Ecol, 2002 Jul, 44(1), 30 - 8 Epub 2002 May 20. Wavelike distributions of infections by an introduced and naturally occurring root pathogen along wheat roots; van Bruggen AH et al.; Previously, we showed that copiotrophic and oligotrophic bacteria fluctuate as moving waves along roots . These waves probably originate as a result of growth and death cycles at any location where a moving nutrient source passed . In this study, we placed sclerotia of Rhizoctonia solani AG8 along growing roots of wheat and showed that the proportions of root sections from which R . solani was isolated fluctuated with distance from the root tip . Similarly, proportions of root sections from which naturally occurring Pythium spp . were isolated fluctuated with distance from the root tip . Fourier analysis showed that these fluctuations constituted significant waves . Cross-correlation analyses demonstrated that there were negative correlations between R . solani infections and colony forming units of copiotrophic bacteria at the time of inoculation at the same locations on the root (lag = 0 cm), indicating that infection by R . solani could have been inhibited by these bacteria . There was a positive correlation between Pythium infections and copiotrophic bacteria at a lag of 6 cm along the roots . It therefore appears that Pythium infection took place shortly after the initial peak in copiotrophic bacteria following the passage of the root tip. Microb Ecol, 2002 Jul, 44(1), 39 - 48 Epub 2002 May 20. Rock phosphate solubilization and colonization of maize rhizosphere by wild and genetically modified strains of Penicillium rugulosum; Reyes I et al.; Maize root colonization and phosphate solubilizing activity of the fungus Penicillium rugulosum were assessed in a greenhouse trial using soil-plant microcosms . The bacterial gene hph conferring resistance to hygromicin B was introduced by electroporation in the wild-type strain IR-94MF1 of P . rugulosum and one transformant, w-T3, was selected . Maize plants were grown for 5 weeks in a P-poor soil and fertilized with a Florida apatite mineral, with Navay, an apatite rock deposit from Venezuela, or with simple superphosphate . Inoculation treatments included strain IR-94MF1, transformant w-T3 and two IR-94MF1 UV-induced mutants with enhanced (Mps++) or reduced (Mps-) in vitro mineral phosphate solubilizing activity . In the absence of P fertilization, inoculation with any P . rugulosum isolate significantly reduced the size of the total and P-solubilizing bacterial community present in maize rhizosphere . The bacterial community significantly increased in maize inoculated with IR-94MF1 and w-T3 when P was added as apatites Navay or Florida . All P . rugulosum strains were able to stimulate the growth of maize plants as indicated by 3.6 to 28.6% increases in dry matter yields . In the presence of rock phosphate, P uptake by maize plants inoculated with the two mutants Mps++ and Mps- was not always in agreement with their P-solubilizing phenotypes . Strain IR-94MF1 and transformant w-T3 increased P assimilation by the plants fertilized with Navay rock phosphate by 26 and 38%, respectively . In this treatment, w-T3 showed its highest significant maize rhizosphere colonization . With the simple superphosphate treatment, w-T3 increased P uptake in plants by 8% over the uninoculated control and also decreased significantly the community size of total bacteria, total fungi, and P-solubilizing fungi in the rhizosphere. Chem Res Toxicol, 2002 May, 15(5), 614 - 22 Bioactivation of tamoxifen by recombinant human cytochrome p450 enzymes; Notley LM et al.; Tamoxifen is a major drug used for adjuvant chemotherapy of breast cancer; however, its use has been associated with a small but significant increase in risk of endometrial cancer . In rats, tamoxifen is a hepatocarcinogen, and DNA adducts have been observed in both rat and human tissues . Tamoxifen has been shown previously to be metabolized to reactive products that have the potential to form protein and DNA adducts . Previous studies have suggested a role for P450 3A4 in protein adduct formation in human liver microsomes, via a catechol intermediate; however, no clear correlation was seen between P450 3A4 content of human liver microsomes and adduct formation . In the present study, we investigated the P450 forms responsible for covalent drug-protein adduct formation and the possibility that covalent adduct formation might occur via alternative pathways to catechol formation . Recombinant P450 3A4 catalyzed adduct formation, and this correlated with the level of uncoupling in the P450 incubation, consistent with a role of reactive oxygen species in potentiating adduct formation after enzymatic formation of the catechol metabolite . Whereas P450s 1A1, 2D6, and 3A5 generated catechol metabolite, no covalent adduct formation was observed with these forms . By contrast, P450 2B6, 2C19, and rat liver microsomes catalyzed drug-protein adduct formation but not catechol formation . Drug protein adducts formed specifically with P450 3A4 in incubations using membranes isolated from bacteria expressing P450 3A4 and reductase, as well as in reconstitutions of purified 3A4, suggesting that the electrophilic species reacted preferentially with the P450 enzymes concerned. J Med Microbiol, 2002 Jun, 51(6), 495 - 502 Helicobacter pylori adherence to gastric epithelial cells: a role for non-adhesin virulence genes; Zhang ZW et al.; Helicobacter pylori is a major aetiological agent in gastroduodenal disorders and adherence of the bacteria to the gastric mucosa is one of the initial stages of infection . Although a number of specific adhesins has been identified, other H . pylori virulence factors may play a role in adherence to gastric epithelial cells directly or through interaction with other adhesins . This study assessed the effect of 16 H . pylori virulence factors on the adherence of the bacteria to gastric AGS cells and on gastric epithelial cell cycle distribution . Defined isogenic H . pylori SS1 mutants were used . After co-incubation of gastric AGS cells and bacteria, adherence of H . pylori to AGS cells was visualised by immunofluorescence microscopy and quantified by flow cytometry . Cell cycle phase distribution was analysed by flow cytometry with propidium iodide staining . Mutants were tested for their ability to adhere to AGS cells and compared with the wild-type SS1 strain . Mutations in genes in the cag pathogenicity island showed that cagP and cagE mutants adhered less than the wild-type strain to AGS cells, whereas a cagF mutant showed no reduction in adherence . Mutations in genes involved in flagellar biosynthesis showed that the adherence ability of fliQ, fliM and fliS mutants was reduced, but a flhB mutant possessed wild-type levels of adherence . Mutations in genes coding for the urease (ureB) and phospholipase (pldA) enzymes did not affect adherence, but mutation of the tlyA gene encoding an H . pylori haemolysin resulted in a reduced adherence . A fliQ mutant, with reduced adherence to AGS cells, was less able to induce AGS cell apoptosis than SS1 . The ability to induce G0G1 cell cycle arrest was also abolished in the fliQ mutant . However, an increased cell number in S phase was observed when AGS cells were exposed to the fliQ mutant compared with SS1, suggesting that unattached bacteria may still be able to stimulate cell proliferation . In addition to known adhesins, other bacterial virulence factors such as CagE, CagP, FliQ, FliM, FliS and TlyA appear to play a role in H . pylori adherence to gastric epithelial cells . Mutations in these genes may affect H . pylori pathogenicity by reducing either the ability of the bacteria to attach to gastric epithelial cells or the intensity of bacteria-host cell interactions. Microb Ecol, 2002 Jul, 44(1), 1 - 9 Epub 2002 May 07. Do neighboring lakes share common taxa of bacterioplankton? Comparison of 16S rDNA fingerprints and sequences from three geographic regions; Lindstrom ES et al.; Bacterioplankton community composition was studied in 12 lakes in three different geographic regions in Scandinavia using denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rDNA . Area-specific abundant taxa were found in the lakes in two of the regions . In the region of Uppland the lakes had an alpha-proteobacterium, belonging to the subgroup Alpha V in common . The Alpha V bacteria appeared to be favored by neutral or higher pH values . The lakes in Lappland were found to harbor Actinobacteria, which appeared to be favored in bog lakes . No abundant taxon was found to be in common for the lakes in Svalbard, the third region studied. J Comput Biol, 2002, 9(2), 447 - 64 A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes; Thijs G et al.; Microarray experiments can reveal important information about transcriptional regulation . In our case, we look for potential promoter regulatory elements in the upstream region of coexpressed genes . Here we present two modifications of the original Gibbs sampling algorithm for motif finding (Lawrence et al., 1993) . First, we introduce the use of a probability distribution to estimate the number of copies of the motif in a sequence . Second, we describe the technical aspects of the incorporation of a higher-order background model whose application we discussed in Thijs et al . (2001) . Our implementation is referred to as the Motif Sampler . We successfully validate our algorithm on several data sets . First, we show results for three sets of upstream sequences containing known motifs: 1) the G-box light-response element in plants, 2) elements involved in methionine response in Saccharomyces cerevisiae, and 3) the FNR O(2)-responsive element in bacteria . We use these data sets to explain the influence of the parameters on the performance of our algorithm . Second, we show results for upstream sequences from four clusters of coexpressed genes identified in a microarray experiment on wounding in Arabidopsis thaliana . Several motifs could be matched to regulatory elements from plant defence pathways in our database of plant cis-acting regulatory elements (PlantCARE) . Some other strong motifs do not have corresponding motifs in PlantCARE but are promising candidates for further analysis. Biochem J, 2002 Aug 15, 366(Pt 1), 315 - 22 Biochemical analysis of the recombinant Fur (ferric uptake regulator) protein from Anabaena PCC 7119: factors affecting its oligomerization state; Hernandez JA et al.; Fur (ferric uptake regulator) protein is a DNA-binding protein which regulates iron-responsive genes . Recombinant Fur from the nitrogen-fixing cyanobacterium Anabaena PCC 7119 has been purified and characterized, and polyclonal antibodies obtained . The experimental data show that Fur from Anabaena dimerizes in solution with the involvement of disulphide bridges . Cross-linking experiments and MALDI-TOF (matrix-assisted laser desorption/ionization time of flight) MS also show several oligomerization states of Fur, and the equilibrium of these forms depends on protein concentration and ionic strength . In intact recombinant Fur, four cysteine residues out of five were inert towards DTNB {5,5'-dithiobis-(2-nitrobenzoic acid)}, and their modification required sodium borohydride . Metal analysis and electrospray ionization MS revealed that neither zinc nor other metals are present in this Fur protein . Purified recombinant Fur bound to its own promoter in gel-shift assays . Fur was shown to be a constitutive protein in Anabaena cells, with no significant difference in its expression in cells grown under iron-sufficient compared with iron-deficient conditions. Appl Microbiol Biotechnol, 2002 May, 58(6), 751 - 5 Epub 2002 Mar 12. Enhancement of entomopathogenic nematode production in in-vitro liquid culture of Heterorhabditis bacteriophoraby fed-batch culture with glucose supplementation; Gil GH et al.; Nematode yield is a decisive factor for successful large-scale commercial production of entomopathogenic nematode . Various carbon sources were tested in in-vitro liquid culture to improve the yield of the entomopathogenic nematode Heterorhabditis bacteriophora . Canola oil was the optimal carbon source for nematode culture compared to carbohydrates when applied as a sole carbon source . However, when some of carbohydrates were applied together with canola oil, significant increases in nematode yield were observed . When 25 mg glucose ml(-1) was supplemented to 25 mg oil-based liquid culture medium ml(-1), the highest nematode yield, 3.62 x 10(5) infective juveniles, was achieved at 12 days, but nematode growth was suppressed at higher than 75 mg glucose ml(-1) . A fed-batch culture process was introduced in nematode liquid culture consisting of two growth phases: bacteria and nematode . In the oil fed-batch culture, in which only glucose was initially added and oil was fed to the culture after the bacterial growth phase concurrent with nematode inoculation, nematode yield increased up to 4.25 x 10(5) infective juveniles ml(-1), while the batch culture resulted in 3.60 x 10(5) infective juveniles ml(-1) . These results indicate that glucose is a superior carbon source for the bacteria, whereas canola oil is optimal for the nematode . The application of fed-batch culture provides significant enhancement of nematode yield in in-vitro liquid culture. Appl Microbiol Biotechnol, 2002 May, 58(6), 704 - 11 Epub 2002 Mar 19. Biological conversion of cyclic alkanes and cyclic alcohols into dicarboxylic acids: biochemical and molecular basis; Cheng Q et al.; Biological oxidation of cyclic alkanes and cyclic alcohols normally results in formation of the corresponding dicarboxylic acids, which are further metabolized in the cell . The biochemical pathways for oxidative conversion of cyclic compounds are similar in various phylogenetically diverse bacteria . Significant progress has been made in the past 2 years in the isolation and characterization of genes involved in cyclic alkane oxidation pathways in several bacterial species . In this article, we review recent advancements in the field of cyclic alcohol oxidation with focus on the biochemical and genetic characterization of the gene functions . Phylogenetic relationships of the analogous enzymes in the pathways are analyzed . Potential biocatalysis applications of these enzymes are also discussed. Biochim Biophys Acta, 2002 May 3, 1575(1-3), 15 - 25 Antisense-RNA regulation and RNA interference; Brantl S; For a long time, RNA has been merely regarded as a molecule that can either function as a messenger (mRNA) or as part of the translational machinery (tRNA, rRNA) . Meanwhile, it became clear that RNAs are versatile molecules that do not only play key roles in many important biological processes like splicing, editing, protein export and others, but can also--like enzymes--act catalytically . Two important aspects of RNA function--antisense-RNA control and RNA interference (RNAi)--are emphasized in this review . Antisense-RNA control functions in all three kingdoms of life--although the majority of examples are known from bacteria . In contrast, RNAi, gene silencing triggered by double-stranded RNA, the oldest and most ubiquitous antiviral system, is exclusively found in eukaryotes . Our current knowledge about occurrence, biological roles and mechanisms of action of antisense RNAs as well as the recent findings about involved genes/enzymes and the putative mechanism of RNAi are summarized . An interesting intersection between both regulatory mechanisms is briefly discussed. New Microbiol, 2002 Apr, 25(2), 265 - 8 Detection of Alloiococcus otitidis in the nasopharynx and in the outer ear canal; Durmaz R et al.; Alloiococcus otitidis has been recovered from the middle ear of children with otitis media with effusion, but its natural habitat is not known . To determine whether the nasopharynx and the outer ear canals are the natural habitats of A . otitidis, 145 swabs (50, nasopharynx; 95 outer ear canal) collected from 50 children were screened by polymerase chain reaction . A . otitidis DNA was detected in seven (4.8%) of the 145 specimens, of which four were nasopharynx, and three outer ear canal . These results indicate that the nasopharynx and outer ear canal may be the body sites for localization of A . otitidis. New Microbiol, 2002 Apr, 25(2), 247 - 52 Different modulation by live or killed Helicobacter pylori on cytokine production from peripheral blood mononuclear cells; Stassi G et al.; The mechanisms by which H . pylori colonizes and persists within the gastric mucosa are poorly understood . The induction and maintenance of gastric inflammation appear to depend on the complex interaction between a number of cytokines and chemokines . The gastric immune response observed "in vivo", during H . pylori infection, is characterized by a polarization of Th1 cell type that seems to be responsible for gastric pathology . The purpose of this study was to test the direct effect of H . pylori (live or gentamicin-killed) on human PBMC in order to evaluate the "in vitro" Th1-Th2 balance by monitoring IL-18, IFNgamma and IL-10 production . This study demonstrates for the first time that "in vitro" pretreatment with gentamicin-killed H . pylori of PBMC, followed by infection with live bacteria, downregulates the production of inflammatory cytokines such as IL-18 and IFNgamma Our results provide a possible strategy to restore the immunological disorders determined by H . pylori infection. J Laparoendosc Adv Surg Tech A, 2002 Apr, 12(2), 123 - 8 Remote complications of spilled gallstones during laparoscopic cholecystectomy: causes, prevention, and management; Hawasli A et al.; In the last 11 years (November 1989-December 2000), 5526 laparoscopic cholecystectomies were performed in a community residency training program . Two cases (0.04%) of remote complications secondary to spilled gallstones were identified . A 75-year-old woman presented with a sterile abscess in the abdominal wall containing gallstones 4 years and 4 months after an elective laparoscopic cholecystectomy . The second patient, a 43-year-old woman, presented with a subdiaphragmatic/subhepatic abscess containing gallstones . The abscess grew the same bacteria that were present 2 years and 3 months previously during a laparoscopic cholecystectomy for acute gangrenous cholecystitis . In both cases, pigmented gallstones were identified . Causes of gallstone spillage, means of prevention, and ways of managing this complication are discussed. J Hosp Infect, 2002 Apr, 50(4), 286 - 92 Mobile zoned/exponential LAF screen: a new concept in ultra-clean air technology for additional operating room ventilation; Friberg B et al.; A mobile screen (0.5 x 0.4 m) producing ultra-clean exponential LAF (air-flow central zone 0.6 m/s and peripheral zone 0.4 m/s) was investigated as an addition to conventional turbulent/mixing operating room ventilation . The evaluation was performed during strictly standardized sham operations reflecting conditions during major surgery . The study consisted of a pilot experiment designed to give high counts of sedimenting aerobic colony forming units (cfu) . In a second main study, recording dust particles, air-borne and sedimenting aerobic cfu, the screen was associated with optimal operating room clothing.In the pilot experiment the use of the screen resulted in a substantial reduction of sedimenting bacteria from 3835-4940 to 0-390 cfu/m(2)/h . In the main study, the use of the additional LAF reduced the surface contamination from 416-329 to 7-78 cfu/m(2)/h up to 1.6 m from the screen (P=0.001-0.0001) . Measured in the wound area the screen reduced the air counts of bacteria from 9-14 to 0.2-0.4 cfu/m(3) (P=0.008-0.0001) and a marked reduction of air-borne dust particles was recorded (P=0.007-0.009).In conclusion, the additional mobile LAF screen reduced the counts of aerobic air-borne and sedimenting bacteria-carrying particles as well as dust particles to the levels gained with complete ultra-clean LAF room ventilation . Thus, the screen might prove a valuable addition to operating room ventilation as well as in other areas where asepsis is essential . Dent Clin North Am, 2002 Apr, 46(2), 211 - 45, v-vi The effects of dentin permeability on restorative dentistry; Pashley DH et al.; The permeability properties of dentin determine its sensitivity and the degree of pulpal response to restorative procedure materials and microleakage . Most pulpal reactions are due to bacteria or bacterial products that permeate across dentin . These reactions can be prevented if dentin is sealed with resins as soon as it is exposed . In the future, restorative dentists may employ topical application of biologic growth factors to permeate across dentin to modify the formation of reactionary or reparative dentin, thereby lowering dentin permeability and protecting the pulp. Rinsho Byori, 2002 Apr, 50(4), 365 - 9 {Function of lung surfactant and its deterioration}; Osanai K; Lung surfactant(LS) is a mixture of several lipids and four apolipoproteins(SP-A, -B, -C and -D) and lowers surface tension at air-liquid interface of alveoli . Most of LS is synthesized and secreted by alveolar type II cells . Although lamellar bodies are storage granules of LS, each component appears to take independent intracellular routes to reside in the granules . Patients with infantile respiratory distress syndrome(IRDS) or acute respiratory distress syndrome(ARDS) develop fatal respiratory failure due to lack of LS . In addition, acute phase of interstitial pneumonia also shows deterioration of LS and increased alveolar surface force resulting in decreased lung compliance . SP-A and SP-D are used as serum marker to evaluated activity of interstitial lung diseases . Recently, growing evidences are accumulating that LS plays a role in innate host defense in the lung against large species of bacteria, mycoplasma, and viruses. Nat Prod Rep, 2002 Apr, 19(2), 181 - 222 The biosynthesis of C5-C25 terpenoid compounds; Dewick PM; This review covers recently-published experimental information on the biosynthesis of terpenoids in the range C5-C25 . In addition to sections on the mevalonate and mevalonate-independent (deoxyxylulose phosphate) pathways, t