Appl Environ Microbiol, 2004 Nov, 70(11), 6473 - 80 Stages of infection during the tripartite interaction between Xenorhabdus nematophila, its nematode vector, and insect hosts; Sicard M et al.; Bacteria of the genus Xenorhabdus are mutually associated with entomopathogenic nematodes of the genus Steinernema and are pathogenic to a broad spectrum of insects . The nematodes act as vectors, transmitting the bacteria to insect larvae, which die within a few days of infection . We characterized the early stages of bacterial infection in the insects by constructing a constitutive green fluorescent protein (GFP)-labeled Xenorhabdus nematophila strain . We injected the GFP-labeled bacteria into insects and monitored infection . We found that the bacteria had an extracellular life cycle in the hemolymph and rapidly colonized the anterior midgut region in Spodoptera littoralis larvae . Electron microscopy showed that the bacteria occupied the extracellular matrix of connective tissues within the muscle layers of the Spodoptera midgut . We confirmed the existence of such a specific infection site in the natural route of infection by infesting Spodoptera littoralis larvae with nematodes harboring GFP-labeled Xenorhabdus . When the infective juvenile (IJ) nematodes reached the insect gut, the bacterial cells were rapidly released from the intestinal vesicle into the nematode intestine . Xenorhabdus began to escape from the anus of the nematodes when IJs were wedged in the insect intestinal wall toward the insect hemolymph . Following their release into the insect hemocoel, GFP-labeled bacteria were found only in the anterior midgut region and hemolymph of Spodoptera larvae . Comparative infection assays conducted with another insect, Locusta migratoria, also showed early bacterial colonization of connective tissues . This work shows that the extracellular matrix acts as a particular colonization site for X . nematophila within insects. Science, 2004 Nov 5, 306(5698), 1042 - 6 Tracking SNARE complex formation in live endocrine cells; An SJ et al.; Syntaxin, synaptosome-associated protein of 25 kD (SNAP25), and vesicle-associated membrane protein/synaptobrevin are collectively called SNAP receptor (SNARE) proteins, and they catalyze neuronal exocytosis by forming a "core complex." The steps in core complex formation are unknown . Here, we monitored SNARE complex formation in vivo with the use of a fluorescent version of SNAP25 . In PC12 cells, we found evidence for a syntaxin-SNAP25 complex that formed with high affinity, required only the amino-terminal SNARE motif of SNAP25, tolerated a mutation that blocks formation of other syntaxin-SNAP25 complexes, and assembled reversibly when Ca2+ entered cells during depolarization . The complex may represent a precursor to the core complex formed during a Ca2+-dependent priming step of exocytosis. FEBS Lett, 2004 Nov 5, 577(1-2), 170 - 4 Structure of the mitochondrial beta-ketoacyl-{acyl carrier protein} synthase from Arabidopsis and its role in fatty acid synthesis; Olsen JG et al.; Mitochondrial fatty acid synthesis is catalyzed by a dissociated fatty acid synthase similar to those of plant plastids and bacteria . The crystal structure of a mitochondrial beta-ketoacyl-{acyl carrier protein} synthase (mtKAS), namely that from Arabidopsis thaliana, has been determined for the first time . This enzyme accomplishes the vital condensation steps in constructing fatty acid carbon skeletons . The product profile of mtKAS is unusual in that C8 and C(14-16) fatty acyl chains predominate . An enzyme architecture that likely is the basis for the observed bimodal profile of mtKAS products can be derived from the shape of the acyl binding pocket. FEBS Lett, 2004 Nov 5, 577(1-2), 141 - 6 Identification of a novel shrimp protein phosphatase and its association with latency-related ORF427 of white spot syndrome virus; Lu L et al.; To characterize the role of latency-associated ORF427 of white spot syndrome virus (WSSV), a shrimp cDNA library was constructed to screen interacting proteins of ORF427 . Employing the yeast two-hybrid system, a novel shrimp protein phosphatase (named PPs), sharing 93% homology with human protein phosphatase 1, has been identified able to bind ORF427 in yeast . Through co-immunoprecipitation assays, the interaction between PPs and ORF427 was further confirmed both in vitro and in vivo . Interestingly, the novel shrimp protein phosphatase consists of only 199 aa and contains almost all the functional catalytic domains of human protein phosphatase, while it lacks the corresponding C-terminal non-catalytic sequence . Transcription and translation products of the identified cDNA can be detected in both normal and WSSV-infected shrimps; and PPs was found to localize mainly in the lysosome of shrimp cells . To characterize its function, the PPs cDNA was highly expressed in bacteria and the purified protein showed phosphatase activity when tested against pNPP in a standard phosphatase assay . Our results suggest that the identified protein phosphatase, PPs, may represent a novel member of protein phosphatase family and might be involved in the regulation of WSSV's life cycle through interaction with latency-related ORF427 of WSSV. Curr Gastroenterol Rep, 2004 Dec, 6(6), 441 - 6 The spectrum of gastric disease associated with Helicobacter pylori and other infectious gastritides; Guarner J; Helicobacter pylori is the most frequent infection of the stomach worldwide . Some of the people infected with H . pylori develop symptoms of dyspepsia that correlate with pathologic evidence of gastritis and peptic ulcers . In addition, H . pylori has been associated with preneoplastic lesions and with two neoplasias: intestinal-type gastric adenocarcinoma and mucosa-associated lymphoid tissue lymphoma . Rarely, gastric pathology can also be caused by other infectious agents, including fungi, other bacteria, parasites, and viruses . This review describes H . pylori-associated pathology and pathologies related to other infectious agents. Curr Gastroenterol Rep, 2004 Dec, 6(6), 429 - 35 Helicobacter pylori infection and gastric cancer: host, bug, environment, or all three? Menaker RJ, Sharaf AA, Jones NL. Helicobacter pylori is a common bacterial pathogen that colonizes the gastric mucosa of over 50% of the world's population . All infected individuals exhibit chronic gastric inflammation, and approximately 1% of patients develop gastric cancers, including adenocarcinomas and mucosal-associated lymphoid tissue lymphomas . In 1994, the World Health Organization International Agency for Research on Cancer classified H . pylori as a type I, or definite carcinogen . Because the prevalence of gastric cancers among H . pylori-infected patients varies between individuals, countries, and geographic areas, H . pylori disease-related outcomes are believed to be determined by an interplay between host factors, bacterial factors, and their interaction with the environment . This review highlights recent advances in our knowledge on H . pylori disease pathogenesis, focusing on the role of the host, bacteria, and environment in the development of gastric carcinoma. Inflammopharmacology, 2004, 12(3), 247 - 60 Effect of Mycobacterium leprae lipids on BCG- and carrageenan-induced cellular recruitment in mouse pleurisy; Moura AC et al.; Pathogenic mycobacteria survive inside macrophages and deactivate these cells, using a mechanism that is still poorly understood . Mycobacterial cell wall lipids constitute the first contact with the host cell . Although Mycobaterium leprae and M . bovis BCG share common antigens, they induce opposite inflammatory responses . Apolar M . leprae lipids have been shown to be anti-inflammatory by down-regulating macrophage activation and T-cell functions . We wonder if these lipids would influence cellular migration to BCG or to other inflammatory agent . We investigated the effect of M . leprae, its lipids or delipidated bacteria on acute and chronic BCG- or carrageenan-induced pleurisy . Previous injection of intact or delipidated M . leprae did not alter either the BCG- or carrageenan-induced pleural inflammatory reaction . However, M . leprae lipids enhanced carrageenan-induced acute cellular migration without impairing BCG inflow; moreover, they reduced BCG chronic response . Together these data suggest distinct mechanisms for intracellular deactivation and pleural cell recruitment exerted by mycobacterial structures. Biochemistry (Mosc), 2004 Oct, 69(10), 1055 - 66 Apoptosis in unicellular organisms: mechanisms and evolution; Gordeeva AV et al.; Data about the programmed death (apoptosis) in unicellular organisms, from bacteria to ciliates, are discussed . Firstly apoptosis appeared in lower eukaryotes, but its mechanisms in these organisms are different from the classical apoptosis . During evolution, the apoptotic process has been improving gradually, with reactive oxygen species and Ca2+ playing an essential role in triggering apoptosis . All eukaryotic organisms have apoptosis inhibitors, which might be introduced by viruses . In the course of evolution, caspases and apoptosis-inducing factor appeared before other apoptotic proteins, with so-called death receptors being the last among them . The functional analogs of eukaryotic apoptotic proteins take parts in the programmed death of bacteria. Indian J Environ Health, 2003 Oct, 45(4), 275 - 80 Influence of Adyar river in the coastal waters of Chennai (Madras), Bay of Bengal; Subramanian B et al.; The impact of the river Adyar which is influenced by industrial wastes and domestic sewage from the city of Chennai (Madras), on the hydrobiology of coastal water in the Bay of Bengal was evaluated . Reduction in pH, dissolved oxygen (DO), nitrite, nitrate, primary productivity and increase of ammonia, phosphate, silicate, heavy metals, biological oxygen demand (BOD), chlorophyll pigments, particulate organic carbon (POC), respiration, suspended solids, ATP, and bacteria in the mixing site during low tide indicated that the Adyar water was heavily polluted and ultimately affect the quality of coastal water near the vicinity of mixing zone . The effects are diluted or nullified as the distance increased from the mixing site due to heavy mixing and littoral current . During high tide, the flow was completely stopped and little or no effect was recorded . The light, water current and wave action are the important factors which minimize the pollution impacts in the receiving coastal water. J Anim Sci, 1999, 77 Suppl 2, 101 - 10 Inflammation in the bovine female reproductive tract; Bondurant RH; Inflammation of the reproductive tract of a cow occurs when the physical and functional barriers to contamination are breached or specific infection occurs . Commonly, contamination occurs at parturition and to a lesser extent at estrus . Uterine contamination following calving is common, but most healthy cows are able to clear the uterus of bacteria in the first 2 to 3 wk after calving . Persistent infections are more likely to be caused by Actinomyces pyogenes . Specific venereal infections tend to be more host-adapted and produce a lower grade inflammation . Nonspecific bacterial contamination of the endometrium generally induces a neutrophilic influx into the stratum compactum and uterine lumen . Neutrophils phagocytize bacteria with the aid of opsonins in the uterine fluid . Mast cells and eosinophils may also contribute to the inflammatory reaction, which may damage the surface epithelium and release vasoactive substances that allow leakage of serum antibodies into the uterine secretions . Specific antibodies of immunoglobulin (Ig) isotype A, M, G1, and G2 in uterine secretions have been described . In model species, the immune capability of the uterus is influenced by steroid hormones, especially estradiol, which increases secretory component and both IgA and IgG content in uterine secretions and increases the activity of antigen-presenting cells in the uterus . Similar cyclic fluctuations in immune components have been described for cows, including changes in the population of subsurface cytotoxic and helper T cells and changes in the expression of major histocompatibility II antigen on surface cells. Nippon Hoigaku Zasshi, 2004 Sep, 58(2), 130 - 40 {Induction mechanism of shock: applying the etiology in judgment of the cause of death in forensic practice}; Tanaka N; In the field of forensic medicine, shock has been identified as a cause of death owing to various kinds of exogenous insults . The etiology and pathogenesis of shock cannot be explained well by the usual gross appearance in medicolegal autopsies, because it is now generally established that the shock is a functional reaction of the vascular system to bodily injury, and that several organs are secondarily impaired during shock . Thus it seemed to forensic pathologists that these morphological changes in several organs after shock did not reveal any significant differences among the causes of death . We approached to the induction mechanism of shock, and we investigated what etiology induced these morphological changes after shock in order to identify shock as the cause of death . It is now generally accepted that the kidney is a target organ of shock, so we mainly investigated the cause of kidney disorder in a case of burn shock and hemorrhagic shock . 1 . Consequences of bacterial translocation (BT) in the shock . The concept of BT indicates that the beginning of shock is induced by the loss of gut barrier function and consequent translocation of bacteria . In general, impaired gut barrier function can be caused either during the shock period by decreased intestinal blood flow and reduced oxygen delivery, resulting during reperfusion in a stage of increased intestinal blood flow, or at a later stage again by reduced flow . A variety of physiological stresses, such as trauma, hemorrhage, thermal injury, surgical operation, various kinds of drags and mental stress, have been shown to cause failure of the gut mucosal barrier, with translocation of bacteria/endotoxin from the gastrointestinal into the mesenteric lymph nodes, and translocation into remote organs and systemic circulation . 2 . Burn shock . We designed to evaluate the BT in a burn shock rat model (following 20% full-thickness scald injury) . The p38 MAPK pathway is an important stress-responsive signal molecule pathway, and it is responsible for the production and signal transduction of cytokines . This pathway is activated by the bacterial LPS or ischemia, so we examined the effects of FR167653, a specific inhibitor of p38 MAPK, on the development of renal failure after the burn-induced intestinal barrier damage . Our study demonstrated that viable bacteria reached the remote organs after burn by quantitative bacterial culture data and FR167653 blocked the burn-induced intestinal barrier damage, and the immunohistochemical data showed that FR167653 prevented the accumulation of polymorphonuclear leukocytes (PMNs) in the glomerular capillaries after burn, and blockaded the burn-induced renal failure by serum UN assay . FR167653 especially decreased the phosphorylation levels of p38 MAPK in the infant kidney after burn, and TNF-alpha and IL-1beta mRNA decreased through the p38 MAPK pathway . The above-mentioned facts do provide additional support for the hypothesis that postburn renal failure is mediated by endotoxin associated with the bacterial translocation, and we identified the pathophysiologic role of p38 MAPK pathway in the development of renal failure after the burn-induced intestinal barrier damage . 3 . Hemorrhagic shock . We evaluated the role of endogenous TNF-alpha in the renal failure and gut bacterial translocation induced by mild hemorrhagic shock (16.7% bleeding of total body blood via a common carotid catheter without fluid resuscitation) . FR167653, a potent inhibitor of TNF-alpha up regulation through p38 MAPK pathway, significantly inhibited these increases of TNF-alpha . Adding to this, our study demonstrated that FR167653 prevented renal failure, such as the infiltration of inflammatory cells and tubular cell necrosis after hemorrhage, and the intestinal barrier damage was also dramatically improved by FR167653 treatment . These results show that derived endogenous TNF-alpha plays a key role in renal failure through p38 MAPK activation during the early phase of mild hemorrhagic shock, including the possible participation of BT . According to these results, we hypothesized that the invading leukocytes induced these organs failures after hemorrhagic shock, so we examined the appearances of leukocytes by the immunohistochemical myeloperoxidase (MPO) staining (marker staining for PMNs) . The incidences of PMNs in these organs after mild hemorrhagic shock increased significantly, and FR157653 prevented the appearance of PMNs . These results showed the possible effective role of the PMNs on the occurrence of organ failure caused by mild hemorrhagic shock . 4 . Forensic practice . Six hundred and seven forensic autopsy cases in our department of forensic medicine during the past 11 years between 1992 and 2002 were analyzed with regard to the cause of death . Shock cases accounted for 18% of all forensic autopsy cases, and among them 65% of cases identified hemorrhagic shock as the cause of death . So we investigated what good grounds to clearly identify the cause of death induced by hemorrhagic shock . Our experimental hemorrhagic shock data showed PMNs activation and priming during hemorrhagic shock, and it might be closely related to BT and remote organ failure . Consequently, we used the MPO staining method, and we immunohistochemically investigated several organs of our practical autopsy cases to detect the appearance of PMNs as a marker of shock induction . We compared the hemorrhagic shock with other causes of death, such as blood loss, asphyxia, drawing and head injury (intracranial hemorrhage) . In every organ, a significant appearance of PMNs was observed in the hemorrhagic shock compared to the other causes of death . Especially, the appearance of PMNs in the heart was clear than that of the other organs in the hemorrhagic shock cases . Therefore, detecting the appearance of PMNs as a marker of shock induction is a very useful and significant method forjudging the cause of death in forensic practice. AORN J, 2004 Oct, 80(4), 652 - 60, 663-5 From handmaiden to right hand--World War I--the mud and the blood; Holder VL; By the beginning of World War I, modern innovations and advances in the field of medicine were common . Physicians knew about bacteria, how disease spread, and the importance of antisepsis . To prepare for the war, Great Britain developed elite corps of army nurses, fully-equipped military hospitals, and trained personnel who established field hospitals and base hospitals . Alice Fitzgerald, a nurse from Baltimore, was drawn into the conflict when she was asked to serve as the Edith Cavell Memorial Nurse with the British Army. Med Arh, 2004, 58(4), 218 - 9 {Acute polyradiculoneuritis--clinical course and outcome during the war and postwar period}; Loncarevic N et al.; The acute polyradiculoneuritis represent acute inflamatory polyneuropathy with unknown cause, frequently induced by prior virus and sometimes bacteria infection . The purpose of this paper is to establish particularities of the clinical course and results of the disease during the war and the post-war time . Within the retrospective study we performed analysis of all patients suffering from the acute polyradiculoneuritis between January 1992 and December 2003 year who during the mentioned period where treated at the Department of Neurology in Sarajevo . In addition to the anamnysis and the clinical examination, diagnostic criteria where laboratory parameters, EKG, cardiological finding, cerebrospinal liquor (LP) and the EMG finding. Phys Rev E Stat Nonlin Soft Matter Phys . 2004 Sep;70(3 Pt 1):031909 . Epub 2004 Sep 23. Topological generalizations of network motifs; Kashtan N et al.; Biological and technological networks contain patterns, termed network motifs, which occur far more often than in randomized networks . Network motifs were suggested to be elementary building blocks that carry out key functions in the network . It is of interest to understand how network motifs combine to form larger structures . To address this, we present a systematic approach to define "motif generalizations": families of motifs of different sizes that share a common architectural theme . To define motif generalizations, we first define "roles" in a subgraph according to structural equivalence . For example, the feedforward loop triad--a motif in transcription, neuronal, and some electronic networks--has three roles: an input node, an output node, and an internal node . The roles are used to define possible generalizations of the motif . The feedforward loop can have three simple generalizations, based on replicating each of the three roles and their connections . We present algorithms for efficiently detecting motif generalizations . We find that the transcription networks of bacteria and yeast display only one of the three generalizations, the multi-output feedforward generalization . In contrast, the neuronal network of C . elegans mainly displays the multi-input generalization . Forward-logic electronic circuits display a multi-input, multi-output hybrid . Thus, networks which share a common motif can have very different generalizations of that motif . Using mathematical modeling, we describe the information processing functions of the different motif generalizations in transcription, neuronal, and electronic networks. Biodegradation, 2004 Oct, 15(5), 327 - 36 Anaerobic degradability of alcohol ethoxylates and related non-ionic surfactants; Mosche M; The anaerobic degradability of alcohol ethoxylates with various degrees of branching and several related substances was studied . Different inocula were employed in order to increase the probability of obtaining capable bacteria, and the degradation assays were fed with several small doses of the test substances in order to avoid inhibition by too high initial concentrations . Mineralization was quantified by monitoring the biogas production and inorganic carbon concentration in the liquid phase . Almost complete mineralization was achieved in the assays with linear alcohol ethoxylate, poly(ethylene glycol), dodecanol, 2-ethyl-hexanoic acid and 3-methyl-valeric acid . No significant degradation was detected in the assays with highly branched alcohol ethoxylate, 2-butyl-branched alcohol ethoxylate, alcohol alkoxylate, poly(propylene glycol) and iso-tridecanol . A 2-ethyl-branched alcohol ethoxylate was transformed to (2-ethyl-hexyloxy)-acetate, which was not further degraded . Apparently already the first step of anaerobic degradation of alcohol ethoxylates, the ethoxylate chain shortening, is sterically hindered by the alkyl branching . Alkyl branching in alcohol ethoxylates and the inclusion of propylene oxide units in alcohol alkoxylates seem to have a clearly more detrimental effect on anaerobic degradability than on aerobic degradability. Gastroenterol Clin Biol, 2004 Oct, 28(10 Pt 1), 913 - 6 {Tropical sprue: two cases in the Paris area}; Macaigne G et al.; Tropical sprue (TS) is a postinfective tropical malabsorption that occurs in tropical countries . TS is associated with a persisting colonization of the small-intestine lumen by enterotoxinogenic bacteria that cause subsequent enterocyte damage affecting all or part of the small-intestine . We report two cases of TS that occurred in inhabitants of Paris area returned from endemic areas . The first observation concerned a 76-year old woman admitted for anorexia, loss of 20 kg and anemia . The second observation concerned a 53-year old man referred for chronic diarrhea and loss of 40 kg within 4 years . In both cases, duodenal lesions consisted of subtotal and total villous atrophy with prominent infiltration of the damaged surface epithelium with lymphocytes and infiltrate of lymphocytes and plasma cells of the lamina propria . The two patients recovered under antibiotics, confirming the diagnosis of TS. J Biol Chem, 2005 Jan 7, 280(1), 326 - 33 Epub 2004 Nov 02. Identification of the namH Gene, Encoding the Hydroxylase Responsible for the N-Glycolylation of the Mycobacterial Peptidoglycan; Raymond JB et al.; The peptidoglycan of most bacteria consists of a repeating disaccharide unit of beta-1,4-linked N-acetylmuramic acid and N-acetylglucosamine . However, the muramic acid moieties of the mycobacterial peptidoglycan are N-glycolylated, not N-acetylated . This is a rare modification seen only in the peptidoglycan of mycobacteria and five other closely related genera of bacteria . The N-glycolylation of sialic acids is a unique carbohydrate modification that has been studied extensively in eukaryotes . However, the significance of the N-glycolylation of bacterial peptidoglycan is unknown . The goal of this project was to identify the gene encoding the hydroxylase responsible for the N-glycolylation of the mycobacterial peptidoglycan . We developed a novel assay for the mycobacterial UDP-N-acetylmuramic acid hydroxylation reaction and demonstrated that Mycobacterium smegmatis has an enzyme activity that can convert UDP-N-acetylmuramic acid to UDP-N-glycolylmuramic acid . We identified the gene namH encoding the mycobacterial UDP-N-acetylmuramic acid hydroxylase by computer data base searching and motif comparisons with the eukaryotic enzymes responsible for the N-glycolyation of sialic acids . The namH gene is not essential for in vitro growth as we were successful in deleting the gene in M . smegmatis . The M . smegmatis mutant is devoid of UDP-N-acetylmuramic acid hydroxylase activity and synthesizes only N-acetylated muropeptide precursors . Furthermore, the mutant exhibits increased susceptibility to beta-lactam antibiotics and lysozyme . Our studies suggest that the N-glycolylation of mycobacterial peptidoglycan may play a role in lysozyme resistance or may contribute to the structural stability of the cell wall architecture. Trends Genet, 2004 Dec, 20(12), 625 - 30 An expanding genetic code; Cropp TA et al.; More than 30 novel amino acids have been genetically encoded in response to unique triplet and quadruplet codons including fluorescent, photoreactive and redox active amino acids, glycosylated and heavy atom derived amino acids in addition to those with keto, azido and acetylenic chains . In this article, we describe recent advances that make it possible to add new building blocks systematically to the genetic codes of bacteria, yeast and mammalian cells . Taken together these tools will enable the detailed investigation of protein structure and function, which is not possible with conventional mutagenesis . Moreover, by lifting the constraints of the existing 20-amino-acid code, it should be possible to generate proteins and perhaps entire organisms with new or enhanced properties. J Mol Biol, 2004 Nov 19, 344(2), 455 - 69 Conformational states of cytochrome P450cam revealed by trapping of synthetic molecular wires; Hays AM et al.; Members of the ubiquitous cytochrome P450 family catalyze a vast range of biologically significant reactions in mammals, plants, fungi, and bacteria . Some P450s display a remarkable promiscuity in substrate recognition, while others are very specific with respect to substrate binding or regio and stereo-selective catalysis . Recent results have suggested that conformational flexibility in the substrate access channel of many P450s may play an important role in controlling these effects . Here, we report the X-ray crystal structures at 1.8A and 1.5A of cytochrome P450cam complexed with two synthetic molecular wires, D-4-Ad and D-8-Ad, consisting of a dansyl fluorophore linked to an adamantyl substrate analog via an alpha,omega-diaminoalkane chain of varying length . Both wires bind with the adamantyl moiety in similar positions at the camphor-binding site . However, each wire induces a distinct conformational response in the protein that differs from the camphor-bound structure . The changes involve significant movements of the F, G, and I helices, allowing the substrate access channel to adapt to the variable length of the probe . Wire-induced opening of the substrate channel also alters the I helix bulge and Thr252 at the active site with binding of water that has been proposed to assist in peroxy bond cleavage . The structures suggest that the coupling of substrate-induced conformational changes to active-site residues may be different in P450cam and recently described mammalian P450 structures . The wire-induced changes may be representative of the conformational intermediates that must exist transiently during substrate entry and product egress, providing a view of how substrates enter the deeply buried active site . They also support observed examples of conformational plasticity that are believed be responsible for the promiscuity of drug metabolizing P450s . Observation of such large changes in P450cam suggests that substrate channel plasticity is a general property inherent to all P450 structures. J Mol Biol, 2004 Nov 19, 344(2), 395 - 407 RNA tertiary structure and cooperative assembly of a large ribonucleoprotein complex; Recht MI et al.; The mechanisms that govern the ordered assembly of multiprotein ribonucleoprotein complexes are not well understood . The in vitro reconstitution of the small subunit of the bacterial ribosome provides a tractable system for the detailed study of ordered assembly . We present a quantitative thermodynamic description of the hierarchical binding of ribosomal proteins to 16S rRNA during assembly of the platform of the 30S ribosomal subunit . The binding of S8, S11, S15, and the S6:S18 heterodimer to the central domain of 16S rRNA has been measured both individually and in combination using isothermal titration calorimetry and gel mobility shift assays . Both enthalpy and free energy measurements demonstrate the cooperative binding of S15 and the S6:S18 heterodimer, but no cooperativity is observed for either S8 or S11 . The results define a thermodynamic framework that describes cooperative platform assembly. Salud Publica Mex, 2004 Sep-Oct, 46(5), 451 - 63 {The role of epidemiology in mental disorder research}; Borges G et al.; Mental disorders, including substance abuse, are part of the Mexican epidemiologic scenario and will remain so during several decades . They may even become more prominent as causes of disease, disability, and death in our country . It is thus imperative to frame appropriate management strategies to curb these problems without delay . This paper aims at outlining epidemiology of mental diseases as a field of study, and to identify its limitations . Emphasis is made on common elements shared with other more traditional fields of epidemiology, as well as on the specific contributions made by this particular field to epidemiology and to psychiatry in general . This paper describes the main study designs and problems in this field of epidemiology, its usefulness in prevention actions, and future challenges . A unique characteristic of mental disorder epidemiology is that its target diseases manifest in two levels: behaviorally (for example, compulsive hand-washing) and as an element of the individual's mental life (e.g., obsession with bacteria being a constant, omnipresent health threat) . It follows that much of the knowledge currently available on the phenomena of mental disorders in general is based on the self-reported insight of individuals . Trained clinicians have collected such reports by interview or with standardized questionnaires . This field of epidemiology is characterized by having two-sides: a mental disorder is a problem in and of itself, causing suffering and prompting the search for specialized care, as it has peculiar clinical manifestations . On the other hand, mental disorder epidemiology also focuses on determining factors (drug use, abuse, or addiction) and on the way these independent variables result in certain processes and outcomes (such as accidents, homicide, suicide, liver cirrhosis, etc.) . Finally, the epidemiology of mental disorders has also been set apart by its focus in series of processes that are not suitably classified as syndromes, but which are germane to public health, for example, violence . The epidemiology of mental disorders faces great challenges in the new millennium, including a complex, changing epidemiologic scenario . Several important issues will influence the future development of mental disorder epidemiology: measurement of mental disorders and risk factors, more efficient sampling design and methods, the relationships among biological research, genetics, social studies, and epidemiology, and the interface between epidemiology and the evaluation of therapies and health services. Nippon Geka Gakkai Zasshi, 2004 Oct, 105(10), 664 - 8 {Hepatic failure following resection of cholestatic liver}; Arai T et al.; Hepatectomy for biliary cancer with obstructive jaundice is often followed by postoperative septic complications associated with hyperbilirubinemia, both of which could lead to cholestatic liver failure by affecting each other . Such septic complications seem to develop from contamination of bile, reduction of intestinal integrity, or impairment of host resistance to bacteria, each resulting from biliary obstruction . Hyperbilirubinemia after hepatectomy is demonstrated to develop due to hepatic mitochondrial dysfunction or impaired expression of bile efflux pumps on the canalicular membrane of hepatocytes . Since no therapeutic strategy is established for liver failure following hepatectomy, it is important to take all possible measures before surgery to enhance the functions of the liver, intestine, and host immunity and to prevent postoperative septic complications. Indian J Med Res, 2004 Oct, 120(4), 305 - 15 Abdominal tuberculosis; Sharma MP et al.; Tuberculosis can involve any part of the gastrointestinal tract and is the sixth most frequent site of extrapulmonary involvement . Both the incidence and severity of abdominal tuberculosis are expected to increase with increasing incidence of HIV infection . Tuberculosis bacteria reach the gastrointestinal tract via haematogenous spread, ingestion of infected sputum, or direct spread from infected contiguous lymph nodes and fallopian tubes . The gross pathology is characterized by transverse ulcers, fibrosis, thickening and stricturing of the bowel wall, enlarged and matted mesenteric lymph nodes, omental thickening, and peritoneal tubercles . Peritoneal tuberculosis occurs in three forms : wet type with ascitis, dry type with adhesions, and fibrotic type with omental thickening and loculated ascites . The most common site of involvement of the gastrointestinal tuberculosis is the ileocaecal region . Ileocaecal and small bowel tuberculosis presents with a palpable mass in the right lower quadrant and/or complications of obstruction, perforation or malabsorption especially in the presence of stricture . Rare clinical presentations include dysphagia, odynophagia and a mid oesophageal ulcer due to oesophageal tuberculosis, dyspepsia and gastric outlet obstruction due to gastroduodenal tuberculosis, lower abdominal pain and haematochezia due to colonic tuberculosis, and annular rectal stricture and multiple perianal fistulae due to rectal and anal involvement . Chest X-rays show evidence of concomitant pulmonary lesions in less than 25 per cent of cases . Useful modalities for investigating a suspected case include small bowel barium meal, barium enema, ultrasonography, computed tomographic scan and colonoscopy . Ascitic fluid examination reveals straw coloured fluid with high protein, serum ascitis albumin gradient less than 1.1 g/dl, predominantly lymphocytic cells, and adenosine deaminase levels above 36 U/l . Laparoscopy is a very useful investigation in doubtful cases . Management is with conventional antitubercular therapy for at least 6 months . The recommended surgical procedures today are conservative and a period of preoperative drug therapy is controversial. Nucleic Acids Res, 2004 Nov 01, 32(19), 5841 - 50 Print 2004. Alleviation of restriction by DNA condensation and non-specific DNA binding ligands; Keatch SA et al.; During conditions of cell stress, the type I restriction and modification enzymes of bacteria show reduced, but not zero, levels of restriction of unmethylated foreign DNA . In such conditions, chemically identical unmethylated recognition sequences also occur on the chromosome of the host but restriction alleviation prevents the enzymes from destroying the host DNA . How is this distinction between chemically identical DNA molecules achieved? For some, but not all, type I restriction enzymes, alleviation is partially due to proteolytic degradation of a subunit of the enzyme . We identify that the additional alleviation factor is attributable to the structural difference between foreign DNA entering the cell as a random coil and host DNA, which exists in a condensed nucleoid structure coated with many non-specific ligands . The type I restriction enzyme is able to destroy the 'naked' DNA using a complex reaction linked to DNA translocation, but this essential translocation process is inhibited by DNA condensation and the presence of non-specific ligands bound along the DNA. Proc Natl Acad Sci U S A, 2004 Nov 9, 101(45), 16040 - 5 Epub 2004 Nov 01. Different functions of HetR, a master regulator of heterocyst differentiation in Anabaena sp . PCC 7120, can be separated by mutation; Khudyakov IY et al.; The HetR protein has long been recognized as a key player in the regulation of heterocyst development . HetR is known to possess autoproteolytic and DNA-binding activities . During a search for mutants of Anabaena sp . PCC 7120 that can overcome heterocyst suppression caused by overexpression of the patS gene, which encodes a negative regulator of differentiation, a bypass mutant strain, S2-45, was isolated that produced a defective pattern (Pat phenotype) of irregularly spaced single and multiple contiguous heterocysts (Mch phenotype) in combined nitrogen-free medium . Analysis of the S2-45 mutant revealed a R223W mutation in HetR, and reconstruction in the wild-type background showed that this mutation was responsible for the Mch phenotype and resistance not only to overexpressed patS, but also to overexpressed hetN, another negative regulator of differentiation . Ectopic overexpression of the hetRR223W allele in the hetRR223W background resulted in a conditionally lethal (complete differentiation) phenotype . Analysis of the heterocyst pattern in the hetRR223W mutant revealed that heterocysts differentiate essentially randomly along filaments, indicating that this mutation results in an active protein that is insensitive to the major signals governing heterocyst pattern formation . These data provide genetic evidence that, apart from being an essential activator of differentiation, HetR plays a central role in the signaling pathway that controls the heterocyst pattern. Hepatol Res, 2004 Oct, 30(2), 57 - 62 Transmission of hepatitis C virus quasispecies between human adults; Saito T et al.; To elucidate how hepatitis C virus (HCV) with multiple variants (quasispecies) is transmitted and adapts to the host during infection, we compared nucleotide and deduced amino acid sequences from hypervariable region1 (HVR1) of the E2 gene of HCV between a donor and a recipient who developed hepatitis after a needlestick accident . Thirty clones from each subject were sequenced after PCR amplification, cloning, and purification of plasmid DNA from single colonies of transformed bacteria . Genetic analysis revealed that the recipient's viral sequences were much less diverse than the donor's . We found a single predominant HCV HVR1 clone of the recipient in 22/30 isolates with the same amino acid sequence, and mimic clones in 8/30 isolates with only one amino acid substitution . These were all absent in the donor, who had 21 highly diverse sequences . Phylogenetic analysis of virus E1/E2 gene sequences showed that the recipient's unique sequences were related to the population of variants from the donor, in whom one isolate had 96% similarity to the recipient's predominant amino acid sequence . These results suggest that a minor subset of the donor's HCV variants is selectively transmitted to the recipient, and that the selection determines the predominant variant in the new host. J Am Soc Mass Spectrom, 2004 Nov, 15(11), 1665 - 74 Strategies and data analysis techniques for lipid and phospholipid chemistry elucidation by intact cell MALDI-FTMS; Jones JJ et al.; Ions attributed to lipids and phospholipids are directly observed by desorption from whole bacteria using intact cell (IC) matrix-assisted laser desorption-ionization (MALDI) Fourier transform mass spectrometry (FTMS) . Saccharomyces cerevisiae are grown in rich media broth, concentrated, and applied directly to the MALDI surface without lysis or chemical treatment . FTMS of MALDI ions gives excellent signal to noise ratios with typical resolving powers of 90,000 and mass precision better than 0.002 Da . Use of accurate mass measurements and a simple set of rules allow assignment of major peaks into one of twelve expected lipid classes . Subsequently, fractional mass versus whole number mass plots are employed to enhance visual interpretation of the high-resolution data and to facilitate detection of related ions such as those representing homologous series or different degrees of unsaturation . This approach, coupled with rules based on bacterial biochemistry, is used to classify ions with m/z up to about 1000 . Major spectral peaks in the range m/z 200-1000 are assigned as lipids and phospholipids . In this study, it is assumed that biologically-derived ions with m/z values lower than 1000 are lipids . This is not unreasonable in view of the facts that molecular weights of lipids are almost always less than 1000 Da, that the copy numbers for lipids in a cell are higher than those for any single protein or other component, and that lipids are generally collections of distinct homologous partners, unlike proteins or other cell components . This paper presents a new rapid lipid-profiling method based on IC MALDI-FTMS. Biochemistry, 2004 Nov 9, 43(44), 13981 - 95 Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor; Copley SD et al.; The thioredoxin fold is found in proteins that serve a wide variety of functions . Among these are peroxiredoxins, which catalyze the reduction of hydrogen peroxide and alkyl peroxides . Although the common structural fold shared by thioredoxins and peroxiredoxins suggests the possibility that they have evolved from a common progenitor, it has been difficult to examine this hypothesis in depth because pairwise sequence identities between proteins in these two superfamilies are statistically insignificant . Using the Shotgun program, we have found that sequences of reductases involved in maturation of cytochromes in certain bacteria bridge the sequences of thioredoxins and peroxiredoxins . Analysis of motifs found in a divergent set of thioredoxins, cytochrome maturation proteins, and peroxiredoxins provides further support for an evolutionary relationship between these proteins . Within the conserved motifs are specific residues that are characteristic of individual protein classes, and therefore are likely to be involved in the specific functions of those classes . We have used this information, in combination with existing structural and functional information, to gain new insight into the structure-function relationships in these proteins and to construct a model for the emergence of peroxiredoxins from a thioredoxin-like ancestor. Biochemistry, 2004 Nov 9, 43(44), 13963 - 71 Biochemical and biophysical characterization of serotonin 5-HT2C receptor homodimers on the plasma membrane of living cells; Herrick-Davis K et al.; While many studies have provided evidence of homodimerization and heterodimerization of G-protein-coupled receptors (GPCRs), few studies have used fluorescence resonance energy transfer (FRET) combined with confocal microscopy to visualize receptor dimerization on the plasma membrane, and there have been no reports demonstrating the expression of serotonin receptor dimers/oligomers on the plasma membrane of living cells . In the study presented here, biochemical and biophysical techniques were used to determine if 5-HT(2C) receptors exist as homodimers on the plasma membrane of living cells . Immunoprecipitation followed by Western blotting revealed the presence of immunoreactive bands the predicted size of 5-HT(2C) receptor monomers and homodimers that were detergent and cross-linker sensitive . Bioluminescence resonance energy transfer (BRET) was assessed in HEK293 cells expressing 5-HT(2C) receptors labeled with Renilla luciferase and yellow fluorescent protein . BRET levels were not altered by pretreatment with serotonin . Confocal microscopy provided direct visualization of FRET on the plasma membrane of live cells expressing 5-HT(2C) receptors labeled with cyan (donor) and yellow (acceptor) fluorescent proteins . FRET, assessed by acceptor photobleaching, was dependent on the donor/acceptor ratio and independent of acceptor expression levels, indicating that FRET resulted from receptor clustering and not from overexpression of randomly distributed receptors, providing evidence for GPCR dimers/oligomers in a clustered distribution on the plasma membrane . The results of this study suggest that 5-HT(2C) receptors exist as constitutive homodimers on the plasma membrane of living cells . In addition, a confocal-based FRET method for monitoring receptor dimerization directly on the plasma membrane of living cells is described. Pol Merkuriusz Lek, 2004 May, 16(95), 430 - 3 {Formation of the selected biochemical markers in the patients with atherosclerotic arterial obliteration and the coexistent infection with Chlamydia psittaci}; Niedziela P et al.; In the arterial wall which is atheromatously changed both basic EB and reticular RB bodies of Chlamydia bacteria may be present . The role of these micro-organisms in the pathogenesis of arteriosclerosis is not thoroughly recognized yet . It is unknown whether Chlamydia initiate or lead to the inflammation of the already existent disease process . That is why it is expedient to carry out the research determining the correlation between the presence of Chlamydia bacteria in the operated arteries and the formation of the selected biochemical indicators . During the operation the imprint specimen was taken from the arterial wall, which was subsequently painted using stamp's method . EB bodies were marked in the immunofluorescence test with the usage of specific antibodies . The concentration of C-reactive protein was marked with the help of the rocket immunoelectrophoresis . The examination of blood lipids and fibrinogens was conducted with the usage of a colorimetric method with the help of ready-made kits . On the basis of the obtained data two groups of patients were distinguished . The first group comprised 16 patients (26%); here elementary EB bodies were detected both in the imprint specimens and the blood serum . In all the patients assigned to the first group the presence of anti-Chlamydia antibodies in the blood serum was observed . The second group consisted of the remaining 47 patients (74%); here no currently lasting Chlamydia infection was stated . On the basis of the conducted research and statistic calculations it is justified to point the correlation between the concentration of C-reactive protein and HDL cholesterol in the group of patients with the detected Chlamydia bacteria in comparison to the group of patients with no infection . However no statistically significant relationship between the concentration of fibrinogen, total cholesterol, LDL cholesterol and triglycerides was observed in the relation to the analyzed groups. Nat Rev Immunol, 2004 Nov, 4(11), 841 - 55 Regulatory T cells: friend or foe in immunity to infection? Mills KH. Homeostasis in the immune system depends on a balance between the responses that control infection and tumour growth and the reciprocal responses that prevent inflammation and autoimmune diseases . It is now recognized that regulatory T cells have a crucial role in suppressing immune responses to self-antigens and in preventing autoimmune diseases . Evidence is also emerging that regulatory T cells control immune responses to bacteria, viruses, parasites and fungi . This article explores the possibility that regulatory T cells can be both beneficial to the host, through limiting the immunopathology associated with anti-pathogen immune responses, and beneficial to the pathogen, through subversion of the protective immune responses of the host. Am J Trop Med Hyg, 2004 Oct, 71(4), 393 - 9 Effect of blocking the CXCL9/10-CXCR3 chemokine system in the outcome of endothelial-target rickettsial infections; Valbuena G et al.; Rickettsiae cause systemic infections such as Rocky Mountain spotted fever and boutonneuse fever . The main cellular target of these obligately intracellular bacteria is the endothelium . T lymphocytes are the most important effectors of immunity, and the CXCR3 ligands CXCL9 and CXCL10 may play an important role in the T cell-mediated clearance of rickettsiae from the infected vasculature as suggested by recent expression studies . Here we showed that antibody-mediated neutralization of CXCL9 and CXCL10, and CXCR3 gene knockout, had no effect on survival or bacterial loads of mice infected with rickettsiae . We also demonstrated that rickettsiae triggered the endothelial expression of intercellular adhesion molecule 1 and vascular cell adhesion molecule 1 in vivo . These findings suggested that antigenic presentation by endothelial cells together with an endothelial inflammatory phenotype induced by the rickettsial infection may be sufficient to arrest T cells and trigger their anti-rickettsial effector mechanisms without the need for chemokines. Huan Jing Ke Xue, 2004 Jul, 25(4), 109 - 12 {Photocatalytic functional ceramic and its speciality of photodecomposition}; Liu P et al.; Photocatalytic ceramic was prepared by coating photocatalytic membrane on ceramic matrix . The photocatalytic behavior of the TiO2 coated ceramic for degradation of oleic acid, ethylene, SO2, NOx and sterilization was studied by using XRD, chromatogram, in-situ IR and spectrophotometer . The results showed that the photocatalytic ceramic prepared by special conditions have the function of environmental conservation such as the photodegradating organic contaminants, removing inorganic baleful gas and killing bacteria . Degradation ratio of ethylene, oleic acid, SO2 and NOx reached 95%-100% respectively for the photocatalytic functional ceramic. Lin Chuang Er Bi Yan Hou Ke Za Zhi, 2002 Oct, 16(10), 550 - 2 {The influence of medicine to the expression of cell adhesion molecule in experimental otitis media with effusion}; Wang S et al.; OBJECTIVE: To study the influence of Cefaclor and Prednisonum to the expression of cell adhesion molecule in experimental otitis media with effusion (OME) . METHOD: SD rats models of OME were made using formalin killed nontypeable Hemophilus influenzae and the expression of adhesion molecules Mac-1 and L-Selectin was analysed by flow cytometry using white blood cell obtained by cardiac puncture in control, bacterial and medicine groups . The pathology of middle ear mucosa was investigated to understand the relationship between the expression of adhesion molecules and the pathology . RESULT: It was found that the expression of adhesion molecules Mac-1 and L-Selection in bacteria group increased obviously with pathological change of the middle ear mucosa . Cefaclor and Prednisonum could decrease the expression of adhesion molecules and inhibited the leukocyte accumulation in the middle ear cavity though there was no significant differences except for the L-Selectin in the Cefaclor group between the bacteria group and the medicine group . CONCLUSION: Dead bacteria in the middle ear may act as an antigen to induce the inflammatory response and effusion of the middle ear . The expression of adhesion molecules Mac-1 and L-Selectin is highly related to the inflammatory response . Cefaclor and Prednisonum may improve otitis media with effusion, which may related to the decreasing expression of Mac-1 and L-Selectin. J Periodontol, 2004 Sep, 75(9), 1209 - 15 Relative proportions of T-cell subpopulations and cytokines that mediate and regulate the adaptive immune response in patients with aggressive periodontitis; Suarez LJ et al.; BACKGROUND: Both the virulence factors of periodontopathic bacteria and the immune response against them have been involved in tissue destruction observed in periodontal disease . Considering the regulatory role of cytokines produced by T cells, the purpose of this study was to compare the CD3+, CD4+, and CD8+ subpopulations of T cells, and to characterize the mRNA of cytokines involved in the adaptive immune response in a group of healthy/gingivitis 1 (HI/G1) individuals and aggressive periodontitis (AgP) patients . METHODS: The percentages of T-cell subpopulations were analyzed in 10 gingival samples of HI/G1 individuals and 10 gingival samples of AgP patients by immunohistochemistry . The presence of interleukin (IL)-2, interferon (IFN)-gamma, IL-4, IL-5, IL-10, IL- 13, and transforming growth factor (TGF)-beta was measured by reverse transcription polymerase chain reaction (RT-PCR) of mRNA extracted from complete gingival biopsies . RESULTS: Significant differences were found in CD3+ and CD4+ cell counts between both groups . The parameters were lower in the gingival biopsies from AgP patients while CD8+ counts were similar in both groups . The cytokine mRNA analysis showed constant expression of IL-2 and IFN-gamma in all cases . The mRNA of IL-5 and IL-10 was present in the majority of HI/G1 (N = 10, N = 9, respectively) but was not in the AgP group (N = 2, N = 1) . IL-13 and TGF-beta were only detected in HI/G1 (N = 2, N = 3) and IL-4 was not detected in any of the individuals . CONCLUSIONS: These results indicate that the role of the CD8+ subpopulation in aggressive periodontitis lesions is limited . On the other hand, cytokines IL-2 and IFN-gamma may not be relevant in the progression of aggressive periodontitis. Int J Toxicol, 2004, 23(5), 335 - 44 Contamination is a frequent confounding factor in toxicology studies with anthraquinone and related compounds; Butterworth BE et al.; Anthraquinone (AQ) (9,10-anthracenedione) is an important compound in commerce . Many structurally related AQ derivatives are medicinal natural plant products . Examples include 1-hydroxyanthraquinone (1-OH-AQ) and 2-hydroxyanthraquinone (2-OH-AQ), which are also metabolites of AQ . Some commercial AQ is produced by the oxidation of anthracene (AQ-OX) . In the recent past, the anthracene used was distilled from coal tar and different lots of derived AQ often contained polycyclic aromatic hydrocarbon contaminants, particularly 9-nitroanthracene (9-NA) . Many toxicology studies on AQ used contaminated anthracene-derived AQ-OX, including a National Toxicology Program (NTP) 2-year cancer bioassay that reported a weak to modest increase in tumors in the kidney and bladder of male and female F344/N rats and in the livers of male and female B6C3F1 mice . The AQ-OX used in that bioassay was mutagenic and contained 9-NA and other contaminants . In contrast, purified AQ is not genotoxic . The purpose of this paper is to provide additional information to help iterpret the NTP cancer bioassay . This paper describes a quantitative analytical study of the NTP anthracene-derived AQ-OX test material, and presents the results of mutagenicity studies with the 1-OH-AQ and 2-OH-AQ metabolites and the primary contaminant 9-NA . Purified 1-OH-AQ and 2-OH-AQ exhibited only weak mutagenic activity in selected strains of tester bacteria and required S9 . Literature reports of potent mutagenic activity for 1-OH-AQ and 2-OH-AQ in bacteria minus S9 are, once again, very likely the result of the presence of contaminants in the test samples . Weak activity and limited production of the 1-OH-AQ and 2-OH-AQ metabolites are possible reasons that AQ fails to exhibit activity in numerous genotoxicity assays . 9-NA was mutagenic in tester strains TA98 and TA100 minus S9 . This pattern of activity is consistent with that seen with the contaminated AQ-OX used in the NTP bioassay . Analysis of all the mutagenicity and analytical data, however, indicates that the mutagenic contamination in the NTP bioassay probably resides with compounds in addition to 9-NA . 9-NA exhibited potent mutagenic activity in the L5178Y mammalian cell mutagenicity assay in the presence of S9 . The positive response was primarily associated with an increase in small colony mutants suggesting a predominance of a clastogenic mechanism . Quantitative mutagenicity and carcinogenicity potency estimates indicate that it is plausible that the contaminants alone in the NTP AQ-OX bioassay could have been responsible for all of the observed carcinogenic activity . Although AQ-OX is no longer commercially used in the United States, many of the reported genotoxicity and carcinogenicity results in the literature for AQ and AQ derivative compounds must be viewed with caution. Semin Ophthalmol, 2002 Mar, 17(1), 11 - 7 Infectious optic neuropathy; Golnik KC; A wide variety of infectious agents are known to cause optic neuropathy . This article will consider the bacteria, spirochetes, fungi, and viruses that most commonly affect the optic nerve . Clinical presentation is variable, but some pathogens often produce a characteristic funduscopic pattern . Diagnosis is usually made on the basis of clinical suspicion and serologic testing . Polymerase chain reaction is also increasingly utilized . Most infectious agents can be effectively treated but visual recovery is highly variable. Biochim Biophys Acta, 2004 Nov 4, 1659(1), 19 - 31 Molecular interference of Cd(2+) with Photosystem II; Sigfridsson KG et al.; Many heavy metals inhibit electron transfer reactions in Photosystem II (PSII) . Cd(2+) is known to exchange, with high affinity in a slow reaction, for the Ca(2+) cofactor in the Ca/Mn cluster that constitutes the oxygen-evolving center . This results in inhibition of photosynthetic oxygen evolution . There are also indications that Cd(2+) binds to other sites in PSII, potentially to proton channels in analogy to heavy metal binding in photosynthetic reaction centers from purple bacteria . In search for the effects of Cd(2+)-binding to those sites, we have studied how Cd(2+) affects electron transfer reactions in PSII after short incubation times and in sites, which interact with Cd(2+) with low affinity . Overall electron transfer and partial electron transfer were studied by a combination of EPR spectroscopy of individual redox components, flash-induced variable fluorescence and steady state oxygen evolution measurements . Several effects of Cd(2+) were observed: (i) the amplitude of the flash-induced variable fluorescence was lost indicating that electron transfer from Y(Z) to P(680)(+) was inhibited; (ii) Q(A)(-) to Q(B) electron transfer was slowed down; (iii) the S(2) state multiline EPR signal was not observable; (iv) steady state oxygen evolution was inhibited in both a high-affinity and a low-affinity site; (v) the spectral shape of the EPR signal from Q(A)(-)Fe(2+) was modified but its amplitude was not sensitive to the presence of Cd(2+) . In addition, the presence of both Ca(2+) and DCMU abolished Cd(2+)-induced effects partially and in different sites . The number of sites for Cd(2+) binding and the possible nature of these sites are discussed. BMC Infect Dis . 2004 Oct 29;4(1):45. Gastro-enteritis outbreak among Nordic patients with psoriasis in a health centre in Gran Canaria, Spain: a cohort study; Eriksen HM et al.; BACKGROUND: Between November 2 and 10, 2002 several patients with psoriasis and personnel staying in the health centre in Gran Canaria, Spain fell ill with diarrhoea, vomiting or both . Patient original came from Norway, Sweden and Finland . The patient group was scheduled to stay until 8 November . A new group of patients were due to arrive from 7 November . METHODS: A retrospective cohort study was conducted to assess the extent of the outbreak, to identify the source and mode of transmission and to prevent similar problems in the following group . RESULTS: Altogether 41% (48/116) of persons staying at the centre fell ill . Norovirus infection was suspected based on clinical presentations and the fact that no bacteria were identified . Kaplan criteria were met . Five persons in this outbreak were hospitalised and the mean duration of diarrhoea was 3 days . The consequences of the illness were more severe compared to many other norovirus outbreaks, possibly because many of the cases suffered from chronic diseases and were treated with drugs reported to affect the immunity (methotrexate or steroids).During the two first days of the outbreak, the attack rate was higher in residents who had consumed dried fruit (adjusted RR = 3.1; 95% CI: 1.4-7.1) and strawberry jam (adjusted RR = 1.9; 95% CI: 0.9-4.1) than those who did not . In the following days, no association was found . The investigation suggests two modes of transmission: a common source for those who fell ill during the two first days of the outbreak and thereafter mainly person to person transmission . This is supported by a lower risk associated with the two food items at the end of the outbreak . CONCLUSIONS: We believe that the food items were contaminated by foodhandlers who reported sick before the outbreak started . Control measures were successfully implemented; food buffets were banned, strict hygiene measures were implemented and sick personnel stayed at home >48 hours after last symptoms. APMIS, 2004 Jun, 112(6), 336 - 41 Identification of Bartonella species in rodents, shrews and cats in Denmark: detection of two B . henselae variants, one in cats and the other in the long-tailed field mouse; Engbaek K et al.; Small mammals and stray cats were trapped in two areas of North Zealand, Denmark, and their blood cultured for hemotrophic bacteria . Bacterial isolates were recovered in pure culture and subjected to 16S rDNA gene sequencing . Bartonella species were isolated from five mammalian species: B . grahamii from Microtus agrestis (field vole) and Apodemus flavicollis (yellow-necked field mouse); B . taylorii from M . agrestis, A . flavicollis and A . sylvaticus (long-tailed field mouse); B . tribocorum from A . flavicollis; B . vinsonii subsp . vinsonii from M . agrestis and A . sylvaticus; and B . birtlesii from Sorex vulgaris (common shrew) . In addition, two variant types of B . henselae were identified: variant I was recovered from three specimens of A . sylvaticus, and B . henselae variant II from 11 cats; in each case this was the only B . henselae variant found . No Bartonella species was isolated from Clethrionomys glareolus (bank vole) or Micromys minutus (harvest mouse) . These results suggest that B . henselae occurs in two animal reservoirs in this region, one of variant I in A . sylvaticus, which may be transmitted between mice by the tick Ixodes ricinus, and another of variant II in cats, which may be transmitted by the cat flea (Ctenocephalides felis) . To our knowledge, this is the first report of the occurrence of B . henselae and B . tribocorum in Apodemus mice. PLoS Biol . 2004 Nov;2(11):e367 . Epub 2004 Nov. Tuberculous granuloma formation is enhanced by a mycobacterium virulence determinant; Volkman HE et al.; Granulomas are organized host immune structures composed of tightly interposed macrophages and other cells that form in response to a variety of persistent stimuli, both infectious and noninfectious . The tuberculous granuloma is essential for host containment of mycobacterial infection, although it does not always eradicate it . Therefore, it is considered a host-beneficial, if incompletely efficacious, immune response . The Mycobacterium RD1 locus encodes a specialized secretion system that promotes mycobacterial virulence by an unknown mechanism . Using transparent zebrafish embryos to monitor the infection process in real time, we found that RD1-deficient bacteria fail to elicit efficient granuloma formation despite their ability to grow inside of infected macrophages . We showed that macrophages infected with virulent mycobacteria produce an RD1-dependent signal that directs macrophages to aggregate into granulomas . This Mycobacterium-induced macrophage aggregation in turn is tightly linked to intercellular bacterial dissemination and increased bacterial numbers . Thus, mycobacteria co-opt host granulomas for their virulence. J Biol Chem, 2005 Jan 14, 280(2), 1327 - 35 Epub 2004 Oct 26. Extended Neck Regions Stabilize Tetramers of the Receptors DC-SIGN and DC-SIGNR; Feinberg H et al.; The human cell surface receptors DC-SIGN (dendritic cell-specific intercellular adhesion molecule-grabbing nonintegrin) and DC-SIGNR (DC-SIGN-related) bind to oligosaccharide ligands found on human tissues as well as on pathogens including viruses, bacteria, and parasites . The extracellular portion of each receptor contains a membrane-distal carbohydrate-recognition domain (CRD) and forms tetramers stabilized by an extended neck region consisting of 23 amino acid repeats . Cross-linking analysis of full-length receptors expressed in fibroblasts confirms the tetrameric state of the intact receptors . Hydrodynamic studies on truncated receptors demonstrate that the portion of the neck of each protein adjacent to the CRD is sufficient to mediate the formation of dimers, whereas regions near the N terminus are needed to stabilize the tetramers . Some of the intervening repeats are missing from polymorphic forms of DC-SIGNR . Two different crystal forms of truncated DC-SIGNR comprising two neck repeats and the CRD reveal that the CRDs are flexibly linked to the neck, which contains alpha-helical segments interspersed with non-helical regions . Differential scanning calorimetry measurements indicate that the neck and CRDs are independently folded domains . Based on the crystal structures and hydrodynamic data, models for the full extracellular domains of the receptors have been generated . The observed flexibility of the CRDs in the tetramer, combined with previous data on the specificity of these receptors, suggests an important role for oligomerization in the recognition of endogenous glycans, in particular those present on the surfaces of enveloped viruses recognized by these proteins. Nihon Hansenbyo Gakkai Zasshi, 2004 Sep, 73(3), 253 - 61 {Functional changes of macrophages in Hansen's disease}; Fukutomi Y; As an obligate intracellular pathogen, the principal host cells for Mycobacterium leprae are mononuclear phagocytes or macrophages . The macrophage is a primitive cell type being found in both early and advanced life forms, and possesses a variety of functions, such as phagocytosis of invaded bacteria, production of cytokines, antigen presentation and tumor killing . Hansen's disease is a chronic infectious disease characterized by specific host immune responses against M . leprae . In this article the macrophage is focused to dissect its functions in the disease. Methods Mol Biol, 2004, 292, 387 - 400 Construction of a Gene Inactivation Library for Bovine herpesvirus 1 Using Infectious Clone Technology; Mahony TJ et al.; The application of infectious clone technology to herpesvirus biology has revolutionized the study of these viruses . Previously the ability to manipulate these large DNA viruses was limited to methods dependent on homologous recombination in mammalian cells . However, the construction of herpesvirus infectious clones using bacterial artificial chromosome vectors has permitted the application of powerful bacterial genetics for the manipulation of these viruses . A method is described for the construction and characterization of a gene inactivation library of Bovine herpesvirus 1 using an infectious clone . The method utilizes transposon-mediated gene inactivation, which permits gene inactivation without any prior knowledge of the viral genomic sequence . Furthermore, as the genetic manipulation is performed in bacteria the inactivation of those viral genes that are essential for viral replication is also possible . The method described here can be readily applied to any herpesvirus clone and provides the tools for precise characterization of all the genes contained within a herpesvirus genome. JAMA, 2004 Oct 27, 292(16), 1955 - 60 Risk of community-acquired pneumonia and use of gastric acid-suppressive drugs; Laheij RJ et al.; CONTEXT: Reduction of gastric acid secretion by acid-suppressive therapy allows pathogen colonization from the upper gastrointestinal tract . The bacteria and viruses in the contaminated stomach have been identified as species from the oral cavity . OBJECTIVE: To examine the association between the use of acid-suppressive drugs and occurrence of community-acquired pneumonia . DESIGN, SETTING, AND PARTICIPANTS: Incident acid-suppressive drug users with at least 1 year of valid database history were identified from the Integrated Primary Care Information database between January 1, 1995, and December 31, 2002 . Incidence rates for pneumonia were calculated for unexposed and exposed individuals . To reduce confounding by indication, a case-control analysis was conducted nested in a cohort of incident users of acid-suppressive drugs . Cases were all individuals with incident pneumonia during or after stopping use of acid-suppressive drugs . Up to 10 controls were matched to each case for practice, year of birth, sex, and index date . Conditional logistic regression was used to compare the risk of community-acquired pneumonia between use of proton pump inhibitors (PPIs) and H2-receptor antagonists . MAIN OUTCOME MEASURE: Community-acquired pneumonia defined as certain (proven by radiography or sputum culture) or probable (clinical symptoms consistent with pneumonia) . RESULTS: The study population comprised 364,683 individuals who developed 5551 first occurrences of pneumonia during follow-up . The incidence rates of pneumonia in non-acid-suppressive drug users and acid-suppressive drug users were 0.6 and 2.45 per 100 person-years, respectively . The adjusted relative risk for pneumonia among persons currently using PPIs compared with those who stopped using PPIs was 1.89 (95% confidence interval, 1.36-2.62) . Current users of H2-receptor antagonists had a 1.63-fold increased risk of pneumonia (95% confidence interval, 1.07-2.48) compared with those who stopped use . For current PPI users, a significant positive dose-response relationship was observed . For H2-receptor antagonist users, the variation in dose was restricted . CONCLUSION: Current use of gastric acid-suppressive therapy was associated with an increased risk of community-acquired pneumonia. Biochem Soc Trans, 2004 Dec, 32(Pt 6), 904 - 9 Structure and chemistry of the Sir2 family of NAD+-dependent histone/protein deactylases; Marmorstein R; The yeast Sir2 (silent information regulator-2) protein functions as an NAD(+)-dependent histone deacetylase to silence gene expression from the mating-type locus, tolomeres and rDNA and also promotes longevity and genome stability in response to calorie restriction . Homologues of yeast Sir2 have been identified in the three domains of bacteria, archaea and eukaryotes; in mammalian cells, Sir2 proteins also deacetylate non-histone proteins such as the p53 tumour suppressor protein, alpha-tubulin and forkhead transcription factors to mediate diverse biological processes including metabolism, cell motility and cancer . We have determined the X-ray crystal structure of a Sir2 homologue from yeast Hst2 (yHst2), in various liganded forms, including the yHst2/acetyl-Lys-16 histone H4/NAD(+) ternary complex; we have also performed related biochemical studies to address the conserved mode of catalysis by these enzymes as well as the distinguishing features that allow different members of the family to target their respective cognate substrates . These studies have implications for the structure-based design of Sir2-specific small molecule compounds, which might modulate Sir2 function for therapeutic application. Ying Yong Sheng Tai Xue Bao, 2004 Jul, 15(7), 1276 - 80 {Significance of senescence study on tree roots and its advances}; Wu C et al.; Root system is one of the important components of trees, and has some important physiological functions such as nutrient and water absorption, transport and storage, anchoring, and supporting . After tree root systems formed, roots often suffer from nutrient- and water-deficient stress, and thus, their absorption of nutrients and water appears more important . Soil nutrient and water have a great spatiotemporal heterogeneity . As the heterogeneity occurs, trees regulate carbon partitioning to roots, resulting in the senescence or death of some roots of the whole root system . In forestry, the senescence of tree roots is closely related to tree productivity, because there is a close relationship between the senescence of tree roots and the absorption of soil nutrient and water . At ecosystem and global scale, the senescence of tree roots influences the cycling of carbon and nutrients, because roots exhaust a great deal of carbon fixed by source leaves through photosynthesis, and there are great amounts of nutrients in tree roots . The senescence of tree roots is influenced by many environmental factors, biotic (e.g., fungi, bacteria, viruses, small edaphic animals) and abiotic (e.g., water, temperature, soil nutrients, heavy metals) . These factors affect the senescence of tree roots by different mechanisms . Although we have much knowledge on the senescence of tree roots and some hypotheses have been proposed, some problems still remain to be resolved, and further experiments are needed to test these hypotheses . Interdisciplinary studies integrating cytology, biochemistry, soil science, and genetics are the prerequisite for rapid advances in understanding the essence of tree root senescence. Med Hypotheses, 2004, 63(6), 925 - 32 Infant mouthing behavior: the immunocalibration hypothesis; Fessler DM et al.; Avid mouthing, the propensity of infants to suck objects and put them in their mouths, is a pattern characteristic of the first 2-3 years of life, with its most intensive manifestation occurring during the first year . Although traditional accounts explain infant mouthing as a source of sensual gratification and/or environmental exploration, these proximate hypotheses are inconsistent with the high costs of mouthing, including choking, poisoning, and exposure to pathogens . We propose that mouthing serves to proactively expose the naive gastrointestinal tract to environmental antigens and commensal bacteria while under the sheltering umbrella of breastfeeding . Mouthing functions to accurately calibrate the developing immune system, including antibody production and mucosal immunity, to the local disease ecology . The critical exposure period is not open-ended, as failure to expose the gut to an adequate number of antigens early in life is associated with an increased risk of allergies, asthma, and atopy . Weaning initiates a number of immune changes that may program the neonatal immune system into certain life-long responses. Biochemistry, 2004 Nov 2, 43(43), 13867 - 74 Micromechanical analysis of the binding of DNA-bending proteins HMGB1, NHP6A, and HU reveals their ability to form highly stable DNA-protein complexes; Skoko D et al.; The mechanical response generated by binding of the nonspecific DNA-bending proteins HMGB1, NHP6A, and HU to single tethered 48.5 kb lambda-DNA molecules is investigated using DNA micromanipulation . As protein concentration is increased, the force needed to extend the DNA molecule increases, due to its compaction by protein-generated bending . Most significantly, we find that for each of HMGB1, NHP6A, and HU there is a well-defined protein concentration, not far above the binding threshold, above which the proteins do not spontaneously dissociate . In this regime, the amount of protein bound to the DNA, as assayed by the degree to which the DNA is compacted, is unperturbed either by replacing the surrounding protein solution with protein-free buffer or by straightening of the molecule by applied force . Thus, the stability of the protein-DNA complexes formed is dependent on the protein concentration during the binding . HU is distinguished by a switch to a DNA-stiffening function at the protein concentration where the formation of highly stable complexes occurs . Finally, introduction of competitor DNA fragments into the surrounding solution disassembles the stable DNA complexes with HMGB1, NHP6A, and HU within seconds . Since spontaneous dissociation of protein does not occur on a time scale of hours, we conclude that this rapid protein exchange in the presence of competitor DNA must occur only via "direct" DNA-DNA contact . We therefore observe that protein transport along DNA by direct transfers occurs even for proteins such as NHP6A and HU that have only one DNA-binding domain. Proc R Soc Lond B Biol Sci, 2004 Aug 7, 271 Suppl 5, S277 - 80 Direct evidence for predation on trilobites in the Cambrian; Zhu MY et al.; A fossil arthropod similar to Fuxianhuia and displaying an exceptionally well-preserved alimentary canal with in situ gut contents is reported from the lower Middle Cambrian (ca . 510 Myr ago) of South China . Three-dimensionally preserved, paired phosphatic nodules, arranged in series along both sides of the gut and containing spherical bacteria, probably represent serial digestive glands . The gut is filled with fragments of the eodiscoid trilobite, Pagetia . The well-developed digestive glands and the fragmentary trilobite remains suggest (i) that the arthropod was a durophagous, possibly selective predator, and (ii) that small trilobites such as eodiscoids were a major food source in Cambrian marine ecosystems . This fossil association augments the small number of previously described associations providing more or less direct evidence of predator-prey relationships in Cambrian epibenthic communities. Refuat Hapeh Vehashinayim, 2004 Jul, 21(3), 67 - 74, 95 {Smoking--a proven risk factor for periodontal disease?}; Klinger A; While bacterial dental plaque is widely considered as the etiological risk factor for the development of periodontal diseases, numerous publications from recent years pointed out the role of environmental factors like smoking as aggravating the severity of disease expression . The present paper reviews the updated literature linking epidemiologically between the presence of smoking habit and disease prevalence in the same population, as well as studies reporting on cell toxicity of nicotine and its by-products on gingival cells, negative effect on humoral and cell-mediated immune system, enhancement of bacterial plaque pathogeneity, and disruption of the wound healing processes . Finally, a negative effect is apparent on the supportive stage of the periodontal treatment, indicating lasting effect of smoking for years to come following the termination of active periodontal treatment. Zhongguo Zhong Yao Za Zhi, 2004 Jul, 29(7), 663 - 6 {Experimental study on anti-pyretic effect of gegen qin lian decoction and its compounds}; Yu LZ et al.; OBJECTIVE: To investigate composition principles of Gegen Qin Lian decoction through anti-pyretic experiment . METHOD: Pharmacological effects of different compounds of Gegen Qin Lian decoction according to six hours temperature response index (TRI6) and average top temperature response height (deltaT) after the decoction was given to feverish animal model by inactived bacteria suspension . RESULT: As for reducing six hour temperature response index, Scutellaria baicalensis root was the main effective drug . Pueraria lobata root could enforce the effect while Coptis chinensis rhizome and Glycyrrhiza uralensis root counteracted it . As for reducing average top temperature response height, the Effects of four herbal drugs were the same as for TRI6 . CONCLUSION: Of the compounds of Gegen Qin Lian decoction, as to the pharmcological anti-pyretic effects, the best one is the compound of Scutellaria baicalensis and Pueraria lobata roots. Zhongguo Zhong Yao Za Zhi, 2004 Jul, 29(7), 624 - 7 {Development of effervescent tablet of Chinese traditional medicine and its technology study}; Tian XF et al.; Effervescent tablets which contain an effervescent mixture of a suitable organic acid and an alkali metal bicarbonate and/or carbonate can give out carbon dioxide when they meet water . The effervescent tablets for oral solution can be dissolved in cool water about 17-20 degrees C, therefore it is convenient to carry and use . It also has a good taste for patient with deodorizing agent added . The foam produced by external effervescent tablets is usually helpful in killing the local bacteria . The review displayed the main supplementary material, preparative technique and the study development of effervescent tablets of Chinese traditional medicine . Effervescent tablets that have been used to clinic were enumerated. J Nanosci Nanotechnol, 2004 May, 4(5), 532 - 8 Initial salivary pellicle formation on solid substrates studied by AFM; Hannig M et al.; Organic layers of salivary biopolymers adsorbed on soft and hard oral tissues, referred to also as salivary pellicle, play a critical role with respect to all surface phenomena taking place in the oral cavity . The initial stages of pellicle formation are of great interest since they determine the ensuing processes of salivary biopolymer adsorption and subsequent adherence of bacteria . In spite of the important physiological role of the pellicle in protecting the enamel surface against short-term acidic attacks, the composition and ultrastructure of the pellicle layer are not yet understood and resolved in detail . The present study utilized atomic force microscopy (AFM), for the first time, to elucidate the morphogenesis and ultrastructural pattern of initial salivary pellicle formation taking place in situ on solid substrates of mica, silicon wafer and graphite . Using tapping mode AFM, salivary pellicles were found in all intraorally exposed specimens and revealed a globular surface morphology of the adsorbed protein layer . The average diameter and height of the adsorbed salivary proteins were determined to be 15 +/- 3 nm and 2.0 +/- 0.5 nm, respectively . It was also found that the surface energy of the substrates affects the rate of pellicle formation, while the overall size of the adsorbed salivary proteins appears to be identical on all studied substrates. Mol Genet Genomics, 2004 Nov, 272(4), 460 - 9 Epub 2004 Nov. Mismatch repair ensures fidelity of replication and recombination in the radioresistant organism Deinococcus radiodurans; Mennecier S et al.; We have characterized the mismatch repair system (MMR) of the highly radiation-resistant type strain of Deinococcus radiodurans, ATCC 13939 . We show that the MMR system is functional in this organism, where it participates in ensuring the fidelity of DNA replication and recombination . The system relies on the activity of two key proteins, MutS1 and MutL, which constitute a conserved core involved in mismatch recognition . Inactivation of MutS1 or MutL resulted in a seven-fold increase in the frequency of spontaneous RifR mutagenesis and a ten-fold increase in the efficiency of integration of a donor point-mutation marker during bacterial transformation . Inactivation of the mismatch repair-associated UvrD helicase increased the level of spontaneous mutagenesis, but had no effect on marker integration--suggesting that binding of MutS1 and MutL proteins to a mismatched heteroduplex suffices to inhibit recombination between non identical (homeologous) DNAs . In contrast, inactivation of MutS2, encoded by the second mutS -related gene present in D . radiodurans, had no effect on mutagenesis or recombination . Cells devoid of MutS1 or MutL proteins were as resistant to gamma-rays, mitomycin C and UV-irradiation as wild-type bacteria, suggesting that the mismatch repair system is not essential for the reconstitution of a functional genome after DNA damage. Pediatr Infect Dis J, 2004 Oct, 23(10 Suppl), S173 - 8 Natural rotavirus infection is not associated to intussusception in Mexican children; Velazquez FR et al.; AIMS: To determine whether natural rotavirus infection or infection by another enteropathogen is associated to intussusception (IS); and to describe the seasonality of IS compared with severe diarrhea (SD) and rotavirus SD in Mexican children . METHODS: A prospective, observational, multicenter and case-control study was conducted in Mexico City from December 1999 to February 2001 . Cases were children younger than 1 year old hospitalized for IS; diagnosis was made by clinical features, radiologic and/or surgery findings . Controls were children younger than 1 year old hospitalized for another disease than a gastrointestinal illness (NGI) . Cases and controls were paired by age and date of admission (+/-3 months; for both), in a 1:2 ratio . A surveillance of IS cases, SD and rotavirus SD episodes was conducted during the study period . Stool samples collected soon after IS resolution or at admission were tested for rotavirus, adenovirus, astrovirus, bacteria and parasites . RESULTS: Thirty cases of IS and 60 controls with NGI were studied . Rotavirus was not detected in any case of IS . Adenovirus (17%) was the only enteropathogen detected in IS . Rotavirus (8%), adenovirus (2%), astrovirus (2%) and bacteria (2%) were detected in NGI . Rotavirus infection was not associated with IS (odds ratio, 0; 95% confidence interval, 0-2.9), whereas adenovirus infection was strongly associated as risk factor for IS (odds ratio undefined; P = 0.003), compared with NGI . Seasonal variation in admissions for IS was small, whereas admissions for SD and rotavirus SD showed a marked seasonal increase during fall-winter . CONCLUSIONS: In Mexican children, rotavirus infection was not associated to IS; whereas a significant association was observed between adenovirus and IS . Also there was no increase in IS cases during the sharply defined fall-winter rotavirus outbreak . Observations from this controlled study suggest that natural rotavirus infection is not a risk factor for IS . This information may have implications for development of a safer and effective rotavirus vaccine. Acta Crystallogr D Biol Crystallogr, 2004 Nov, 60(Pt 11), 2003 - 5 Epub 2004 Oct 20. Crystallization and preliminary X-ray crystallographic analysis of chorismate synthase from Mycobacterium tuberculosis; Dias MV et al.; The enzymes of the shikimate pathway are potential targets for the development of new therapies because they are essential for bacteria but absent from mammals . The last step in this pathway is performed by chorismate synthase (CS), which catalyzes the conversion of 5-enolpyruvylshikimate-3-phosphate to chorismate . Optimization of crystallization trials allowed the crystallization of homogeneous recombinant CS from Mycobacterium tuberculosis (MtCS) . The crystals of MtCS belong to space group P6(4)22 (or P6(2)22) and diffract to 2.8 A resolution, with unit-cell parameters a = b = 129.7, c = 156.8 A . There are two molecules in the asymmetric unit . Molecular-replacement trials were not successful . Heavy-atom derivative screening is in progress. Methods Mol Biol, 2004, 291, 337 - 50 An immunoassay for measuring repair of ultraviolet photoproducts; McCready S; A method is described that makes use of a polyclonal antiserum to measure repair of the principal photoproducts induced in DNA by short-wave ultraviolet light (UVC)-pyrimidine-pyrimidone 6-4 photoproducts ({6-4}PPs) and cyclobutane pyrimidine dimers (CPDs) . DNA extracted from irradiated cells is applied to a nitrocellulose dot blot and quantitated using an enzyme-conjugated secondary antibody and a color assay . Although the polyclonal antiserum contains antibodies to both {6-4}PPs and CPDs, repair of these can be measured separately by differential destruction or repair of one or other photoproduct . The method is useful for measuring repair in total genomic DNA and is sufficiently sensitive to measure repair of damage induced by doses of 10 J/m2 of UVC and less . The method is very versatile and has been used to measure repair in human cells, yeasts, plants, archaea, bacteria, and filamentous fungi. Nucleic Acids Res, 2004 Oct 22, 32(19), 5703 - 11 Print 2004. Unidirectional translocation from recognition site and a necessary interaction with DNA end for cleavage by Type III restriction enzyme; Raghavendra NK et al.; Type III restriction enzymes have been demonstrated to require two unmethylated asymmetric recognition sites oriented head-to-head to elicit double-strand break 25-27 bp downstream of one of the two sites . The proposed DNA cleavage mechanism involves ATP-dependent DNA translocation . The sequence context of the recognition site was suggested to influence the site of DNA cleavage by the enzyme . In this investigation, we demonstrate that the cleavage site of the R.EcoP15I restriction enzyme does not depend on the sequence context of the recognition site . Strikingly, this study demonstrates that the enzyme can cleave linear DNA having either recognition sites in the same orientation or a single recognition site . Cleavage occurs predominantly at a site proximal to the DNA end in the case of multiple site substrates . Such cleavage can be abolished by the binding of Lac repressor downstream (3' side) but not upstream (5' side) of the recognition site . Binding of HU protein has also been observed to interfere with R.EcoP15I cleavage activity . In accordance with a mechanism requiring two enzyme molecules cooperating to elicit double-strand break on DNA, our results convincingly demonstrate that the enzyme translocates on DNA in a 5' to 3' direction from its recognition site and indicate a switch in the direction of enzyme motion at the DNA ends . This study demonstrates a new facet in the mode of action of these restriction enzymes. J Biol Chem, 2005 Jan 7, 280(1), 469 - 475 Epub 2004 Oct 22. Crystal Structure of the Human Cytosolic Sialidase Neu2: EVIDENCE FOR THE DYNAMIC NATURE OF SUBSTRATE RECOGNITION; Chavas LM et al.; Gangliosides play key roles in cell differentiation, cell-cell interactions, and transmembrane signaling . Sialidases hydrolyze sialic acids to produce asialo compounds, which is the first step of degradation processes of glycoproteins and gangliosides . Sialidase involvement has been implicated in some lysosomal storage disorders such as sialidosis and galactosialidosis . Neu2 is a recently identified human cytosolic sialidase . Here we report the first high resolution x-ray structures of mammalian sialidase, human Neu2, in its apo form and in complex with an inhibitor, 2-deoxy-2,3-dehydro-N-acetylneuraminic acid (DANA) . The structure shows the canonical six-blade beta-propeller observed in viral and bacterial sialidases with its active site in a shallow crevice . In the complex structure, the inhibitor lies in the catalytic crevice surrounded by ten amino acids . In particular, the arginine triad, conserved among sialidases, aids in the proper positioning of the carboxylate group of DANA within the active site region . The tyrosine residue, Tyr(334), conserved among mammalian and bacterial sialidases as well as in viral neuraminidases, facilitates the enzymatic reaction by stabilizing a putative carbonium ion in the transition state . The loops containing Glu(111) and the catalytic aspartate Asp(46) are disordered in the apo form but upon binding of DANA become ordered to adopt two short alpha-helices to cover the inhibitor, illustrating the dynamic nature of substrate recognition . The N-acetyl and glycerol moieties of DANA are recognized by Neu2 residues not shared by bacterial sialidases and viral neuraminidases, which can be regarded as a key structural difference for potential drug design against bacteria, influenza, and other viruses. Infect Immun, 2004 Nov, 72(11), 6676 - 9 Mucosal administration of flagellin induces innate immunity in the mouse lung; Honko AN et al.; Nonsurgical intratracheal instillation of 1 microg of purified, recombinant flagellin in several strains of mice stimulated a transient innate immune response in the lung characterized by the infiltration of neutrophils and the rapid production of tumor necrosis factor alpha, interleukin 6, granulocyte colony-stimulating factor, and the chemokines keratinocyte-derived chemokine, MIP1alpha, and MIP-2. Infect Immun, 2004 Nov, 72(11), 6615 - 21 Differences in cell activation by Chlamydophila pneumoniae and Chlamydia trachomatis infection in human endothelial cells; Krull M et al.; Seroepidemiological studies and demonstration of viable bacteria in atherosclerotic plaques have linked Chlamydophila pneumoniae infection to the development of chronic vascular lesions and coronary heart disease . In this study, we characterized C . pneumoniae-mediated effects on human endothelial cells and demonstrated enhanced phosphorylation and activation of the endothelial mitogen-activated protein kinase (MAPK) family members extracellular receptor kinase (ERK1/2), p38-MAPK, and c-Jun-NH2 kinase (JNK) . Subsequent interleukin-8 (IL-8) expression was dependent on p38-MAPK and ERK1/2 activation as demonstrated by preincubation of endothelial cells with specific inhibitors for the p38-MAPK (SB202190) or ERK (U0126) pathway . Inhibition of either MAPK had almost no effect on intercellular cell adhesion molecule 1 (ICAM-1) expression . While Chlamydia trachomatis was also able to infect endothelial cells, it did not induce the expression of endothelial IL-8 or ICAM-1 . These effects were specific for a direct stimulation with viable C . pneumoniae and independent of paracrine release of endothelial cell-derived mediators like platelet-activating factor, NO, prostaglandins, or leukotrienes . Thus, C . pneumoniae triggers an early signal transduction cascade in target cells that could lead to endothelial cell activation, inflammation, and thrombosis, which in turn may result in or promote atherosclerosis. Infect Immun, 2004 Nov, 72(11), 6324 - 9 RNA encoding the MPT83 antigen induces protective immune responses against Mycobacterium tuberculosis infection; Xue T et al.; We have previously demonstrated that vaccination of mice with plasmid DNA vectors expressing immunodominant mycobacterial genes induced cellular immune responses and significant protection against challenge with Mycobacterium tuberculosis . We demonstrate here, using in vitro-synthesized RNA, that vaccination with DNA or RNA constructs expressing the M . tuberculosis MPT83 antigen are capable of inducing specific humoral and T-cell immune responses and confer modest but significant protection against M . tuberculosis challenge in mice . This is the first report of protective immunity conferred against intracellular bacteria by an RNA vaccine . This novel approach avoids some of the drawbacks of DNA vaccines and illustrates the potential for developing new antimycobacterial immunization strategies. Ultrason Sonochem, 2005 Mar, 12(4), 301 - 6 Bioleaching with ultrasound; Swamy KM et al.; Application of bioleaching of metals in a large-scale operation is reviewed briefly . Continued technical innovation is vital for the wider utilisation of this extraction process within the mineral industries . Therefore, the use of power ultrasound in combination with bioleaching (referred to as sonobioleaching) has been studied and is shown to be beneficial in the recovery of nickel from lean grade ores . The role of ultrasound in improving the benefits and lowering the drawbacks of bioleaching to an acceptable level are described . A possible mechanism for improving and intensifying this process is hypothesised. Peptides, 2004 Nov, 25(11), 1899 - 907 The crustacean hyperglycemic hormone precursors a and b of the Norway lobster differ in the preprohormone but not in the mature peptide; Mettulio R et al.; The neuro-endocrine X-organ sinus-gland complex of crustaceans produces and releases the neuropeptides of the crustacean hyperglycemic hormone (cHH)/molt-inhibiting hormone (MIH)/gonad-inhibiting hormone (GIH) family that regulate important physiological processes, such as growth, reproduction and molting . We cloned two full-length cDNAs encoding the preprocHH-A and preprocHH-B of the Norway lobster Nephrops norvegicus of 132 and 131 amino acid residues . The two cHHs differ in the preprohormone but not in the mature peptide sequence . The mature cHH was expressed in bacteria as GST fusion protein that, in bioassay, shows a hyperglycemic activity similar to that of native cHH present in an eyestalk extract. J Theor Biol, 2004 Dec 7, 231(3), 357 - 76 Identifying control mechanisms of granuloma formation during M . tuberculosis infection using an agent-based model; Segovia-Juarez JL et al.; Infection with Mycobacterium tuberculosis is a major world health problem . An estimated 2 billion people are presently infected and the disease causes approximately 3 million deaths per year . After bacteria are inhaled into the lung, a complex immune response is triggered leading to the formation of multicellular structures termed granulomas . It is believed that the collection of host granulomas either contain bacteria resulting in a latent infection or are unable to do so, leading to active disease . Thus, understanding granuloma formation and function is essential for improving both diagnosis and treatment of tuberculosis . Granuloma formation is a complex spatio-temporal system involving interactions of bacteria, specific immune cells, including macrophages, CD4+ and CD8+ T cells, as well as immune effectors such as chemokine and cytokines . To study this complex dynamical system we have developed an agent-based model of granuloma formation in the lung . This model combines continuous representations of chemokines with discrete agent representations of macrophages and T cells in a cellular automata-like environment . Our results indicate that key host elements involved in granuloma formation are chemokine diffusion, prevention of macrophage overcrowding within the granuloma, arrival time, location and number of T cells within the granuloma, and an overall host ability to activate macrophages . Interestingly, a key bacterial factor is its intracellular growth rate, whereby slow growth actually facilitates survival. J Hosp Infect, 2004 Nov, 58(3), 233 - 7 In situ endoluminal brushing: a safe technique for the diagnosis of catheter-related bloodstream infection; Dobbins BM et al.; We assessed the safety of the endoluminal brush technique for the in situ diagnosis of central-venous-catheter (CVC)-related bloodstream infection (CRBSI) . The endoluminal brush was used to investigate patients with suspected CRBSI by sampling the CVC lumen to within 3-5 cm of the catheter tip (the brush was kinked to mark the length required) . Quantitative peripheral blood cultures were taken 1 min pre-brushing and 1 min and 1h post-brushing . In addition, a 1 mL sample of through-catheter blood was aspirated immediately pre- and post-brushing, and aliquots were directly plated on to blood agar to determine the load of CVC-associated bacteria . After CVC removal, catheter tips were sent for culture using the Maki roll and modified Cleri flush techniques . Of 139 suspected cases, 61 (45%) had confirmed episodes of CRBSI . No patients experienced fever or rigors, or had evidence of embolic phenomena after CVC endoluminal brushing . There was no difference overall in pre-brushing and 1-min post-brushing peripheral blood bacterial counts (P < 0.702) . Peripheral and CVC blood bacterial counts were significantly reduced 1h post-brushing (P < 0.03 and P < 0.001, respectively), possibly due to removal of endoluminal biomass . The endoluminal brush technique can be safely used to diagnose CRBSI without the need for CVC removal, provided that the brush is not allowed to protrude beyond the tip of the catheter. Trends Plant Sci, 2004 Nov, 9(11), 523 - 8 Plant fructan exohydrolases: a role in signaling and defense? Van den Ende W, De Coninck B, Van Laere A. Fructans are fructose oligomers and polymers synthesized by a small number of plant and bacterial species and mainly function as reserve carbohydrates . The terminal fructosyl-fructose linkages can be degraded by fructan exohydrolases (FEHs), occurring in bacteria, fungi and fructan plants . Unexpectedly, it was found that FEHs also occur in non-fructan plants such as Beta vulgaris and Arabidopsis thaliana that apparently lack endogenous fructan substrates . FEHs might have defense-related roles acting on bacterial fructan-containing slimes or might act on minute (up to now undetected) amounts of fructans acting as signals in plants. Mol Biochem Parasitol, 2004 Nov, 138(1), 29 - 36 Malaria parasite-inhibitory antibody epitopes on Plasmodium falciparum merozoite surface protein-1(19) mapped by TROSY NMR; Morgan WD et al.; Plasmodium falciparum merozoite surface protein 1 (MSP1)(19), the C-terminal fragment of merozoite surface protein 1, is a leading candidate antigen for development of a vaccine against the blood stages of the malaria parasite . Many human and animal studies have indicated the importance of MSP1(19)-specific immune responses . Anti-MSP1(19) antibodies can prevent invasion of red blood cells by P . falciparum parasites in vitro . However, the fine specificity of anti-MSP1(19) antibodies is also important, as only a fraction of monoclonal antibodies (mAbs) have parasite-inhibitory activity in vitro . Human sera from malaria-endemic locations show strong MSP1(19) reactivity, but individual serum samples vary greatly in inhibitory activity . NMR is an excellent method for studying protein-protein interactions, and has been used widely to study binding of peptides representing known epitopes (as well as non-protein antigens) to antibodies and antibody fragments . The recent development of transverse relaxation optimized spectroscopy (TROSY) and related methods has significantly extended the maximum size limit of molecules that can be studied by NMR . TROSY NMR experiments produce high quality spectra of Fab complexes that allow the mapping of epitopes by the chemical shift perturbation technique on a complete, folded protein antigen such as MSP1(19) . We studied the complexes of P . falciparum MSP1(19) with Fab fragments from three monoclonal antibodies . Two of these antibodies have parasite-inhibitory activity in vitro, while the third is non-inhibitory . NMR epitope mapping showed a close relationship between binding sites for the two inhibitory antibodies, distinct from the location of the non-inhibitory antibody . Together with a previously published crystal structure of the P . falciparum MSP1(19) complex with the Fab fragment of another non-inhibitory antibody, these results revealed a surface on MSP1(19) where inhibitory antibodies bind . This information will be useful in evaluating the anti-MSP1(19) immune response in natural populations from endemic areas, as well as in vaccine trials . It will also be valuable for optimizing the MSP1(19) antigen by rational vaccine design . This work also shows that TROSY NMR techniques are very effective for mapping conformational epitopes at the level of individual residues on small- to medium-sized proteins, provided that the antigen can be expressed in a system amenable to stable isotope labelling, such as bacteria or yeast. Adv Protein Chem, 2004, 68, 313 - 49 Ionotropic glutamate receptor recognition and activation; Oswald RE; Ionotropic glutamate receptors are the major excitatory neurotransmitters in mammalian brain but are found throughout the animal kingdom as well as in plants and bacteria . A great deal of progress in understanding the structure of these essential neurotransmitter receptors has been made since the first examples were cloned and sequenced in 1989 . The atomic structure of the ligand-binding domain of several ionotropic glutamate receptors has been determined, and a great deal of progress has been made in relating the structural properties of the binding site to the function of the intact receptor . In addition, the identification of glutamate receptors from a wide variety of organisms ranging from several types of bacteria to Arabidopsis to a range of animal species has made glutamate receptors a molecular laboratory for studying the evolution of proteins . The fact that glutamate receptors are a particularly ancient intercellular signaling molecule suggests a potential role in the transition from single celled to multicellular organisms . This review focuses on the structure and dynamics of ionotropic glutamate receptors and their relation to the function and evolution of these proteins. Biochem J . 2004 Oct 25; {Epub ahead of print} Characterization of phylogenetically distant members of the adenylyl cyclase family from mycobacteria: Rv1647 from M . tuberculosis and its ortholog ML1399 from M . leprae; Shenoy AR et al.; Analysis of the genome sequence of Mycobacterium tuberculosis H37Rv has identified 16 genes that are similar to the mammalian adenylyl and guanylyl cyclases . Rv1647 was predicted to be an active adenylyl cyclase but its position in a phylogenetically distant branch from the other enzymes characterized so far from M . tuberculosis, makes it an interestingly divergent nucleotide cyclase to study . In agreement with its divergence at the sequence level from other nucleotide cyclases, cloning, expression and purification of Rv1647 revealed differences in its biochemical properties from the earlier characterized Rv1625c adenylyl cyclase . Adenylyl cyclase activity of Rv1647 was activated by detergents but was resistant to high concentrations of salt . Mutations of substrate specifying residues to those present in guanylyl cyclases failed to convert the enzyme to a guanylyl cyclase, but did not alter its oligomeric status . Orthologs of Rv1647 could be found in M . leprae, M . avium and M . smegmatis . The ortholog from M . leprae (ML1399) was cloned, protein expressed, purified and shown biochemically to be an adenylyl cyclase, thus representing the first adenylyl cyclase to be described from M . leprae . Importantly, Western blot analysis of subcellular fractions from M . tuberculosis and M . leprae revealed that Rv1647 and ML1399 gene products were expressed in these bacteria respectively . Additionally, M . tuberculosis was also found to express the Rv1625c adenylyl cyclase, suggesting that multiple adenylyl cyclase proteins may be expressed simultaneously in this organism . These results suggest that Class III cyclase-like gene products are likely to have an important role to play in the physiology and perhaps the pathology of these medically important bacteria. Lin Chuang Er Bi Yan Hou Ke Za Zhi, 2004 Jul, 18(7), 411 - 3 {The expression of RANTES interleukin 1beta and endotoxin in the effusion of secretory otitis media}; Liang G et al.; OBJECTIVE: To study the protein expression of endotoxin, interleukin 1beta (IL-1beta) and regulated upon activation, normal T expressed and secreted (RANTES) in effusions of secretory otitis media and their roles in the pathogenesis of secretory otitis media . METHOD: Seventy-two effusion samples were taken from 53 patients with secretory otitis media by tympanocentesis . After swabs they were taken for bacteria culture . Limulus amebocyte lysate (LAL) test was used to quantify the content of endotoxin, radioimmunoassay to analyze the level of IL-1beta and enzyme-linked immunosorbent assay (ELISA) to detect the concentration of RANTES . RESULT: Endotoxin, IL-1beta and RANTES were detectable in 80.9%, 77.8% and 70.8% of middle ear effusion, with mean levels of (35.2 +/- 51.6) EU/ml, (1.10 +/- 0.84) microg/L and (0.52 +/- 0.43) microg/L respectively . All of them showed higher concentration in the mucoid-type effusions than those in the serous-type effusions (P<0.05) . Higher levels of the endotoxin and RANTES (P<0.05) were found in longer course patients . The effusions with positive bacteria culture displayed more abundant endotoxin, IL-1beta and RANTES protein than those with negative culture . Significant correlations were found between endotoxin and IL-1beta (r = 0.74, P<0.01), also between IL-1beta and RANTES (r = 0.48, P<0.01) . CONCLUSION: Endotoxin, IL-1beta and RANTES may take part in maintaining the inflammatory response in the tympanic cavity and stimulating mucin secretion . It indicates that they play an important role in the immune pathogenesis of secretory otitis media. Cutis, 2004 Sep, 74(3 Suppl), 9 - 12, 32-4 Rosacea and the pilosebaceous follicle; Powell FC; The pathophysiology of rosacea remains unknown . A leading theory suggests a vascular basis; however, clinical observations and histopathologic studies suggest that inflammation of the pilosebaceous follicle may be central to the pathogenesis of rosacea . Demodex folliculorum is a frequently seen commensal in the follicles of facial skin . According to evidence from biopsies of the skin surface, individuals with rosacea have a higher density of this parasite . This increased mite density may play a role in the pathophysiology of rosacea by triggering inflammatory or specific immune reactions, mechanically blocking the follicles, or acting as a vector for bacteria . Ongoing research has shown that bacteria from patients with rosacea may behave differently at the higher skin temperature that may be present in patients with rosacea . Another group has isolated bacteria from the Demodex mites; these bacteria may play a pathogenic role in papulopustular rosacea by facilitating follicular-based inflammatory changes. Am J Physiol Heart Circ Physiol . 2004 Oct 21; {Epub ahead of print} Human neutrophils promote angiogenesis by a paracrine feedforward mechanism involving endothelial interleukin-8; Schruefer R et al.; Neovascularization by sprouting angiogenesis is critical for inflammation-mediated tissue remodeling and wound healing . We report here that human polymorphonuclear neutrophils (PMN) stimulated for 1 h with 100 nM N-formyl-Met-Leu-Phe (fMLP) released a proangiogenic entity which induced sprouting of capillary-like structures in an in vitro angiogenesis assay . The effect was comparable to the response obtained upon stimulation with 100 ng/ml basic fibroblast growth factor . The PMN-mediated response was inhibited by neutralizing antibodies against VEGF or IL-8 . As measured by ELISA technique, we found that fMLPactivated PMN (5 x 10(6)/ml) released 78 pg/ml IL-8 and 39 pg/ml VEGF within 1 h after stimulation . The IL-8 release was blocked by actinomycin D or cycloheximide, but the inhibitors had no effect on the VEGF release suggesting that the IL-8 secretion required de novo synthesis whereas VEGF was secreted from preformed stores . Accordingly, RT-PCR analysis revealed that the IL-8 mRNA was upregulated upon PMN stimulation whereas the expression of the VEGF mRNA was not affected . Moreover, the supernatant derived from activated PMN induced an upregulation of the endothelial IL-8 mRNA expression suggesting that the release of VEGF and IL-8 from activated PMN may activate a paracrine feedforward mechanism involving endothelial IL-8 . Moreover, the VEGF-induced upregulation of endothelial IL-8 expression as well as the sprouting of capillary-like structures was inhibited by a neutralizing anti-IL-8 antibody . These findings suggest that bacteria-derived tripeptides stimulate human PMN to release VEGF and IL-8 which activate endothelial cells and induce angiogenesis by a paracrine feedforward mechanism involving endothelial IL-8 upregulation. Mol Plant Microbe Interact, 2004 Oct, 17(10), 1086 - 94 Enhancer trapping identifies TRI, an Arabidopsis gene up-regulated by pathogen infection; Fridborg I et al.; Enhancer trap Arabidopsis thaliana plants were screened for genes up-regulated by virus infection . The plants carried T-DNA insertions comprising a minimal -60-bp Cauliflower mosaic virus 35S promoter fused to the beta-