Z Naturforsch {C}, 1998 Nov-Dec, 53(11-12), 1061 - 71 Increased levels of lipid oxidation products in rheumatically destructed bones of patients suffering from rheumatoid arthritis; Jira W et al.; The new indicator for lipid peroxidation (LPO) processes--9-hydroxy-10,12-octadecadienoic acid (9-HODE)--was used to investigate, whether LPO processes are increased in destructed bone material of patients suffering from rheumatoid arthritis (RA) in comparison to surrounded non destructed bone material . The HODE content in destructed bones exceeded that of non destructed ones of the same patient for a factor of about 3 . In addition similar increases in leukotoxines and epoxy oleic acid in the destructed bone material were observed, indicating an increase of LPO processes in affected bone parts of patients. Can J Microbiol, 1998 Oct, 44(10), 1012 - 7 Characterization of the expression and immunogenicity of the ns4b protein of human coronavirus 229E; Chagnon F et al.; Sequencing of complementary DNAs prepared from various coronaviruses has revealed open reading frames encoding putative proteins that are yet to be characterized and are so far only described as nonstructural (ns) . As a first step in the elucidation of its function, we characterized the expression and immunogenicity of the ns4b gene product from strain 229E of human coronavirus (HCV-229E), a respiratory virus with a neurotropic potential . The gene was cloned and expressed in bacteria . A fusion protein of ns4b with maltose-binding protein was injected into rabbits to generate specific antibodies that were used to demonstrate the expression of ns4b in HCV-229E-infected cells using flow cytometry . Given a previously reported contiguous five amino acid shared region between ns4b and myelin basic protein, a purified recombinant histidine-tagged ns4b protein and (or) human myelin basic protein were injected into mice to evaluate whether myelin-viral protein cross-reactive antibody responses could be generated . Each immunogen induced specific but not cross-reactive antibodies . We conclude that ns4b is expressed in infected cells and is immunogenic, although this does not involve amino acids shared with a self protein, at least in the experimental conditions used. Langenbecks Arch Chir Suppl Kongressbd, 1998, 115, 596 - 8 {Pancreatitis and translocation--approaches for nutritional strategies}; Foitzik T; Translocation of intestinal bacteria from the gut into pancreatic necrosis is an important factor in the development of septic complications in acute pancreatitis . Bacterial translocation is promoted by an impaired intestinal mucosal barrier, which can be attributed to the reduced oxygen and substrate supply of the intestine . A rat model of severe acute pancreatitis has been used to confirm the hypothesis that an impaired mucosal barrier can be stabilized by supplying certain nutrients, vitamins, and trace elements . A reduction in secondary pancreas infections with intestinal bacteria and improved survival was achieved under intravenous glutamine substitution, an essential amino acids in stress situations for enterocytes, colonocytes and immunocompetent cells . The positive experimental results are currently being investigated in a controlled randomized multicenter trial . Comparable studies need to be performed for verifying the effect of other nutritive factors on bacterial translocation and the disease course in acute pancreatitis. Gene Ther, 1998 Nov, 5(11), 1538 - 44 Safety study and characterization of E1A-liposome complex gene-delivery protocol in an ovarian cancer model; Xing X et al.; A phase I clinical trial of E1A-liposome complex is currently ongoing in patients with HER-2/neu-overexpressing breast or ovarian cancers . To optimize the E1A-liposome complex for a further stage of clinical trial, several aspects of the current protocol have been examined in an animal model . In the orthotopic ovarian cancer model, different doses of lipid in the the E1A-liposome complex, which is currently used in clinical trials, were tested for the in vivo gene-transfer efficacy and tumor-suppression function . A lowered lipid dose--1/13 of the previous amount--produced gene expression level and E1A tumor-suppression efficacy similar to that of the original protocol . Mini-E1A, an E1A construct without its immortalization domain and yet capable of repressing HER-2/neu, was proved to be as potent as E1A in suppressing tumor development in vivo . These changes in the E1A-liposome complex will significantly reduce any potential adverse effects caused by lipid vector and E1A DNA . To examine further whether residual E1A DNA may still exist in normal organs after the E1A-liposome treatment, PCR was used to detect E1A DNA in mice that survived for 1 1/2 years after the last treatment . E1A DNA was detected only in the lungs and kidneys, but not in livers, hearts, spleens, brains, uterus or the ovaries . Furthermore, resistance of the E1A DNA extracted from tissues to the digestion of Dpnl restriction enzyme, which can cleave the methylated E1A plasmid DNA generated by methylation-competent bacteria, suggested integration of E1A DNA into the chromosome of the lungs and kidneys . Experimental results presented here provide important information for safety concerns and for the design of future phase II and phase III trials. Microb Ecol, 1999 Feb, 37(2), 95 - 106 Protozoan Bacterivory in the Ice and the Water Column of a Cold Temperate Lagoon; Sime-Ngando T et al.; > Abstract Bacterial abundance and bacterivorous protist abundance and activity were examined in ice-brine and water column communities of a cold temperate Japanese lagoon (Saroma-Ko Lagoon, Hokkaido, 44 degreesN, 144 degreesE), during the late winter phase of ice community development (February-March 1992) . Bacterial abundance averaged 6 and 1 x 10(5) cells ml-1 in the ice-brine and plankton samples, respectively, and generally decreased during the sampling period . Bacterivorous protists, identified based on direct observation of short-term (<1 h) ingested fluorescently labeled bacteria (FLB) in their food vacuoles, were largely dominated by flagellates, mainly cryothecomonad-type and chrysomonad-like cells and small dinoflagellates of the genus Gymnodinium . Bacterivorous ciliates included mainly the prostomatid Urotricha sp., the scuticociliates Uronema and Cyclidium, the choreotrichs Lohmaniella oviformis and Strobilidium, and the hypotrich Euplotes sp . Protist abundance averaged 4 x 10(3) and 8.1 cells ml-1 in the ice-brine and 0.3 x 10(3) and 1.2 cells ml-1 in the plankton, for flagellates and ciliates, respectively . In contrast to bacteria, the abundance of protists generally increased throughout the sampling period, indicating predator-prey interactions . Protistan bacterivory, measured from the rate of FLB disappearance over 24 h, averaged 36% (ice) and 24% (plankton) of bacterial standing stock and exhibited the same seasonal pattern as for protist abundance . The calculated specific clearance (range, 2-67 nl protozoa-1 h-1) and ingestion (<1-26 particles protozoa-1 h-1) rates were likely to be minimal estimates and grazing impact may have been higher on occasion . Indications for the dependence of "bacterivorous protists" on nonbacterial food items were also provided . Although alternative sources of bacterial loss are likely to be of importance, this study provides evidence for the potential of protozoan assemblages as bacterial grazers in both sea ice-brine biota and water column at the southern limit of sea ice in the northern hemisphere. Proc AMIA Symp . 1998;:750-4. Updating a bibliography using the related articles function within PubMed; Liu X et al.; Comprehensive bibliographies are useful for conducting reviews of the literature, and for assessing the progress within a field . These bibliographies may be broad and inclusive, or focused and precise in their inclusion criteria . In either case, the task of maintaining a complete bibliography within a particular area of research is made difficult by the diversity, complexity and huge volume of newly published literature . In an effort to effectively and automatically retrieve relevant literature, different search strategies and indexing tools have been developed, including the RELATED ARTICLES function provided with the PubMed system . In this paper, we report a program for incremental updates of a bibliography using the PubMed RELATED ARTICLES function . Given a highly specialized starting bibliography of experimental measurements of the structure of the 30S bacterial ribosomal subunit, the system was applied to find additional relevant references . For this particular task, the system has a recall of 75%, a strict precision of 32% and a partial precision of 42% . Our results are notable because although the RELATED ARTICLES function is purely statistical, it is nonetheless able to select a very narrowly defined set of articles from the literature . We discuss the tradeoffs between having a user to evaluate many articles of possible interest in a single session, versus asking a user to evaluate a small set of articles on a periodic basis. Baillieres Clin Rheumatol, 1998 Nov, 12(4), 611 - 26 Animal models and in vitro models for the study of aetiopathogenesis of spondyloarthropathies; Breban M; Among several animal models, HLA-B27 transgenic rodents proved useful for investigating the interplay between genetic factors and the bacterial environment in the aetiopathogenesis of the spondyloarthropathies (SpA) . HLA-B27 transgenic rats spontaneously develop a multisystemic inflammatory disease resembling human SpA . This disease is dependent on the presence of a normal bacterial flora and implicates the immune system . The presence of both T cells and antigen-presenting cells expressing high levels of HLA-B27 seems of critical importance in its pathogenesis . HLA-B27 transgenic mice also develop arthritis, under the influence of the bacterial flora . In both types of model, CD8+ T cells seem not to be necessary, arguing against the 'arthritogenic peptide' hypothesis . In vitro models have been used to study the immune response against bacterial agents and the role of HLA-B27 in human SpA . It appears that an impaired immune response against bacteria could be involved in the triggering of human SpA . HLA-B27 could be implicated at the level of interaction between host cells and bacteria in the driving of a specific immune response against bacterial antigens or as a target of an autoimmune response. Bull Tokyo Dent Coll, 1998 Aug, 39(3), 165 - 74 Relationships between chronic oral infectious diseases and systemic diseases; Okuda K et al.; There are over 300 species of bacteria forming populations of several hundred billion in the human oral cavity . The number of bacteria reaches a thousand billion when the mouth is not sufficiently cleaned . Using saliva and gingival crevicular fluid as their main nutrients, these bacteria create their ecological niches on tooth surfaces, gingival crevices, saliva, dorsum linguae, and buccal and pharyngeal mucosa, threatening oral and systemic health . It is known that primary lesions of these chronic bacterial infections secondarily cause nephritis, rheumatoid arthritis, and dermatitis . Further, it has been demonstrated in recent years that bacteria inhabiting the oral cavity can cause bacterial pneumonia and endocarditis and that the periodontal-disease-associated bacteria become causative agents for pregnancy troubles and are involved in blood circulation problem and coronary heart disease . Dentistry reviewed the theme of World Health Day, Oral Health for a Healthy Life, in 1994 . The 8020 campaign to promote tooth care is also becoming established in Japan; however, the authors emphasized that this achievement is not the goal of dental health care . In this article, we explain the bases supporting the concept that oral health care, primarily mouth cleaning, is important for not only oral disease but also a healthy life. Nucleic Acids Res, 1999 Feb 15, 27(4), 1104 - 17 DNA binding specificity and transactivation properties of SREBP-2 bound to multiple sites on the human apoA-II promoter; Kan HY et al.; DNase I footprinting of the apoA-II promoter using sterol regulatory element binding protein-2 {(SREBP-2 (1-458)} expressed in bacteria identified four protected regions, designated AIIAB (-64 to -48), AIICD (-178 to -154), AIIDE (-352 to -332) and AIIK (-760 to -743), which bind SREBP-2 and contain either palindromic or direct repeat motifs . Potassium permanganate and dimethyl sulfate interference experiments using the AIIAB region as probe showed that the nucleotides of a decameric palindromic repeat RTCAMVTGMY and two 5' T residues participate in DNA-protein interactions . SREBP-2 transactivated the intact (-911/+29) apoA-II promoter 1.7-fold and truncated apoA-II promoter segments which contain one, two or three SREBP-2 sites 11- to 17-fold in HepG2 cells . Transactivation of a promoter construct containing the binding site AIIAB and the apoA-II enhancer, which includes the binding site AIIK, was abolished by mutations in element AIIAB . An SREBP-2 mutant defective in DNA binding caused a dose-dependent repression of the apoA-II promoter activity . Repression was also caused by an SREBP-2 mutant which lacks the N-terminal activation domain (residues 1-93) but binds normally to its cognate sites . In contrast, a double SREBP-2 mutant which lacks both the DNA binding and the activation domains has no effect on the apoA-II promoter activity . Overall, the findings suggest that SREBP-2 can transactivate the apoA-II promoter by binding to multiple sites . Furthermore, the repression caused by the DNA binding deficient mutants results from squelching of positive activator(s) which appear to recognize the activation domain of SREBP-2. Proc Natl Acad Sci U S A, 1999 Feb 2, 96(3), 1059 - 64 Enhancing versus suppressive effects of stress hormones on skin immune function; Dhabhar FS et al.; Delayed-type hypersensitivity (DTH) reactions are antigen-specific cell-mediated immune responses that, depending on the antigen, mediate beneficial (e.g., resistance to viruses, bacteria, and fungi) or harmful (e.g., allergic dermatitis and autoimmunity) aspects of immune function . Contrary to the idea that stress suppresses immunity, we have reported that short-duration stressors significantly enhance skin DTH and that a stress-induced trafficking of leukocytes to the skin may mediate this immunoenhancement . Here, we identify the hormonal mediators of a stress-induced enhancement of skin immunity . Adrenalectomy, which eliminates the glucocorticoid and epinephrine stress response, eliminated the stress-induced enhancement of skin DTH . Low-dose corticosterone or epinephrine administration significantly enhanced skin DTH and produced a significant increase in the number of T cells in lymph nodes draining the site of the DTH reaction . In contrast, high-dose corticosterone, chronic corticosterone, or low-dose dexamethasone administration significantly suppressed skin DTH . These results suggest a role for adrenal stress hormones as endogenous immunoenhancing agents . These results also show that hormones released during an acute stress response may help prepare the immune system for potential challenges (e.g., wounding or infection) for which stress perception by the brain may serve as an early warning signal. Genome Res, 1999 Jan, 9(1), 17 - 26 Distribution of protein folds in the three superkingdoms of life; Wolf YI et al.; A sensitive protein-fold recognition procedure was developed on the basis of iterative database search using the PSI-BLAST program . A collection of 1193 position-dependent weight matrices that can be used as fold identifiers was produced . In the completely sequenced genomes, folds could be automatically identified for 20%-30% of the proteins, with 3%-6% more detectable by additional analysis of conserved motifs . The distribution of the most common folds is very similar in bacteria and archaea but distinct in eukaryotes . Within the bacteria, this distribution differs between parasitic and free-living species . In all analyzed genomes, the P-loop NTPases are the most abundant fold . In bacteria and archaea, the next most common folds are ferredoxin-like domains, TIM-barrels, and methyltransferases, whereas in eukaryotes, the second to fourth places belong to protein kinases, beta-propellers and TIM-barrels . The observed diversity of protein folds in different proteomes is approximately twice as high as it would be expected from a simple stochastic model describing a proteome as a finite sample from an infinite pool of proteins with an exponential distribution of the fold fractions . Distribution of the number of domains with different folds in one protein fits the geometric model, which is compatible with the evolution of multidomain proteins by random combination of domains . {Fold predictions for proteins from 14 proteomes are available on the World Wide Web at . The FIDs are available by anonymous ftp at the same location.} Insect Mol Biol, 1999 Feb, 8(1), 107 - 18 Insect immunity: molecular cloning, expression, and characterization of cDNAs and genomic DNA encoding three isoforms of insect defensin in Aedes aegypti; Lowenberger CA et al.; Aedes aegypti were immune activated by injection with bacteria, and the expression of insect defensins was measured over time . Northern analyses indicated that defensin transcriptional activity continued for at least 21 days after bacterial injection, and up to 10 days after saline inoculation . Mature defensin levels in the haemolymph reached approximately 45 microM at 24 h post inoculation . cDNAs encoding the preprodefensins of three previously described mature Ae . aegypti defensins were amplified by PCR, cloned and sequenced . Genomic clones were amplified using primers designed against the cDNA sequence . Sequence comparison indicates that there is significant inter- and intra-isoform variability in the signal peptide and prodefensin sequences of defensin genes . Preprodefensin sequences of isoforms A and B are very similar, consisting of a signal peptide region of twenty amino acids, a prodefensin region of thirty-eight amino acids and a forty amino acid mature peptide domain . The sequence encoding isoform C is significantly different, comprising a signal peptide region of twenty-three amino acids, a prodefensin region of thirty-six amino acids, and the mature protein domain of forty amino acids . Analysis of the genomic clones of each isoform revealed one intron spatially conserved in the prodefensin region of all sequences . The intron in isoforms A and B is 64 nt long, and except for a 4 nt substitution in one clone, these intron sequences are identical . The intron in isoform C is 76 nt long and does not share significant identity with the intron sequences of isoforms A or B . The defensin gene mapped to chromosome 3, between two known loci, blt and LF168. Insect Mol Biol, 1999 Feb, 8(1), 67 - 72 Phylogenetic status of a fecundity-enhancing Wolbachia that does not induce thelytoky in Trichogramma; Vavre F et al.; Wolbachia are widespread bacteria which infect a number of species of insects and other arthropods . They manipulate the reproduction of their hosts at their own advantage . In Trichogramma species all Wolbachia known so far induce thelytoky and form a monophyletic group in the B subdivision of Wolbachia . Here we show that some strains of the arrhenotokous species Trichogramma bourarachae harbour Wolbachia symbionts that locate in the A subdivision, and which do not induce thelytoky . Although the symbiont of T . bourarachae is closely related to Wolbachia that induce cytoplasmic incompatibility in other insects, no cytoplasmic incompatibilities were found in crosses involving infected and uninfected strains . In T . bourarachae the presence of this Wolbachia is associated with a higher fecundity of strains . Our results strongly suggest that Wolbachia are involved in this increased fecundity . Theoretical models on the evolution of host-Wolbachia interaction predict that a reduced effect on reproduction can be selected for if cost of infection is reduced . The effect in T . bourarachae should illustrate this prediction. Insect Mol Biol, 1999 Feb, 8(1), 39 - 53 Four serine proteinases expressed in Manduca sexta haemocytes; Jiang H et al.; Several putative serine proteinases were detected in Manduca sexta larval plasma by labelling with radioactive diisopropyl fluorophosphate . To begin to identify and characterize such enzymes, a polymerase chain reaction was carried out using haemocyte cDNA as template and primers designed to amplify conserved sequences from serine proteinases . Four serine proteinase cDNA fragments were cloned . These were used as probes to screen an M . sexta larval haemocyte cDNA library to obtain full-length clones encoding haemocyte proteinases 1-4 (HP1, HP2, HP3 and HP4) . HP1 and HP2 contain an aminoterminal 'clip' domain similar to those found in horseshoe crab clotting enzyme and clotting factor B and also in the Drosophila melanogaster proteinases snake and easter . HP3 and HP4 are most similar to proteinases from mammalian leucocytes . HP1 and HP2 are both present in plasma . HP1 is expressed in haemocytes (granular cells and oenocytoids) and not in fat body . HP2 is expressed in fat body and in granular haemocytes, plasmatocytes and oenocytoids . After injection of larvae with bacteria, the level of HP2 mRNA decreased in haemocytes and increased in fat body. Virus Genes, 1998, 17(3), 219 - 32 DNA-antiviral vaccines: new developments and approaches--a review; Giese M; Current vaccines can be divided into "live," "recombinant" and "killed" vaccines . Live vaccines are traditionally composed of attenuated viruses or bacteria, selected for their reduced pathogenicity . Recombinant vaccines, driven by a viral or bacterial vector express foreign antigens, or only recombinant proteins injected as antigen . Killed vaccines consist of inactivated whole pathogens . But all these traditional vaccines have some disadvantages: Attenuated live vaccine are able to undergo mutation and as mutated viruses or bacteria can now provoke the diseases against which the vaccine should protect the organism . A further disadvantage of live vaccines is the possibility of shedding which is a real problem especially in veterinary medicine . Clearly, there is a need for better vaccines to protect against diseases without the disadvantages associated with vaccines presently in use . Modern vaccines might be characterized as safe, no risk of reversion to pathogenicity, and they should be stable without the necessity of a "cold chain." Production should be simple, standardized and inexpensive . Vaccine development has now been improved by the ability to use direct inoculations of plasmid DNA encoding viral or bacterial proteins . One of the major benefits of DNA-vaccines, variously termed "DNA-, genetic- or nucleic acid-immunization," is the endogenous synthesis of the encoded protein . Therefore DNA vaccines mimic natural infection and provoke both strong humoral and cellular immune response . This review summarizes new developments and approaches of DNA vaccination and explains the construction of expression plasmids as well as possible mechanisms of immune responses. Theor Popul Biol, 1999 Feb, 55(1), 94 - 109 Dynamics of co-infection with M . Tuberculosis and HIV-1; Kirschner D; Since 1985, there has been a renewed epidemic of tuberculosis (TB) that was previously thought to be in check . There is evidence to believe the main factor for this resurgence has been the human immunodeficiency virus (HIV) . Co-infection with HIV and M . Tuberculosis has profound implications for the course of both diseases . This study represents a first attempt to understand how the introduction of an opportunistic infection, namely Mycobacterium tuberculosis, the bacteria that causes TB, affects the dynamic interaction of HIV-1 and the immune system . We create a mathematical model using ordinary differential equations to describe the interaction of HIV and TB with the immune system . It is known that infection with TB can decrease the CD4(+) T cell counts-a key marker of AIDS progression; thus, it shortens survival in HIV infected individuals . Another main marker for HIV progression is the viral load . If this load is increased due to the presence of opportunistic infections, the disease progression is much more rapid . We also explore the effects of drug treatment on the TB infection in the doubly-infected patient . Br J Nutr, 1998 Oct, 80(4), S213 - 8 Development of consumer probiotics for the US market; Sanders ME; Curiosity about probiotic bacteria is high . This is not surprising given the rapid growth of the natural products market in the USA, which was 22% in 1995 (New Hope Natural Media, Boulder, CO) . Although probiotic cultures are only one component of that market, this trend shows that consumers in the USA are increasingly taking a pro-active stance towards their health and are purchasing products not only to eliminate what is perceived as dietary negatives but to increase the levels of dietary positives (Wrick, 1995) . This shift in consumer attitude bodes well for the development of the American probiotic market . This article describes the composition, promotion and labelling of probiotic-containing products, discusses attributes of commercial probiotic bacteria, and estimates the size of the probiotic market in the USA . This market information was obtained from several published (Anon, 1996a,b) and unpublished but commercially available (SPINS Information Services, San Francisco, CA and New Hope Natural Media, Boulder, CO) sources. Appl Environ Microbiol, 1999 Feb, 65(2), 438 - 43 Anaerobic versus aerobic degradation of dimethyl sulfide and methanethiol in anoxic freshwater sediments; Lomans BP et al.; Degradation of dimethyl sulfide and methanethiol in slurries prepared from sediments of minerotrophic peatland ditches were studied under various conditions . Maximal aerobic dimethyl sulfide-degrading capacities (4.95 nmol per ml of sediment slurry . h-1), measured in bottles shaken under an air atmosphere, were 10-fold higher than the maximal anaerobic degrading capacities determined from bottles shaken under N2 or H2 atmosphere (0.37 and 0 . 32 nmol per ml of sediment slurry . h-1, respectively) . Incubations under experimental conditions which mimic the in situ conditions (i . e., not shaken and with an air headspace), however, revealed that aerobic degradation of dimethyl sulfide and methanethiol in freshwater sediments is low due to oxygen limitation . Inhibition studies with bromoethanesulfonic acid and sodium tungstate demonstrated that the degradation of dimethyl sulfide and methanethiol in these incubations originated mainly from methanogenic activity . Prolonged incubation under a H2 atmosphere resulted in lower dimethyl sulfide degradation rates . Kinetic analysis of the data resulted in apparent Km values (6 to 8 microM) for aerobic dimethyl sulfide degradation which are comparable to those reported for Thiobacillus spp., Hyphomicrobium spp., and other methylotrophs . Apparent Km values determined for anaerobic degradation of dimethyl sulfide (3 to 8 microM) were of the same order of magnitude . The low apparent Km values obtained explain the low dimethyl sulfide and methanethiol concentrations in freshwater sediments that we reported previously . Our observations point to methanogenesis as the major mechanism of dimethyl sulfide and methanethiol consumption in freshwater sediments. J Gastrointest Surg, 1998 Mar-Apr, 2(2), 174 - 85 Role of the ileocecal junction in the motor response to intestinal resection; Thompson JS et al.; Extensive resections of the distal small intestine are associated with motor disruption in the proximal remnant . Luminal contents such as bacteria and short-chain fatty acids may play a role . We evaluated the effect of bypass of the ileocecal junction (ICJ) on the motor response to a 50% distal resection . Thirty-five dogs were divided into three groups: transection control (TC, n = 11); 50% distal resection with intact ICJ (DR, n = 12), and 50% distal resection with jejunocolostomy to bypass the ICJ (DRBP, n = 12) . Motor activity, intestinal transit, nutrition, absorption, and motor active hormones were studied over a 3-month period . Caloric intake was reduced and nutritional status similarly impaired in both resected groups . Steatorrhea, however, was significantly greater after DRBP . Intestinal structural adaptation was similar in both resected groups at 12 weeks . Animals in the bypass group demonstrated elevated intraluminal short-chain fatty acid and anaerobic bacterial counts . Migrating motor complex frequency was similar in the three groups; distal starts, however, were more frequent in both resected groups . Clustered contractile activity was prominent in the remnant after both DR and DRBP (50% and 32% recording time occupied by clusters, respectively {not significant}) . Basal levels of peptide YY were increased following resection and this increase was unaffected by ICJ bypass . Postprandial neurotensin concentrations were transiently increased after distal bowel resection . In contrast, the postprandial neurotensin response was abolished following resection with bypass of the ICJ . Basal motilin levels were reduced following resection alone but not after resection with ICJ bypass . The motor response to resection does not appear to be related to alterations in circulating levels of hormones localized to the distal ileum; neither does it seem to be influenced by luminal bacteria and short-chain fatty acids or retention of a sphincteric mechanism at the ICJ . These findings also raise questions about the role of short-chain fatty acids and bacteria in the generation of the various distinctive motor patterns of the distal ileum . Resection of the distal ileum through loss of the receptor site for either retarding reflexes or bile salt absorption may be of greater importance in determining the motor response to resection. J Vet Diagn Invest, 1999 Jan, 11(1), 45 - 9 Detection of Lawsonia intracellularis in swine using polymerase chain reaction methodology; Jordan DM et al.; The polymerase chain reaction (PCR) was evaluated for its usefulness as a diagnostic tool to detect Lawsonia (ileal symbiont) intracellularis . Porcine ilea were collected from swine cases submitted to the Iowa State University Veterinary Diagnostic Laboratory between December 1, 1994, and June 30, 1995 . Sampling was random, with no regard to health status . There were 621 ileum scrapings evaluated using the PCR technique . Thirty-five of the samples were positive, either by PCR or conventional diagnostic methods such as histology and Warthin-Starry silver stain . These 35 samples were further evaluated by Warthin-Starry silver stain and indirect immunofluorescent antibody test (IFAT) to confirm the presence of L . intracellularis in the tissue sections . Of the 26 samples positive by PCR, 22 were positive by IFAT . Sixteen of the 22 were also positive when stained with Warthin-Starry and evaluated microscopically for typical bacteria . Nine of the original samples were negative by all 3 techniques . PCR appears more sensitive and specific for L . intracellularis detection than Warthin-Starry stain and IFAT . This study provides evidence that PCR may be useful as a reference standard for the detection of L . intracellularis . PCR may be an appropriate monitoring tool for swine herds because it is a rapid procedure that could be applied to batch testing . Although the test is currently too laborious and expensive for routine diagnostic use, there may be situations in which it is justified because of the advantages of greater sensitivity and specificity. Scand J Urol Nephrol, 1998 Dec, 32(6), 411 - 4 Internal jugular vein haemodialysis catheter-induced right atrium endocarditis--case report and review of the literature; Tarng DC et al.; We present a case of right-sided endocarditis as a life-threatening complication of having a jugular vein haemodialysis catheter inadvertently placed in the right atrium . The mechanisms of direct traumatization of the endocardium by the catheter tip and continuous inoculation of bacteria onto the endocardial surface make dual lumen catheter-induced endocarditis similar to the pathophysiology of experimental endocarditis in animals . Therefore, the catheter tip should be placed in the distal superior vena cava during cannulation . Once endocarditis is present, removal of catheters and a 4-6-week course of intravenous antibiotics guided by the sensitivity test are recommended. Syst Appl Microbiol, 1998 Dec, 21(4), 618 - 31 Group specific PCR-detection of potential trichothecene-producing Fusarium-species in pure cultures and cereal samples; Niessen ML et al.; A PCR based assay (Tox5 PCR) which analyses Fusarium species potentially producing trichothecenes was developed using a pair of primers derived from the DNA-sequence of the trichodiene synthase gene (tri5) . The primer pair was tested using DNA isolated from a variety of strains representing 64 species and varieties of Fusarium as well as from other fungi, bacteria and cereals . A 658 bp PCR fragment was specifically amplified with DNA isolated from strains of species belonging to the Fusarium sections Discolor, Sporotrichiella, Arthrosporiella, Gibbosum, and "Dlaminia" . PCR products obtained were sequenced . Alignment to tri5 sequences given in the literature revealed a high degree of homology . Results of the PCR developed correlated well with literature data on the trichothecene producing capabilities of the respective species . Potential trichothecene producing fusaria were detected in contaminated cereals and malts using the Tox5 PCR assay . Intensity of the signals produced were well correlated with the concentration of deoxynivalenol (DON) in samples of wheat. Syst Appl Microbiol, 1998 Dec, 21(4), 478 - 86 Adenylosuccinate synthetase genes: molecular cloning and phylogenetic analysis of a highly conserved archaeal gene; Cann IK et al.; Adenylosuccinate synthetase (PurA) catalyzes the first step in the de novo AMP synthesis and has been extensively studied in both Bacteria and Eukarya . We cloned the purA gene from the hyperthermophilic archaeon, Pyrococcus furiosus . The gene appears to be individually transcribed and encodes a protein of 339 amino acids . The amino acid sequence comparison with other archael PurAs found from recent genome analyses indicated that two deletions, one central and the other C-terminal, are a common feature of archaeal PurAs . None of the 21 PurA homologues analyzed from Eukarya and Bacteria exhibited this feature . Amino acid sequences of PurAs in Archaea showed 64% average identities which were significantly higher than the 50% and 55% calculated for Bacteria and Eukarya, respectively . Several residues conserved in PurAs of both Eukarya and Bacteria and shown to be of catalytic importance are missing in the archaeal PurAs . Phylogenetic analysis using PurA as the marker grouped life into 3 domains, hence it was consistent with results derived from 16-18S ribosomal RNA sequences . The topology within the three domains, in general, portrayed the hitherto accepted evolutionary relationship among the organisms utilized . PurA can, thus, serve as an additional marker to evaluate phylogenetic inferences drawn from sequence data from rRNA and other conserved genes . The presence of two unique deletions in both euryarchaeal and crenarchaeal PurAs, but not in those of Bacteria and Eukarya, is a strong evidence confirming the common lineage of these two subdomains of Archaea. Reprod Nutr Dev, 1998 Sep-Oct, 38(5), 567 - 76 In vitro study of molecular weight, hydrophobicity and amino acid composition of peptides during breakdown of a casein hydrolysate by two strains of Prevotella ruminicola; Depardon N et al.; The molecular weight, amino acid composition and hydrophobicity of the peptide residue produced by hydrolysis of protein by two strains of Prevotella ruminicola (23 and S17/3) were determined . These last two characteristics could play a role in the control of proteolysis . Both strains produced dipeptidyl peptidases (DAP-1) but only P . ruminicola 23 synthesised alanine aminopeptidase . The area of 3-5 kDa peptides decreased, while the peptides directly assimilable by bacteria (0.5-1 kDa and < 0.5 kDa) increased with strain S17/3, but decreased with P . ruminicola 23 . The amino acid compositions showed that the proportions of these compounds changed little with time and there was proline enrichment . Similarly, reverse phase HPLC showed no evidence of enrichment of the culture medium by hydrophobic peptides during the growth phase of P . ruminicola . These experiments show that the changes in the various peptide classes resulting from the hydrolysis and uptake of peptides by P . ruminicola differed with time and depended on the strain used . The nature of the enzyme activity and the use of other nitrogen sources may explain the difference between the two strains. J Bacteriol, 1999 Feb, 181(3), 907 - 15 Diversity of radA genes from cultured and uncultured archaea: comparative analysis of putative RadA proteins and their use as a phylogenetic marker; Sandler SJ et al.; Archaea-specific radA primers were used with PCR to amplify fragments of radA genes from 11 cultivated archaeal species and one marine sponge tissue sample that contained essentially an archaeal monoculture . The amino acid sequences encoded by the PCR fragments, three RadA protein sequences previously published (21), and two new complete RadA sequences were aligned with representative bacterial RecA proteins and eucaryal Rad51 and Dmc1 proteins . The alignment supported the existence of four insertions and one deletion in the archaeal and eucaryal sequences relative to the bacterial sequences . The sizes of three of the insertions were found to have taxonomic and phylogenetic significance . Comparative analysis of the RadA sequences, omitting amino acids in the insertions and deletions, shows a cladal distribution of species which mimics to a large extent that obtained by a similar analysis of archaeal 16S rRNA sequences . The PCR technique also was used to amplify fragments of 15 radA genes from uncultured natural sources . Phylogenetic analysis of the amino acid sequences encoded by these fragments reveals several clades with affinity, sometimes only distant, to the putative RadA proteins of several species of Crenarcheota . The two most deeply branching archaeal radA genes found had some amino acid deletion and insertion patterns characteristic of bacterial recA genes . Possible explanations are discussed . Finally, signature codons are presented to distinguish among RecA protein family members. J Food Prot, 1999 Jan, 62(1), 86 - 90 Effect of chemical cleaning agents and commercial sanitizers on ATP bioluminescence measurements; Green TA et al.; Nine chemical cleaning agents at three concentrations were studied to determine the effect on ATP bioluminescence measurements from pure ATP (PATP) and ATP from chicken exudate (CJATP) . The nine commercial cleaning and sanitizing chemicals were concentrated foaming acid (FA), acid sanitizer (AS), iodine cleaner-disinfectant (ZI), alkaline cleaner-degreaser (PC), chlorinated alkaline cleaner (CA), chlorinated sanitizer (CS), quaternary ammonium (QA), antibiofilm agent (AB), and acidic peroxygen sanitizer (HP) . Effect was reported as a percent change from the log10 relative light unit (LRLU) measurements of the control groups . All cleaners and sanitizers were tested at one-tenth of the manufacturer's recommended level (MRL), MRL, and two times MRL . FA, PC, and CA at all three concentrations significantly decreased PATP and CJATP LRLU . AS decreased PATP and CJATP LRLU at 200 and 400 ppm quaternary ammonium . ZI decreased PATP LRLU at MRL or greater, while CJATP LRLU were decreased by all concentrations of ZI tested . CS decreased PATP LRLU in a dose-dependent manner; however, for CJATP, LRLU decreased slightly at the two lower concentrations but were not affected by 1,200 ppm CS . QA at MRL or above for PATP or at all concentrations for CJATP significantly increased LRLU . AB decreased LRLU at all concentrations tested for PATP or at MRL or greater for CJATP . HPA at MRL or greater for PATP or at all concentrations for CJATP significantly reduced LRLU . These results demonstrate that commercial sanitizers and cleansers may squelch or increase LRLU measurements when the chemical comes into direct contact with the ATP bioluminescence reagents . Hence, when using ATP bioluminescence as a means of determining sanitary quality of food-processing equipment, it is essential to consider the type and concentration of chemical cleaner or sanitizer being used on the equipment prior to testing. Vet Pathol, 1999 Jan, 36(1), 1 - 13 An epizootic of lymphoplasmacytic gastritis attributed to Helicobacter pylori infection in cynomolgus monkeys (Macaca fascicularis); Reindel JF et al.; An epizootic of subclinical lymphoplasmacytic gastritis occurred in cynomolgus monkeys maintained at our research facility . Gastric pathology data and histologic sections of 63 adolescent monkeys (2.5-3.5 years old) sacrificed during the epizootic were reviewed . Localized to multifocal reddening of the gastric mucosa was noted grossly in 7 of 44 (16%) monkeys harboring Helicobacter pylori, but not in any of 19 monkeys in which these bacteria were not seen . Gastritis, characterized by accentuation of lymphoplasmacytic infiltrates in antral and to a lesser degree cardiac mucosa, occurred in 42 of 63 (67%) monkeys evaluated and in 42 of 44 (93%) monkeys in which H . pylori was observed microscopically . Two monkeys with H . pylori infection had infiltrate scores that overlapped with the upper limit of scores of H . pylori-negative animals . Coincident with accentuated infiltrates were gastric gland epithelial hyperplasia, reduction in mucin content of surface and gland epithelia, and comparatively minor infiltrates of neutrophils in superficial lamina propria and gastric glands . Antral mucosa thickness often exceeded 1.5 to 2 times normal . Antral mucosal erosions occurred in 7 of 44 (16%) monkeys with H . pylori . Argyrophilic bacteria morphologically consistent with H . pylori were present in antral and less commonly cardiac mucosal glands . Intensity of bacterial colonization correlated with lymphoplasmacytic infiltrates (r = 0.754) and hyperplasia (r = 0.700), although responses were quite variable . These bacteria were not detected in fundic mucosa except in instances where parietal cells were substantially depleted in glands coincident with localized increases in lamina propria inflammatory cell infiltrates . Helicobacter heilmannii-like organisms (HHLOs) were present in fundic glands of all 63 monkeys; colonization was often pronounced . Scores for fundic mucosal inflammation did not correlate with presence or intensity of colonization with HHLOs (r = 0.005) . Rather, fundic inflammation scores positively correlated with the antral inflammation scores (r = 0.548) . Bacteria morphologically, biochemically, and genetically consistent with H . pylori were cultured from gastric mucosal specimens confirming bacterial identification . These findings demonstrate that adolescent cynomolgus monkeys are susceptible to natural infection with H . pylori and develop many morphologic hallmarks of H . pylori-related gastritis in humans. Biochem Biophys Res Commun, 1999 Jan 8, 254(1), 109 - 13 Extended X-ray absorption fine structure evidence for a single metal binding domain in Xenopus laevis nucleotide excision repair protein XPA; Buchko GW et al.; Nucleotide excision repair (NER) is an important cellular mechanism, conserved from bacteria to humans, responsible for eliminating multiple types of structurally distinct DNA lesions from the genome . The protein XPA appears to play a central role in NER, recognizing and/or verifying damaged DNA and recruiting other proteins, including RPA, ERCC1, and TFIIH, to repair the damage . Sequence analysis and genetic evidence suggest that zinc, which is essential for DNA binding, is associated with a C4-type motif, C-X2-C-X17-C-X2-C . Sequence analysis suggests that a second, H2C2-type zinc-binding motif may be present near the C-terminal . Seventy percent of the amino acid sequence of Xenopus laevis XPA (xXPA) is identical to human XPA and both putative zinc-binding motifs are conserved in all known XPA proteins . Electrospray ionization-mass spectroscopy data show that xXPA contains only one zinc atom per molecule . EXAFS spectra collected on full-length xXPA in frozen (77 K) 15% glycerol aqueous solution unequivocally show that the zinc atom is coordinated to four sulfur atoms with an average Zn--S bond length of 2.33 +/- 0.02 A . Together, the EXAFS and mass spectroscopy data indicate that xXPA contains just one C4-type zinc-binding motif . Biochim Biophys Acta, 1998 Dec 8, 1429(1), 1 - 17 Pyroglutamyl peptidase: an overview of the three known enzymatic forms; Cummins PM et al.; Pyroglutamyl peptidase can be classified as an omega peptidase which hydrolytically removes the amino terminal pyroglutamate (pGlu) residue from specific pyroglutamyl substrates . To date, three distinct forms of this enzyme have been identified in mammalian tissues . Type I is typically a cytosolic, cysteine peptidase displaying a broad pyroglutamyl substrate specificity and low molecular mass . Type II has been shown to be a membrane anchored metalloenzyme of high molecular mass with a narrow substrate specificity restricted to the hypothalamic releasing factor, thyrotropin-releasing hormone (TRH, pGlu-His-Pro-NH2) . A third pyroglutamyl peptidase activity has also been observed in mammalian serum which displays biochemical characteristics remarkably similar to those of tissue Type II, namely a high molecular mass, sensitivity to metal chelating agents, and a narrow substrate specificity also restricted to TRH . This serum activity has subsequently been designated 'thyroliberinase' . This review surveys the biochemical, enzymatic, and structural properties of this interesting and unique class of peptidases . It also addresses the putative physiological roles which have been ascribed to these enzymes . Pyroglutamyl peptidase activities isolated and characterized from bacterial sources are also reviewed and compared with their mammalian counterparts. J Parasitol, 1998 Dec, 84(6), 1190 - 5 One fate of epimastigote forms of Trypanosoma cruzi injected in mice . An ultrastructural study; Umekita LF et al.; Recently, we suggested that epimastigote forms of Trypanosoma cruzi are cleared from circulation of mice by a mechanism independent of lysis and that platelets play an important role in this process . These observations prompted us to look at the fate of epimastigotes in the lung, liver, and spleen of mice injected intravenously with these parasite forms . Using transmission electron microscopy, we observed clumps of epimastigotes and platelets in direct contact with phagocytes in the lumen of capillaries . However, the platelets and parasites were probably separated before phagocytosis because only parasites were found inside the phagocytes . Indeed, most of the phagocytes, although containing epimastigotes in different stages of disintegration, contained no platelets . The removal of parasites from platelets was probably mediated by phagocytes through a mechanism similar to the removal of bacteria from the surface of erythrocytes in humans . These observations suggest that the nonvirulence of T . cruzi epimastigotes in mice is not due to lysis but probably to the inability of these parasite forms to escape destruction by the phagocytes. Transfusion, 1999 Jan, 39(1), 63 - 9 Effects of methylene blue-treated plasma on red cells and stored platelet concentrates; Perrotta PL et al.; BACKGROUND: Photochemical methods can effectively inactivate extracellular viruses and bacteria found in blood components . Treatment of plasma with methylene blue (MB), a phenothiazine dye, and visible light inactivates enveloped viruses including HIV-1 . The effects of MB-treated plasma on cellular components stored in vitro have not been well characterized . STUDY DESIGN AND METHODS: MB-treated plasma (83 microg MB/250 mL plasma) was added to single-donor platelets, stored AS-1 red cells (RBCs), irradiated RBCs, and frozen-deglycerolized RBCs . In vitro platelet assays performed after 1 and 5 days of storage in MB-treated plasma included pH, pO2, pCO2, HCO3, platelet number, lactate dehydrogenase, glucose, osmotic recovery, and CD62 expression . RBC components were examined at specific intervals for leakage of potassium, plasma hemoglobin level, and percentage of hemolysis . Direct antiglobulin tests, osmotic fragilities, and RBC antigen stability tests were also performed on RBCs stored in MB-treated plasma . Components stored with autologous plasma or nontreated allogeneic plasma served as controls . RESULTS: Similar storage-induced changes in pH, glucose, and platelet numbers, as well as increases in lactate dehydrogenase, CD62 expression, and lactate were seen in single-donor platelets stored with MB-treated and control plasma . Platelet morphology scores and osmotic recoveries were not altered . Plasma hemoglobin and potassium and percentage of hemolysis increased equally in the various RBC components stored with MB-treated or nontreated plasma . Osmotic fragility and RBC antigen stability were not appreciably altered by MB-treated plasma . CONCLUSION: Plasma treated by MB photoinactivation can be used for in vitro resuspension and storage of platelets or RBCs, because of the lack of influence of MB-treated plasma on a variety of in vitro platelet and RBC assays. J Hematother, 1998 Dec, 7(6), 481 - 91 Ex vivo expansion and differentiation of unselected peripheral blood progenitor cells in serum-free media; Paquette RL et al.; The ability to expand and differentiate unselected PBPC was investigated . Cells were grown in serum-free media containing stem cell factor, GCSF and megakaryocyte growth and development factor (pegylated PEG-rHuMGDF) with or without supplemental serum . Optimal proliferation occurred when PBPC were cultured without prior Ficoll-Paque separation in serum-free media . Cell yields after 17 days of culture were proportional to the percentage of CD34+ cells in the starting population and were 1170+/-302-fold higher than the starting numbers of CD34+ cells . Granulocyte-macrophage colony-forming units increased over 12 days of culture, whereas the numbers of erythroid colony-forming cells peaked between 4 and 7 days . Elimination of PEG-rHuMGDF from cell cultures resulted in significantly lower yields of myeloid and erythroid colony-forming cells and total cell numbers . Cell differentiation into neutrophils was indicated by progressive increases in CD11b, CD15, and CD66b expression . Expanded neutrophils phagocytosed and killed bacteria as efficiently as neutrophils from normal donors . Large-scale expansion studies yielded similar proliferation and differentiation results as parallel small-scale cultures . Therefore, unselected PBPC can be efficiently expanded and differentiated into large numbers of functional mature neutrophils. Bratisl Lek Listy, 1998 Nov, 99(11), 617 - 20 Construction of a quantitative PCR system to determine expression of tumor associated antigen; Buchler T; Cancer immunotherapy is a strategy for cancer treatment by induction of anti tumor responses . The identification of candidate tumor associated antigens (TAA) suggested their potential use as immunogens for vaccination studies . Quantification of a TAA expression by cancerous cells is an important factor in determination of induced immune response efficiency against tumors and thus enables us to devise optimal immunotherapy protocol to cure cancer . The quantitative polymerase chain reaction (PCR) enables us to compare the TAA expression in highly metastatic tumor clones with that in less metastatic ones and in normal cells . It allows us to gain more insight into genome rearrangements that occur in malignant transformation as well as broaden our knowledge about tumor cell gene expression regulation . One of the peptides isolated previously in our lab from a murine lung carcinoma is the mutated Connexin 37 (cx37), a gap-junction protein . Research is underway to determine the expression level of the TAA in various Lewis lung carcinoma cells . This evaluation is achieved by means of quantitative PCR . A quantitative PCR experiment includes preparation of a control template, which is added in known amounts together with the target template in a series of amplification reactions . The control template uses the same primers as the target sequence, yet their PCR products differ in size so as to be distinguishable . Two methods were used to produce this control template . The first one included specific deletion of a sequence of approximately 100 bp that lay between the two primers, insertion of the new template into a plasmid vector, transformation of competent bacteria, detection of transformed bacterial colonies and isolation of the plasmid DNA in a large quantity . The non-mutated, deleted Connexin 37 cDNA was also isolated from bacteria and used for another experiment aimed at producing deleted, mutated Connexin 37 cDNA by means of primer mutagenesis . (Fig . 5, Ref 8.) FEMS Microbiol Lett, 1999 Jan 1, 170(1), 1 - 12 Purification and characterization of a hydroperoxidase from the cyanobacterium Synechocystis PCC 6803: identification of its gene by peptide mass mapping using matrix assisted laser desorption ionization time-of-flight mass spectrometry; Regelsberger G et al.; A cytosolic catalase-peroxidase from the cyanobacterium Synechocystis PCC 6803 was purified to homogeneity by a six-step purification procedure . It is a homodimeric enzyme with a subunit molecular mass of 85 kDa . The isoelectric point of the protein is at pH 5.5; Michaelis constant, turnover number, and catalytic efficiency of the catalase activity for H2O2 were measured to be 4.8 mM, 3450 s-1, and 7.2 x 10(5) M-1 s-1, respectively . Preparation and spectroscopy of the pyridine ferrohemochrome identified an iron protoporphyrin IX as the prosthetic group . The enzyme was shown to exhibit both catalase and peroxidase activities, both of which were inhibited by cyanide, leading to a high-spin to low-spin transition of the heme iron center as detected by a shift of the Soret peak from 405 to 421 nm . The catalase-specific inhibitor 3-amino-1,2,4-triazole proved ineffective . o-Dianisidine, pyrogallol and guaiacol functioned as a peroxidatic substrate, but no reaction was detected with NADH, NADPH, glutathione, and ascorbate . Peptide mass mapping using matrix assisted laser desorption ionization time-of-flight mass spectrometry showed the identity between the purified protein and a putative katG gene derived from the genome of Synechocystis PCC 6803 . A comparison of amino acid sequences of the catalase-peroxidase from Synechocystis PCC 6803 and those from other bacteria showed a high homology around the assumed distal and proximal histidine residues, suggesting a highly conserved histidine as the fifth ligand of the heme iron. Can J Vet Res, 1999 Jan, 63(1), 69 - 78 Pathogenesis of porcine Actinobacillus pleuropneumonia, part II: roles of proinflammatory cytokines; Huang H et al.; The in vitro production of proinflammatory cytokines after stimulation with Actinobacillus pleuropneumoniae and the relation of these cytokines in vivo with the disease caused by A . pleuropneumoniae were investigated . Within 24 h, in vitro stimulation by A . pleuropneumoniae (serotype 1) preparations, including killed bacteria, bacterial culture supernatant, lipopolysaccharide, and bacterial extracts, porcine pulmonary alveolar macrophages (PAM) produced significant (P < 0.05) amounts of tumor necrosis factor-alpha (TNF-alpha) and interleukin-1 (IL-1) as measured by bioassays . The supernatants containing interleukin-8 from PAM after stimulation by bacterial preparations showed significant neutrophil chemotaxis, while bacterial preparations alone did not . After in vivo infection with A . pleuropneumoniae, the mean levels of TNF-alpha and IL-1 in serum, as measured by bioassays, were elevated 37- to 27836-fold for TNF-alpha and 11- to 5941-fold higher for IL-1 within 4 d post-infection, depending on the treatments, and remained elevated up to Day 7 . Both cytokines were also detected in porcine lungs by bioassays and immunocytochemistry . The results indicated that both secreted and surface components of A . pleuropneumoniae can stimulate PAM to produce proinflammatory mediators . Neutrophil chemoattractants rather than bacterial components are the major factor causing acute lung inflammation . The elevation of TNF-alpha and IL-1 in pigs occurred coincident with the onset of acute clinical disease. Arch Biochem Biophys, 1999 Feb 1, 362(1), 12 - 21 Geranoyl-CoA carboxylase: a novel biotin-containing enzyme in plants; Guan X et al.; Geranoyl-CoA carboxylase (EC 6.4.1.4) is a biotin-containing enzyme previously described in two genera of bacteria . Here we report the presence of geranoyl-CoA carboxylase in kingdom Plantae . Geranoyl-CoA carboxylase was purified 180-fold from maize leaves . The enzyme has a biotin-containing subunit of 122 kDa . The pH optimum for activity is 8.3 . The apparent Km values for the substrates geranoyl-CoA, bicarbonate, and ATP are 64 +/- 5 microM, 0 . 58 +/- 0.04 mM, and 8.4 +/- 0.4 microM, respectively . Subcellular fractionations indicate that geranoyl-CoA carboxylase is located in plastids . Geranoyl-CoA carboxylase activity is ubiquitous in organs of monocots and dicots and varies with development . We postulate that geranoyl-CoA carboxylase plays an important role in isoprenoid catabolism in plants, in a pathway analogous to that shown in Psuedomonas sp . In plants, this catabolic pathway would require the interaction of at least three subcellular compartments (plastids, microbodies, and mitochondria) and two biotin-containing enzymes, geranoyl-CoA carboxylase and 3-methylcrotonyl-CoA carboxylase . Nat Genet, 1999 Jan, 21(1), 108 - 10 Genome phylogeny based on gene content; Snel B et al.; Species phylogenies derived from comparisons of single genes are rarely consistent with each other, due to horizontal gene transfer, unrecognized paralogy and highly variable rates of evolution . The advent of completely sequenced genomes allows the construction of a phylogeny that is less sensitive to such inconsistencies and more representative of whole-genomes than are single-gene trees . Here, we present a distance-based phylogeny constructed on the basis of gene content, rather than on sequence identity, of 13 completely sequenced genomes of unicellular species . The similarity between two species is defined as the number of genes that they have in common divided by their total number of genes . In this type of phylogenetic analysis, evolutionary distance can be interpreted in terms of evolutionary events such as the acquisition and loss of genes, whereas the underlying properties (the gene content) can be interpreted in terms of function . As such, it takes a position intermediate to phylogenies based on single genes and phylogenies based on phenotypic characteristics . Although our comprehensive genome phylogeny is independent of phylogenies based on the level of sequence identity of individual genes, it correlates with the standard reference of prokarytic phylogeny based on sequence similarity of 16s rRNA . Thus, shared gene content between genomes is quantitatively determined by phylogeny, rather than by phenotype, and horizontal gene transfer has only a limited role in determining the gene content of genomes. Cancer Gene Ther, 1998 Nov-Dec, 5(6), 401 - 7 Transfer of chimeric receptor gene made of variable regions of tumor-specific antibody confers anticarbohydrate specificity on T cells; Mezzanzanica D et al.; The antitumor specificity of T cells can be induced by gene transfer using a recently developed therapeutic approach (T body) . In this work, we genetically conferred anticarbohydrate specificity onto T cells using the variable regions of monoclonal antibody MLuC1, which binds the Lewis(Y) (LeY) tumor-associated antigen that is overexpressed on several human carcinomas . The variable regions of MLuC1, which are in a single-chain Fv (ScFv) configuration, were cloned and spliced in a eukaryotic expression vector with both the gene encoding the signal-transducing gamma-chain of the human Fcgamma receptor and a flexible hinge domain . The chimeric ScFv-gamma gene was expressed in a murine cytotoxic T-cell hybridoma . Transfectants receiving vector only served as a negative control (mock) . Screening for functional transfectants was carried out using a tumor growth inhibition assay . The soluble form of MLuC1 ScFv was recovered from bacteria periplasm and tested for binding to LeY-expressing cells by the fluorescence-activated cell sorter analysis . Despite the low binding ability of the soluble MLuC1 ScFv, 7 of 13 genetically engineered cytotoxic T lymphocyte clones inhibited the growth of LeY-positive cells and did not affect growth of LeY-negative cells . None of the mock clones tested specifically inhibited tumor growth . These data indicate that, by chimeric MLuC1 ScFv-gamma gene transfer, it is possible to confer anticarbohydrate specificity onto T cells and extend the applicability of the T-body approach to tumor-associated antigens that are naturally not recognized by T cells. Rinsho Byori, 1998 Dec, 46(12), 1258 - 63 {Semi-quantitative detection of Helicobacter pylori using immunohistochemical staining}; Shirahase H et al.; Several methods have been used for the detection of Helicobacter pylori (HP) infection . However, few reports have evaluated the accuracy of each method and compared the level of HP infection . HP infection was evaluated semi-quantitatively using immunohistochemical staining and accuracy of several methods to detect HP infection were compared . Biopsy specimens, obtained from a total 64 patients who underwent endoscopy for evaluation of gastroduodenal diseases, were studied using a rapid urease test, culture method, and immunohistochemical method . The infection was graded according to the number of the individual bacteria seen in a highly magnified visual field, and defined as follows: (0) = 0; (1+) < 10; (2+) = 10-29; (3+) = 30-99, (4+) > 100 . The rapid urease test had a sensitivity of 53%, specificity of 100%, and accuracy of 73% . The culture method had a sensitivity of 75%, specificity of 100%, and accuracy of 86% . Sensitivity of rapid urease test and the culture method decreased in a positive correlation to the decrease in total number of HP bacteria counted . Using the rapid urease test, sensitivity was < 30% when the grade of HP infection was (2+) or less, while 100% sensitivity was obtained only when the grade of HP infection was (4+) . On the other hand, sensitivity of culture method, remained between 80 and 90% when HP infection was (2+) or more . The rapid urease test and culture of HP may result in false negative tests for mild infection although those have high sensitivity and specificity for moderate to severe infection . Immunohistochemical stain provides a reliable semi-quantitative diagnosis of HP infection . Clinicians should be aware of the characteristics of each method to detect HP infection, and select the appropriate ones for their purpose. Khirurgiia (Mosk), 1998, (12), 24 - 7 {Some immunologic aspects in postoperative peritonitis}; Perfil'ev DF; Examination of blood serum and cellular elements of 45 patients with postoperative diffuse purulent peritonitis shows that in the majority of examined persons before and in the first days after the operation immunodepression exists . The dynamics of immunologic disturbances (antibody titers, phagocytosis, immunoglobulines, T- and B-lymphocytes) are sufficiently informative and as a rule, correlate with clinical course of peritonitis . Adequate reaction of the organism to infection resulted in a favourable outcome . Low values of immunologic indices in postoperative period necessitate the use of stimulant therapy in combined treatment of this complication. Zentralbl Hyg Umweltmed, 1998 Dec, 201(4-5), 377 - 86 {Emissions from building products and investigation of their toxicity with the bioluminescence inhibition test}; Mucke W et al.; The investigation of building products in test chambers contains so far only analytical and sensory measurements . In this paper, first experiments for the direct testing of the acute toxicity of building product emissions with the bioluminescence inhibition test are presented . The test specimen was a solvent-free dispersion paste for gluing carpets . Two tests with different air change rates were performed in a 1 m3 stainless steel test chamber . The emissions were concentrated at uniform timesteps in impinger-bottles and measured with the bioluminescence inhibition test . At the same time the concentrations of the emissions in the test chamber were measured both with charcoal adsorbent tubes (carbon disulphide desorption) and with tenax tubes (thermal desorption) . The results of the bioluminescence inhibition test show, that the decrease of the toxicity over a period of 28 days is far lower at a low air change rate than at a higher air change rate . We also found, that from the multitude of the emitted substances the toxicity for the luminescence bacteria was only caused by Ethanol-{2-(2-butoxyethoxy)}-acetate. Infect Immun, 1999 Feb, 67(2), 653 - 8 An in vitro tissue culture bilayer model to examine early events in Mycobacterium tuberculosis infection; Birkness KA et al.; A tissue culture bilayer system that mimics some aspects of early alveolar infection by Mycobacterium tuberculosis was developed . This model incorporates human lung epithelial type II pneumocyte (A549) (upper chamber) and endothelial cell (lower chamber) layers separated by a microporous membrane . This construction makes it possible to observe and quantify the passage of bacteria through the two layers, to observe the interaction of the bacteria with the various cell types, and to examine the basic mechanisms of immune cell recruitment to the site of infection . After 10(7) organisms were added to the upper chamber we microscopically observed large numbers of bacteria attached to and within the pneumocytes and we determined by viable-cell counting that a small percentage of the inoculum (0.02 to 0.43%) passed through the bilayer into the lower chamber . When peripheral blood mononuclear cells were added to the lower chamber, microscopic examination indicated a migration of the mononuclear cells through the bilayer to the apical surface, where they were seen associated with the mycobacteria on the pneumocytes . The added complexity of the bilayer system offers an opportunity to define more precisely the roles of the various lung cell types in the pathogenesis of early tuberculosis. Infect Immun, 1999 Feb, 67(2), 576 - 80 Binding and utilization of human transferrin by Prevotella nigrescens; Duchesne P et al.; To survive and multiply within their hosts, pathogens must possess efficient iron-scavenging mechanisms . In the present study, we investigate the capacity of Prevotella nigrescens and Prevotella intermedia to use various sources of iron for growth and characterize the transferrin-binding activity of P . nigrescens . Iron-saturated human transferrin and lactoferrin, but not ferric chloride and the iron-free form of transferrin, could be used as sources of iron by P . nigrescens and P . intermedia . Neither siderophore activity nor ferric reductase activity could be detected in P . nigrescens and P . intermedia . However, both species showed transferrin-binding activity as well as the capacity to proteolytically cleave transferrin . To various extents, all strains of P . nigrescens and P . intermedia tested demonstrated transferrin-binding activity . The activity was heat and protease sensitive . The capacity of P . nigrescens to bind transferrin was decreased when cells were grown in the presence of hemin . Preincubation of bacterial cells with hemin, hemoglobin, lactoferrin, fibrinogen, immunoglobulin G, or laminin did not affect transferrin-binding activity . The transferrin-binding protein could be extracted from the cell surface of P . nigrescens by treatment with a zwitterionic detergent . Subjecting the cell surface extract to affinity chromatography on an agarose-transferrin column revealed that it contained a protein having an estimated molecular mass of 37 kDa and possessing transferrin-binding activity . The transferrin-binding activity of P . nigrescens and P . intermedia may permit the bacteria to obtain iron for survival and growth in periodontal pockets. Biophys J, 1999 Feb, 76(2), 1034 - 42 The temperature dependence of internal molecular motions in hydrated and dry alpha-amylase: the role of hydration water in the dynamical transition of proteins; Fitter J; Internal molecular motions of proteins are strongly affected by environmental conditions, like temperature and hydration . As known from numerous studies, the dynamical behavior of hydrated proteins on the picosecond time scale is characterized by vibrational motions in the low-temperature regime and by an onset of stochastic large-amplitude fluctuations at a transition temperature of 180-230 K . The present study reports on the temperature dependence of internal molecular motions as measured with incoherent neutron scattering from the globular water-soluble protein alpha-amylase and from a protein-lipid complex of rhodopsin in disk membranes . Samples of alpha-amylase have been measured in a hydrated and dehydrated state . In contrast to the hydrated sample, which exhibits a pronounced dynamical transition near 200 K, the dehydrated alpha-amylase does not show an appreciable proportion of stochastic large-amplitude fluctuations and no dynamical transition in the measured temperature range of 140-300 K . The obtained results, which are compared to the dynamical behavior of protein-lipid complexes, are discussed with respect to the influence of hydration on the dynamical transition and in the framework of the glass transition. J Biol Chem, 1999 Jan 29, 274(5), 2631 - 6 CPG16, a novel protein serine/threonine kinase downstream of cAMP-dependent protein kinase; Silverman MA et al.; Gene expression is necessary for the formation and consolidation of long term memory in both invertebrates and vertebrates . Here, we describe the expression and characterization of candidate plasticity gene 16 (cpg16), a protein serine/threonine kinase that was previously isolated from rat hippocampus as a plasticity-related gene . CPG16, when expressed in and purified from bacteria and COS7 cells, was only capable of autophosphorylation and phosphorylation of myelin basic protein but failed to phosphorylate many other peptides and proteins in in vitro phosphorylation assays . Recombinant CPG16, when overexpressed and purified from COS7 cells, had a relatively low level of autophosphorylation activity . This activity was significantly stimulated when cAMP-elevating agents (forskolin, 8-bromo-cAMP) were added to the cells but not by any other extracellular stimuli tested, e.g . serum, phorbol esters, and a calcium ionophore . Although the stimulation of CPG16 activity was inhibited by the cAMP-dependent protein kinase inhibitor H-89, it did not serve as a direct substrate for this kinase . This suggests that CPG16 may be activated by a cAMP-stimulated protein kinase cascade . Immunolocalization studies in COS7 and NIH-3T3 cells showed mostly cytoplasmic localization of CPG16 that turned partially nuclear upon stimulation with 8-bromo-cAMP . Moreover, overexpression of CPG16 seems to partially inhibit cAMP-stimulated activity of the transcription factor CREB (cAMP response element-binding protein), suggesting its involvement in the down-regulation of cAMP-induced transcription . Thus, CPG16 is a protein serine/threonine kinase that may be involved in a novel signaling pathway downstream of cAMP-dependent protein kinase. Nat Genet, 1999 Jan, 21(1 Suppl), 48 - 50 DNA microarrays in drug discovery and development; Debouck C et al.; DNA microarrays can be used to measure the expression patterns of thousands of genes in parallel, generating clues to gene function that can help to identify appropriate targets for therapeutic intervention . They can also be used to monitor changes in gene expression in response to drug treatments . Here, we discuss the different ways in which microarray analysis is likely to affect drug discovery. Eur J Biochem, 1999 Jan, 259(1-2), 449 - 55 Binding of heptapeptides or unfolded proteins to the chimeric C-terminal domains of 70-kDa heat shock cognate protein; Wu SJ et al.; Seventy-kDa heat shock cognate protein (hsc70) and its homologs in bacteria, yeast and vertebrates are known to form complexes with S-carboxymethyl-alpha-lactalbumin (CMLA), an unfolded protein; and, this activity has been attributed to its C-terminal 30-kDa domain . Herein, we show that hsc70s isolated from the seeds of mung bean and peas, however, are not effective in complexing with CMLA, and that the 30-kDa domain of Arabidopsis hsc70 (At30) cannot form stable complexes with CMLA either . Moreover, chimeric 30-kDa domains, either composed of rat 18-kDa and Arabidopsis 10-kDa subdomains (R18At10) or with Arabidopsis 18-kDa and rat 10-kDa subdomains (At18R10), were prepared and tested for their ability to complex with CMLA or a heptapeptide FYQLALT . At18R10 cannot complex with both CMLA and FYQLALT . On the other hand, R18At10 is capable of forming complexes with FYQLALT at a level similar to that of the rat 30-kDa domain (R30) . R18At10 also forms complexes with CMLA, but the amount of the R18At10/CMLA complexes is much less than that of R30/CMLA . The results imply that the 18-kDa subdomain dictates the binding specificity for heptapeptide, and that the C-terminal 10-kDa subdomain may also provide some selection or restriction for unfolded proteins to form complexes with hsc70. Mol Gen Genet, 1998 Dec, 260(5), 475 - 9 Upregulation of a histone-like protein in dormant Mycobacterium smegmatis; Lee BH et al.; The aerobic saprophyte Mycobacterium smegmatis, like its pathogenic counterpart M . tuberculosis, has the ability to adapt to anaerobiosis by shifting down to a dormant state . Here, we report the identification and molecular genetic characterisation of the first dormancy-induced protein in M . smegmatis . Comparative SDS-polyacrylamide gel electrophoresis of protein extracts of aerobically growing and dormant anaerobic M . smegmatis cultures revealed the upregulation of a 27-kDa protein in the dormant state . Peptide sequencing showed that the induced protein is a homologue of the histone-like protein H1p, predicted by the M . tuberculosis genome project . The corresponding hlp gene was cloned from M . smegmatis and sequenced . Disruption of the hlp gene eliminated the histone-like protein but did not affect the viability of the dormant culture. J Drug Target, 1998, 6(4), 243 - 9 Adjuvants and delivery issues related to immunization: a survey of the recent patent literature; Mrsny RJ; Vaccines have provided generations of individuals with protection against a number of devastating childhood diseases and, in the case of smallpox, have eradicated the disease . Arguably, this preventive approach to health care may have saved more lives than all other therapeutic approaches combined . Being commonly composed of killed-whole or live-attenuated organisms, successful vaccines have been capable of not only presenting crucial epitopes required for protective immunity but also components which stimulate the immune system provide a response of sufficient intensity to provide sustained protection . It is unlikely, however, that these same vaccines would be approved in today's regulatory climate where manufacturers must validate a highly reproducible manufacturing process and demonstrate the exact composition of the final product through stringent quality control (Gupta, 1997) . Therefore, companies involved in the identification of new vaccines and their production appear to be moving away from the ill-defined and poorly-controlled immunogens of the past . Instead, they have started employing recombinant biotechnology to produce large quantities of specific antigens with the hope that these antigens will provide protective immunity . Antigen identification can take years of investigation . This process could be speeded up, however, by understanding the mechanisms which pathogens such as viruses and bacteria use to infect the host, their replication cycle and the steps they frequently take to evade the host immune system . Such a rational approach to immunogen design results in what has been termed an "intelligent" vaccine (Plough, 1998) . "Intelligent" vaccines will likely be completely composed of artificial or synthetically derived products using recombinant and cell culture technologies and hopefully will allow manufacturers to develop products with the desired efficacy and safety profiles required by regulatory authorities . But unlike the complex and ill-defined immunogens of the past, these specific antigens are frequently poorly antigenic by themselves when compared to whole organisms . Co-delivery with a variety of agents, known as adjuvants, has been shown to increase the antigenicity of these poorly antigenic immunogens . In this editorial, I review the recent patent literature as it pertains to targeting of specific antigens and the role played by various classes of adjuvants to enable or enhance such targeted deliveries. Proc Natl Acad Sci U S A, 1999 Jan 19, 96(2), 721 - 5 Purification of serine racemase: biosynthesis of the neuromodulator D-serine; Wolosker H et al.; High levels of D-serine occur in mammalian brain, where it appears to be an endogenous ligand of the glycine site of N-methyl-D-aspartate receptors . In glial cultures of rat cerebral cortex, D-serine is enriched in type II astrocytes and is released upon stimulation with agonists of non-N-methyl-D-aspartate glutamate receptors . The high levels of D-serine in discrete areas of rat brain imply the existence of a biosynthetic pathway . We have purified from rat brain a soluble enzyme that catalyzes the direct racemization of L-serine to D-serine . Purified serine racemase has a molecular mass of 37 kDa and requires pyridoxal 5'-phosphate for its activity . The enzyme is highly selective toward L-serine, failing to racemize any other amino acid tested . Properties such as pH optimum, Km values, and the requirement for pyridoxal phosphate resemble those of bacterial racemases, suggesting that the biosynthetic pathway for D-amino acids is conserved from bacteria to mammalian brain. J Theor Biol, 1999 Jan 7, 196(1), 9 - 17 Prediction of photosynthetic production rate of ethylene using a recombinant cyanobacterium Wang JS, Araki T, Ogawa T, Sakai M, Matsuoka M, Fukuda H. A model of substrate inhibition for enzyme kinetics is applied to photosynthetic production of ethylene by a recombinant cyanobacterium, which exhibits light inhibition behavior . Kinetic parameters of the model were evaluated from a linear plot of the data . Parameter values obtained in this way described well the light-intensity dependence of ethylene production rate . The inhibition model was then extended to predict the production rate at higher cell concentrations, taking account of the light absorption effect by the bacteria . An explicit expression for the production rate was derived and the predicted results agreed with experimental data . An expression is also derived for the optimum light intensity which will result in a maximum production rate . In addition, predicted features of light-intensity dependence of total production conformed to reported results of another photosynthetic product . The approach of the present work may be applicable to a number of other photosynthetic processes . Mol Pathol, 1998 Aug, 51(4), 209 - 14 Simultaneous detection and strain differentiation of Mycobacterium tuberculosis complex in paraffin wax embedded tissues and in stained microscopic preparations; van der Zanden AG et al.; AIMS: To detect and differentiate Mycobacterium tuberculosis simultaneously by polymerase chain reaction (PCR) in clinical samples prepared for histopathological analysis and for microscopic detection of acid fast bacteria . METHODS: Paraffin wax embedded tissue samples and Ziehl-Neelsen (ZN) and auramine stained microscopic preparations from culture positive tuberculosis patients were subjected to DNA extraction and amplification by PCR . PCR was performed with primers specific for direct repeats and the product was detected by hybridisation to a set of 43 different oligonucleotides, a procedure designated as "spoligotyping" . RESULTS: Mycobacterium tuberculosis complex DNA was detected in all of the 23 paraffin wax embedded tissues analysed . Strain differentiation was possible in 20 of the 23 paraffin wax embedded tissues . Mycobacterium tuberculosis complex DNA was also detected and typed in eight of 10 ZN stained microscopic preparations . The hybridisation patterns obtained from virtually all of these samples were identical to those obtained from DNA extracted from cultures . CONCLUSION: Simultaneous detection and strain differentiation of M . tuberculosis complex bacteria is possible in clinical samples prepared by current methods for microscopic and histopathological analysis, without the need to culture . The methodology described opens the way to rapid disclosure of outbreaks in high risk settings, such as hospitals and prisons, where dissemination of tuberculosis might be very fast as a result of a high prevalence of human immunodeficiency virus infected patients. Mol Mar Biol Biotechnol, 1998 Dec, 7(4), 270 - 9 Sensitive detection of Renibacterium salmoninarum in whole fry, blood, and other tissues of pacific salmon by reverse transcription-polymerase chain reaction; Rhodes LD et al.; A sensitive, reproducible assay for detecting Renibacterium salmoninarum in a variety of tissues, including blood, has been developed . This assay, based on reverse transcription-polymerase chain reaction (RT-PCR) of 16S ribosomal RNA, exhibited sensitivity to </=10 cells per milligram of tissue by ethidium bromide detection, and this sensitivity was increased 10-fold by Southern blotting . There was a strong association (p <.001) between blood and ovarian fluid for the presence of bacteria in spawning salmon, and in 17.9% of the infected fish, bacteria were detected in blood but not in ovarian fluid . The ability to analyze multiple tissues, the reproducibility, and sensitivity of 16S RT-PCR make it a useful tool for both research and husbandry applications. Proc Natl Acad Sci U S A, 1999 Jan 19, 96(2), 766 - 71 Involvement of specific calmodulin isoforms in salicylic acid-independent activation of plant disease resistance responses; Heo WD et al.; The Ca2+ signal is essential for the activation of plant defense responses, but downstream components of the signaling pathway are still poorly defined . Here we demonstrate that specific calmodulin (CaM) isoforms are activated by infection or pathogen-derived elicitors and participate in Ca2+-mediated induction of plant disease resistance responses . Soybean CaM (SCaM)-4 and SCaM-5 genes, which encode for divergent CaM isoforms, were induced within 30 min by a fungal elicitor or pathogen, whereas other SCaM genes encoding highly conserved CaM isoforms did not show such response . This pathogen-triggered induction of these genes specifically depended on the increase of intracellular Ca2+ level . Constitutive expression of SCaM-4 and SCaM-5 in transgenic tobacco plants triggered spontaneous induction of lesions and induces an array of systemic acquired resistance (SAR)-associated genes . Surprisingly, these transgenic plants have normal levels of endogenous salicylic acid (SA) . Furthermore, coexpression of nahG gene did not block the induction of SAR-associated genes in these transgenic plants, indicating that SA is not involved in the SAR gene induction mediated by SCaM-4 or SCaM-5 . The transgenic plants exhibit enhanced resistance to a wide spectrum of virulent and avirulent pathogens, including bacteria, fungi, and virus . These results suggest that specific CaM isoforms are components of a SA-independent signal transduction chain leading to disease resistance. Annu Rev Microbiol, 1998, 52, 191 - 230 Something from almost nothing: carbon dioxide fixation in chemoautotrophs; Shively JM et al.; The last decade has seen significant advances in our understanding of the physiology, ecology, and molecular biology of chemoautotrophic bacteria . Many ecosystems are dependent on CO2 fixation by either free-living or symbiotic chemoautotrophs . CO2 fixation in the chemoautotroph occurs via the Calvin-Benson-Bassham cycle . The cycle is characterized by three unique enzymatic activities: ribulose bisphosphate carboxylase/oxygenase, phosphoribulokinase, and sedoheptulose bisphosphatase . Ribulose bisphosphate carboxylase/oxygenase is commonly found in the cytoplasm, but a number of bacteria package much of the enzyme into polyhedral organelles, the carboxysomes . The carboxysome genes are located adjacent to cbb genes, which are often, but not always, clustered in large operons . The availability of carbon and reduced substrates control the expression of cbb genes in concert with the LysR-type transcriptional regulator, CbbR . Additional regulatory proteins may also be involved . All of these, as well as related topics, are discussed in detail in this review. Annu Rev Cell Dev Biol, 1998, 14, 197 - 230 Bioluminescence; Wilson T et al.; Bioluminescence has evolved independently many times; thus the responsible genes are unrelated in bacteria, unicellular algae, coelenterates, beetles, fishes, and others . Chemically, all involve exergonic reactions of molecular oxygen with different substrates (luciferins) and enzymes (luciferases), resulting in photons of visible light (approximately 50 kcal) . In addition to the structure of luciferan, several factors determine the color of the emissions, such as the amino acid sequence of the luciferase (as in beetles, for example) or the presence of accessory proteins, notably GFP, discovered in coelenterates and now used as a reporter of gene expression and a cellular marker . The mechanisms used to control the intensity and kinetics of luminescence, often emitted as flashes, also vary . Bioluminescence is credited with the discovery of how some bacteria, luminous or not, sense their density and regulate specific genes by chemical communication, as in the fascinating example of symbiosis between luminous bacteria and squid. Methods Cell Biol, 1999, 60, 235 - 58 Zebrafish YAC, BAC, and PAC genomic libraries; Amemiya CT et al.; Numerous positional cloning projects directed at isolating genes responsible for the myriads of observed developmental defects in the zebrafish are anticipated in the very near future . In this chapter, we have reviewed the YAC, BAC, and PAC large-insert genomic resources available to the zebrafish community . We have discussed how these resources are screened and used in a positional cloning scheme and have pointed out frequently formidable logistical considerations in the approach . Despite being extremely tedious, positional cloning projects in the zebrafish will be comparatively easier to accomplish than in human and mouse, because of unique biological advantages of the zebrafish system . Moreover, the ease and speed at which genes are identified and cloned should rapidly increase as more mapping reagents and information become available, thereby paving the way for meaningful biological studies. J Biol Chem, 1999 Jan 22, 274(4), 2401 - 7 Molecular cloning of mouse glycolate oxidase . High evolutionary conservation and presence of an iron-responsive element-like sequence in the mRNA; Kohler SA et al.; Iron regulatory proteins (IRPs) control the synthesis of several proteins in iron metabolism by binding to iron-responsive elements (IREs), a hairpin structure in the untranslated region (UTR) of corresponding mRNAs . Binding of IRPs to IREs in the 5' UTR inhibits translation of ferritin heavy and light chain, erythroid aminolevulinic acid synthase, mitochondrial aconitase, and Drosophila succinate dehydrogenase b, whereas IRP binding to IREs in the 3' UTR of transferrin receptor mRNA prolongs mRNA half-life . To identify new targets of IRPs, we devised a method to enrich IRE-containing mRNAs by using recombinant IRP-1 as an affinity matrix . A cDNA library established from enriched mRNA was screened by an RNA-protein band shift assay . This revealed a novel IRE-like sequence in the 3' UTR of a liver-specific mouse mRNA . The newly identified cDNA codes for a protein with high homology to plant glycolate oxidase (GOX) . Recombinant protein expressed in bacteria displayed enzymatic GOX activity . Therefore, this cDNA represents the first vertebrate GOX homologue . The IRE-like sequence in mouse GOX exhibited strong binding to IRPs at room temperature . However, it differs from functional IREs by a mismatch in the middle of its upper stem and did not confer iron-dependent regulation in cells. Biotechnol Annu Rev, 1998, 4, 259 - 84 Archaeon Pyrococcus kodakaraensis KOD1: application and evolution; Fujiwara S et al.; Archaea is the third domain which is phylogenetically differentiated from the other two domains, bacteria and eucarya . Hyperthermophile within the archaea domain has evolved most slowly retaining many ancestral features of higher eukaryotes . Pyrococcus kodakaraensis KOD1, which grows at 95 degrees C optimally, is a newly isolated hyperthermophilc archaeon . The KOD1 strain possesses a circular genome, whose size is estimated to be approximately 2,036 kb . KOD1 enzymes involved in the genetic information processing system, such as DNA polymerase, Rec protein, aspartyl tRNA synthetase and molecular chaperonin, share features of eukaryotic enzymes . Rapid and accurate PCR method by KOD1 DNA polymerase and enzyme stabilization system by KOD1 chaperonin are also introduced in this article. Eur Cytokine Netw, 1998 Dec, 9(4), 633 - 8 Absence of regulation of human polymorphonuclear oxidative burst by interleukin-10, interleukin-4, interleukin-13 and transforming growth factor-beta in whole blood; Reglier-Poupet H et al.; Cytokines such as IL-10, IL-4, IL-13 and TGF-beta play a major role in the regulation of immune responses and are considered as anti-inflammatory agents mainly due to their actions on monocytes . These cytokines are also known to participate in the regulation of PMN activities . However, few and contradictory results have been reported on their direct and priming effects on the PMN oxidative burst, which is essential for killing bacteria . We used a flow cytometry method to study the effects of these cytokines on the PMN oxidative burst; we also used whole blood to avoid PMN activation related to isolation procedures and in order to simulate the in vivo situation more closely . None of the cytokines tested had direct or priming effects on PMN H2O2 production . We also show for the first time that these cytokines do not modulate TNF priming of the PMN oxidative burst in response to N-formyl peptides (fMLP) . These results show that the anti-bacterial activity of PMN, in terms of the PMN respiratory burst, is not down regulated by these anti-inflammatory cytokines in whole blood. Biochim Biophys Acta, 1999 Jan 12, 1416(1-2), 92 - 100 Functional reconstitution of bacterially expressed human potassium channels in proteoliposomes: membrane potential measurements with JC-1 to assay ion channel activity; Chanda B et al.; Structure-function studies on ion channels have been greatly facilitated by the cloning of cDNAs from a variety of sources . However, obtaining detailed structural information on these proteins requires overexpression, purification and reconstitution in a functionally competent form . In this communication, we report on the functional reconstitution of a human potassium channel, Kv1.4, overexpressed in bacteria . We have assessed the activity of these channels using a spectroscopic assay with a potential-sensitive dye, JC-1 . The presence of ion channels renders proteoliposomes selectively permeable to potassium ions as monitored by measurements of transmembrane electrical potential . We have optimised conditions wherein a 12% change in the fluorescence signal of the carbocyanine dye JC-1 per 10 mV change in membrane potential is obtained . Using this assay, we find that the reconstituted protein is potassium selective and its activity is blocked by 4-aminopyridine, a known potassium channel blocker. Curr Biol, 1998 Dec 17-31, 8(25), R925 - 7 DNA segregation: putting chromosomes in their place; Gordon GS et al.; Recent studies provide evidence that bacterial chromosomes are replicated by an enzyme factory, the replisome, located at a fixed position at the center of the cell; the fixed replisome could be a major factor in determining chromosome order in the cell, and may provide the force that drives chromosome segregation. Hum Mutat, 1999, 13(1), 38 - 43 Novel splice site mutation at IVS8 nt 5 of HEXB responsible for a Greek-Cypriot case of Sandhoff disease; Furihata K et al.; Sandhoff disease is caused by abnormalities in HEXB gene encoding the beta-subunit of beta-hexosaminidase . In this study, we analyzed the HEXB gene of a Sandhoff carrier in the Greek-Cypriot community . A G to C transversion was identified in one allele of her HEXB gene at position 5 of the 5'-splice site of intron 8 (IVS8 nt5) . One of 13 cDNA clones derived from her lymphocyte HEXB mRNA lacked the last four nucleotides "GTTG" of exon 8, which created a premature termination codon at 11 codons downstream . In vivo transcription of the mutant HEXB gene fragment in CHO cells resulted in deletion of the "GTTG." The mutation has not been found in 40 DNA samples from anonymous donors, indicating that this is not a polymorphism in the Cypriot population . These results clearly indicate that the splice site mutation at IVS8 nt5 is responsible for this case of Sandhoff disease. Phytochemistry, 1998 Dec, 49(8), 2245 - 53 Biochemical and immunochemical characterization of Brassica juncea glyoxalase I; Deswal R et al.; A homogenous preparation of glyoxalase I (S-lactoylglutathione-lyase, EC 4.4.1.5) was obtained from Brassica juncea seedlings . The enzyme is a heterodimer with 27,000 and 29,000 M(r) subunits and native M(r) of 56,000 . The circular dichroic spectra of the protein showed characteristics of a distinctly helical protein, and magnesium affected the secondary structure . It is a zinc metalloenzyme . Amino acid modification studies suggested the involvement of histidine residues in catalysis . Apo-glyoxalase I was reactivated by divalent cations Mn2+ (0.5 Mm) > Mg2+ (5 Mm) > Zn2+ (0.05 Mm) and Ca2+ (0.01 Mm) . Monospecific, polyclonal anti-glyoxalase I antibodies were raised, which showed its presence in seeds, roots, hypocotyl, cotyledon and different flower parts . They showed varied degree of cross reactivity with the extracts from various plants, yeast, bacteria and animal system. Crit Rev Biotechnol, 1998, 18(4), 257 - 82 Approaches to new vaccines; Mahon BP et al.; The explosive technological advances in the fields of immunology and molecular biology in the last 5 years had an enormous impact on the identification of candidate vaccines against diseases, which until a few years ago seemed uncontrollable . Increased knowledge of the immune system has helped to define the mechanisms that underlie successful immunization and is now being exploited to develop improved versions of existing vaccines and new vaccines against emerging pathogens, tumors, or autoimmune diseases . An understanding of the mechanisms of action of novel adjuvants and the development of new vector and delivery systems will have a major impact on vaccine strategies . The use of DNA encoding antigens from pathogenic viruses, bacteria, and parasites as vaccines is a new approach that is receiving considerable attention . This and other innovative approaches, including vaccine production in plants, are appraised in this review . The successful eradication of smallpox and the imminent eradication of poliomyelitis by worldwide immunization campaigns provide positive examples of how the vaccine-mediated approach can lead to disease elimination; with the advent of new vaccines and improved delivery systems, there is no scientific reason why these successes cannot be repeated. Ultrastruct Pathol, 1998 Sep-Oct, 22(5), 357 - 67 Biology and pathology of the mitochondrion; Lloreta-Trull J et al.; The mitochondrion is a highly efficient organelle that is essential for the function of cells . It is currently accepted that mitochondria originated from primitive nonphotosynthetic bacteria that were engulfed by early eucharyotic cells . Most of the normal and pathologic interactions between mitochondria and the cells that contain them can be viewed as symbiotic processes . The main features of mitochondrial structure and function and some of the pathological disorders that involve this organelle are reviewed. Skin Pharmacol Appl Skin Physiol, 1998, 11(4-5), 214 - 26 In vitro cross-linking of recombinant human involucrin; LaCelle PT et al.; Human involucrin (hINV) is a constituent of the scaffolding of the cornified envelope . In the present study, we describe an in vitro model system to study the role of hINV in scaffold formation . We characterize the in vitro cross-linking of full-length (585 amino acid) recombinant hINV, rhINV(1-585) . When reacted with detergent-solubilized, particulate transglutaminase type 1 (TG1) or partially purified type 2 transglutaminase (TG2), rhINV(1-585) functions as a TG substrate in a calcium-dependent manner . When the reaction is supplemented with 14C-putrescine tracer, the radiolabeled cosubstrate is incorporated into a high-molecular-weight product in a calcium-, rhINV(1-585)- and time-dependent manner . 35S-rhINV(1-585) is also cross-linked to form a high-molecular-weight product . These results suggest that rhINV(1-585) is extensively multimerized . Products having a molecular weight smaller than authentic rhINV(1-585) are also formed, providing evidence for intramolecular cross-link formation . Transmission electron microscopy of cross-linked product reveals immunoreactive large-molecular-weight loop-string-loop and branched structures . Our studies (1) show that rhINV(1-585) is a substrate for both TG1 and TG2, (2) indicate that rhINV(1-585) can be cross-linked to form macromolecular products having distinct structural features, (3) demonstrate that rhINV(1-585) forms intramolecular cross-links when hINV concentration is limiting and (4) establish that hINV possesses reactive Gln and Lys residues. Carcinogenesis, 1998 Dec, 19(12), 2163 - 8 Carcinogenicity and DNA adduct formation observed in ACI rats after long-term treatment with madder root, Rubia tinctorum L; Westendorf J et al.; Madder root, Rubia tinctorum L., is a traditional herbal medicine used against kidney stones . Recently we reported that lucidin, a hydroxyanthraquinone derivative present in this plant, is mutagenic in bacteria and mammalian cells . We also demonstrated the formation of DNA adducts in tissue culture and mice after treatment with this compound . To elucidate the possible carcinogenicity of madder root, three groups of male and female ACI rats received either a normal diet or a diet supplemented with 1 or 10% drug for a total period of 780 days . Weight gain and morbidity were not different among the three groups . Non-neoplastic lesions related to the treatment were evident in the liver and kidneys of both sexes . Moreover, dose-dependent increases in benign and malignant tumour formation were observed in the liver and kidneys of treated animals . 32P-post-labelling analysis showed an increase in the overall level of DNA adducts observed in the liver, kidney and colon of rats treated with 10% madder root in the diet for 2 weeks . HPLC analysis of 32P-labelled DNA adducts revealed a peak co-migrating with an adduct obtained after in vitro treatment of deoxyguanosine-3'-phosphate with lucidin . These observations suggest that the use of madder root for medicinal purposes is associated with a carcinogenic risk. Am J Ind Med, 1999 Jan, 35(1), 58 - 67 Metal working fluid-associated hypersensitivity pneumonitis: an outbreak investigation and case-control study; Fox J et al.; Occupational exposure to bacterial or fungal antigens has been associated with hypersensivity pneumonitis (HP), an immunologically-mediated pulmonary disease . Between August 1995 and April 1996, 34 employees working in machining and assembly areas of an engine manufacturing plant were clinically diagnosed with HP . Of these, 20 employees met an epidemiologic case definition . In a case-control study, no exposure variables, including duration and intensity of metal working fluid (MWF) exposure, were statistically associated with an increased risk of disease . Neither cases nor controls demonstrated precipitin reactivity against unused samples of the seven MWF and two biocides used in the plant . HP cases had a significantly higher prevalence of positive precipitin reactions to used oil soluble and synthetic MWFs . Reactivity to used but not unused MWF suggests a biocontaminant, probably bacteria or fungi, is the causative antigen in the development of HP in this setting. Klin Oczna, 1998, 100(5), 315 - 8 {The evaluation of surface deposits on frequent replacement lenses by scanning electron microscopy (SEM)}; Kaluzny JJ et al.; PURPOSE: The aim of our study was to find the method of preparation of soft contact lenses for examination by SEM and next evaluation of deposits on the surfaces of frequent replacement lenses . MATERIAL AND METHODS: Frequent replacement contact lenses (Acuvue) stored in physiological saline, distilled water and sterile, dry container were prepared for examination by SEM (Novoscan 30) . The best quality preparations were made from contact lenses stored in sterile, dry container and dried at room temperature . Acuvue contact lenses were taken from five young, healthy persons after one, two, three and four weeks of wearing . All the lenses were examined by SEM . RESULTS: We observed nearly all the components of tear film on the surfaces of the lenses . Flat, amorphic protein, crystalline deposits, fibrinous structures were usually observed . Sometimes the nectrotic cell were seen . In one preparation we found bacteria . The amount of deposits was not high and did not increase with four weeks time of lens usage . The quality and quantity of deposits were individually variable . CONCLUSIONS: The methods we choose let us to prepare good quality preparations of soft contact lenses for examination by SEM . On the surfaces of the frequent replacement contact lenses we found only a small quantity of deposits. Kansenshogaku Zasshi, 1998 Nov, 72(11), 1182 - 7 {Experimental study of the relationship between Bordetella pertussis and B . parapertussis infections in suckling mice}; Kawai H; Bordetella parapertussis can occasionally be isolated in the late period of epidemic pertussis and even from the same patient infected with B . pertussis, thereby closely related to B . pertussis . Compared with B . pertussis, it is more frequently isolated from vaccinated individuals as well . Based on the findings, we carried out an experimental study to establish their interrelationship in mice infected with B . parapertussis alone or with both bacteria . The total of 4 groups, each of which constituted ten 10-12 day-day-old mice were in this study . Each 10 mice from mothers which were either unimmunized or immunized with filamentous hemagglutinin-predominant pertussis vaccine were infected with either freshly isolated 1.2 x 10(4) CFU strain 422 of B . parapertussis alone or mixed with 6 x 10(3) CFU strain 18-323 of B . pertussis and 6 x 10(3) CFU strain 422 of B . parapertussis transnasally . We then compared bacterial colonization 1, 2 and 3 weeks after challenge, using the numbers of bacteria in the lungs and peripheral white blood cell count . In the B . parapertussis infection group, B . parapertussis could colonize neither the lungs regardless of pertussis antibodies . In the group infected with a mixture of B . pertussis and B . parapertussis, 10(6) CFU of B . pertussis was primarily found in mice not given the pertussis antibodies, however, 10(5) CFU of B . parapertussis was found in mice given the pertussis antibodies . These results suggest that B . pertussis helps B . parapertussis to colonize in the presence of the pertussis antibodies, thus explaining above the clinical findings. Nippon Rinsho, 1998 Dec, 56(12), 3082 - 6 {Principles of antituberculosis chemotherapy and drug susceptibility tests}; Suzuki K; Principles of antituberculosis chemotherapy and the present situation of the drug susceptibility testing in Japan were reviewed . There are three types of the bacteria in patients with tuberculosis: 1) actively replicating bacteria in cavities, 2) slowly replicating bacteria in caseous necrosis, and 3) fully dormant bacteria . The type 1) bacteria are the most vulnerable to all antituberculosis drugs, particularly INH, while the type 2) bacteria are susceptible to either RFP or PZA alone . In Japan, the drug susceptibility testing have been done by the absolute concentration method using Ogawa egg slants . However, there are many drawbacks pointed out in the system . Therefore, the Japanese society for tuberculosis has recommended a new testing system using the proportion method with the Ogawa medium since 1997. Nippon Rinsho, 1998 Dec, 56(12), 3017 - 22 {Nucleic acid components of mycobacteria: recent studies on secreted protein genes}; Matsuo K; Among the nucleic acid components of mycobacteria, secreted protein genes have been attractive targets in relation to the role in the bacteria-host cell interaction . The alpha antigen gene family is of particular interest from its evolutional constitution process and as a candidate of protective antigen for tuberculosis (TB) . Recent studies on DNA vaccination revealed that the antigen 85A, a member of the alpha antigen family, could induce protective immunity against TB . The other studies on the development of recombinant BCG vaccines demonstrated that alpha antigen gene is applicable to a foreign antigen carrier which could obtain protective immunity against human immunodeficiency virus and malaria parasite infections . In this paper, advanced applications of such mycobacterial secreted protein genes are reviewed. Arch Immunol Ther Exp (Warsz), 1998, 46(6), 341 - 6 Novel protein toxin-based strategy for development of cytotoxic T lymphocyte vaccines; Wiedlocha A; Specific activation of CD8+ cytotoxic T lymphocytes (CTL) is crucial to elicit immunity against intracellular pathogens including viruses, bacteria and protozoa . CTLs recognize mainly intracellularly processed peptides of pathogen origin associated with major histocompatibility complex class I molecules (MHC class I) at the cell surface of infected cells . It implicates the way how to induce specific CTL response and develop an efficient vaccine against intracellular pathogens . Therefore, the general strategy is to mimic the infection by introducing the target antigen into the cytosol of host cells in vivo . Several approaches have been proposed so far, including self replicating vectors, adjuvants and liposomes . However, none of them are ready for practical use . Recently, it has been shown that a number of protein toxins can be used to carry passenger proteins across cellular membranes into the cytosol . This suggested new possibilities for how to deliver a protein antigen into the cytosol for intracellular processing and presentation by MHC class I and to develop CTL vaccines . Here the use of protein toxins as translocation vehicles for delivery of antigen peptides into the cytosol is discussed . Experimental data already obtained demonstrating in vivo elicited immunity by the toxin systems are reviewed and considered. J Bacteriol, 1999 Jan, 181(2), 469 - 76 Transcription of two sigma 70 homologue genes, sigA and sigB, in stationary-phase Mycobacterium tuberculosis; Hu Y et al.; The sigA and sigB genes of Mycobacterium tuberculosis encode two sigma 70-like sigma factors of RNA polymerase . While transcription of the sigA gene is growth rate independent, sigB transcription is increased during entry into stationary phase . The sigA gene transcription is unresponsive to environmental stress but that of sigB is very responsive, more so in stationary-phase growth than in log-phase cultures . These data suggest that SigA is a primary sigma factor which, like sigma70, controls the transcription of the housekeeping type of promoters . In contrast, SigB, although showing some overlap in function with SigA, is more like the alternative sigma factor, sigmaS, which controls the transcription of the gearbox type of promoters . Primer extension analysis identified the RNA start sites for both genes as 129 nucleotides upstream to the GTG start codon of sigA and 27 nucleotides from the ATG start codon of sigB . The -10 promoter of sigA but not that of sigB was similar to the sigma70 promoter . The half-life of the sigA transcript was very long, and this is likely to play an important part in its regulation . In contrast, the half-life of the sigB transcript was short, about 2 min . These results demonstrate that the sigB gene may control the regulons of stationary phase and general stress resistance, while sigA may be involved in the housekeeping regulons. Arch Biochem Biophys, 1999 Jan 15, 361(2), 183 - 94 Closely related form I ribulose bisphosphate carboxylase/oxygenase molecules that possess different CO2/O2 substrate specificities; Horken KM et al.; The deduced primary sequence (cbbL and cbbS) of form I ribulose 1, 5-bisphosphate carboxylase/oxygenase (rubisco) from Bradyrhizobium japonicum places this enzyme within the Type IC subgroup of red-like rubisco enzymes . In addition, B . japonicum appears to organize most of the structural genes of the Calvin-Benson-Bassham (CBB) pathway in at least one major operon . Functional expression and characterization of the B . japonicum and Xanthobacter flavus enzymes from this group revealed that these molecules exhibit diverse kinetic properties despite their relatively high degree of sequence relatedness . Of prime importance was the fact that these closely related enzymes exhibited CO2 and O2 substrate specificities that varied from relatively low values {tau = (VcKo)/(VoKc) = 45} to values that approximated those obtained for higher plants (tau = 75) . These results, combined with the metabolic and genetic versatility of the organisms from which these enzymes were derived, suggest a potential rich resource for future biological selection and structure-function studies aimed at elucidating structural features that govern key enzymological properties of rubisco . Anal Biochem, 1998 Dec 15, 265(2), 260 - 8 Analysis of 3- and 6-linked sialic acids in mixtures of gangliosides using blotting to polyvinylidene difluoride membranes, binding assays, and various mass spectrometry techniques with application to recognition by Helicobacter pylori; Johansson L et al.; A convenient approach to analyze 3- and 6-linked sialic acids in mixtures of biologically active gangliosides was developed . The procedure was adapted to work on small amounts of material and included parallel tests, which allowed direct analysis of structure and activity . The initial step in the procedure was separation of a mixture of gangliosides by thin-layer chromatography (TLC) and blotting to a polyvinylidene difluoride membrane . The gangliosides were then analyzed (a) by direct desorption from the membrane and fast atom bombardment mass spectrometry (FAB MS), (b) by membrane-binding assay using the NeuAcalpha3- and NeuAca