bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measuring chromosome dynamics on different time scales using resolvases with varying half‐lives
Authors: Stein Richard A. , Deng Shuang , Higgins N. Patrick 
Published: April 2005

SummaryThe bacterial chromosome is organized into multiple independent domains, each capable of constraining the plectonemic negative supercoil energy introduced by DNA gyrase. Different experimental approaches have estimated the number of domains to be between 40 and 150. The site‐specific resolution systems of closely related transposons Tn3 and γδ are valuable tools for measuring supercoil diffusion and analysing bacterial chromosome dynamics in vivo. Once made, the wild‐type resolvase persists in cells for time periods greater than the cell doubling time. To examine chromosome dynamics over shorter time frames that are more closely tuned to processes like inducible transcription, we constructed a set of resolvases with cellular half‐lives ranging from less than 5 min to 30 min. Analysing chromosomes on different time scales shows domain structure to be dynamic. Rather than the 150 domains detected with the Tn3 resolvase, wild‐type cells measured over a 10 min time span have more than 400 domains per genome equivalent, and some gyrase mutants exceed 1000.
A yeast genetic system for the identification and characterization of substrate proteins transferred into host cells by the Legionella pneumophila Dot/Icm system
Authors: Campodonico Eva M. , Chesnel Laurent , Roy Craig R. 
Published: April 2005

SummaryThe Dot/Icm system is a type IVb secretion system used by Legionella pneumophila to modulate vesicular transport in both protozoan and mammalian host cells. It has been shown that proteins and processes that are highly conserved in all eukaryotic cells are targets for some of the proteins injected by the Dot/Icm system. For example, the Legionella protein RalF was shown previously to be a Dot/Icm substrate that functions as a guanine nucleotide exchange factor (GEF) for the Arf family of eukaryotic small GTP‐binding proteins. Here we show that ectopic production of the RalF protein in Saccharomyces cerevisiae interferes with yeast growth. Inhibition of yeast growth was found to be dependent on the ability of RalF to function as an Arf‐GEF in vivo. The possibility that other Dot/Icm substrate proteins would have the capacity to interfere with yeast growth was used as a rationale to screen plasmid libraries containing random fragments of Legionella chromosomal DNA positioned downstream of a galactose‐inducible promoter. This screen identified Legionella proteins that conferred a conditional growth defect when overproduced by yeast cultured in the presence of galactose. Most of the Legionella proteins identified were determined to be substrates of the Dot/Icm system. This screen led to the identification of a new Dot/Icm substrate protein that was called YlfA, for yeast lethal factor A. A paralogue of YlfA was identified on an unlinked region of the Legionella chromosome and this protein was also translocated by the Dot/Icm system. It was determined that a hydrophobic region near the N‐terminus of the YlfA protein and an adjacent region predicted to form a coiled‐coil domain were necessary for a biological activity that interfered with yeast growth. The YlfA protein did not decorate the Legionella‐containing vacuole during the first 7 h of infection but could be observed on the endoplasmic reticulum (ER)‐derived replicative vacuole and on punctate structures throughout the host cell at later stages. Ectopic production of YlfA in mammalian cells revealed that the N‐terminal hydrophobic domain in YlfA was able to localize the protein to early secretory organelles, including endoplasmic reticulum. These studies show that yeast genetics can be exploited to identify and characterize proteins that are injected into host cells by bacterial pathogens that utilize type IV secretion systems for pathogenesis.
Silkworm pathogenic bacteria infection model for identification of novel virulence genes
Authors: Kaito Chikara , Kurokawa Kenji , Matsumoto Yasuhiko , Terao Yutaka , Kawabata Shigetada , Hamada Shigeyuki , Sekimizu Kazuhisa 
Published: April 2005

SummarySilkworms are killed by injection of pathogenic bacteria, such as Staphylococcus aureus and Streptococcus pyogenes, into the haemolymph. Gene disruption mutants of S. aureus whose open reading frames were previously uncharacterized and that are conserved among bacteria were examined for their virulence in silkworms. Of these 100 genes, three genes named cvfA, cvfB, and cvfC were required for full virulence of S. aureus in silkworms. Haemolysin production was decreased in these mutants. The cvfA and cvfC mutants also had attenuated virulence in mice. S. pyogenes cvfA‐disrupted mutants produced less exotoxin and had attenuated virulence in both silkworms and mice. These results indicate that the silkworm‐infection model is useful for identifying bacterial virulence genes.
DksA represses ribosomal gene transcription in Pseudomonas aeruginosa by interacting with RNA polymerase on ribosomal promoters
Authors: Perron Karl , Comte Rachel , Van Delden Christian 
Published: April 2005

SummaryIn Escherichia coli transcription of ribosomal RNA (rRNA) is regulated by the H‐NS and Fis proteins, as well as by the small signal molecule ppGpp and the initiating nucleotides. During amino acid starvation, the concentration of ppGpp increases, and binding of this alarmone to RNA polymerase (RNAP) leads to inhibition of rRNA transcription, a regulatory event called stringent response. Here we show that in Pseudomonas aeruginosa DksA, a protein with pleiotropic effects, is a negative regulator of rRNA transcription both during exponential growth and stringent conditions. A dksA mutant overexpresses rRNA, without being affected in the production of ppGpp. Cell‐fractionation and chromosome immunoprecipitation experiments demonstrate that DksA is associated with DNA, in particular with promoters of ribosomal genes in vivo. The binding to rRNA promoters specifically increases during stringent response, and correlates with the binding of RNAP to these regions. Moreover DksA can be copurified with RNAP subunits in vivo. DNA band shift experiments show that DksA, in synergy with ppGpp, increases the binding of RNAP to ribosomal promoters. Therefore DksA might be a new regulator of rRNA transcription in P. aeruginosa.
The role of nucleoid‐associated proteins in the organization and compaction of bacterial chromatin
Authors: Dame Remus T. 
Published: April 2005

SummaryThe bacterial chromosomal DNA is folded into a compact structure called nucleoid. The shape and size of this ‘body’ is determined by a number of factors. Major players are DNA supercoiling, macromolecular crowding and architectural proteins, associated with the nucleoid, which are the topic of this MicroReview. Although many of these proteins were identified more than 25 years ago, the molecular mechanisms involved in the organization and compaction of DNA have only started to become clear in recent years. Many of these new insights can be attributed to the use of recently developed biophysical techniques.
Biosynthesis of the red antibiotic, prodigiosin, in Serratia: identification of a novel 2‐methyl‐3‐n‐amyl‐pyrrole (MAP) assembly pathway, definition of the terminal condensing enzyme, and implications for undecylprodigiosin biosynthesis in Streptomyces
Authors: Williamson Neil R. , Simonsen Henrik T. , Ahmed Raef A. A. , Goldet Gabrielle , Slater Holly , Woodley Louise , Leeper Finian J. , Salmond George P. C. 
Published: April 2005

SummaryThe biosynthetic pathway of the red‐pigmented antibiotic, prodigiosin, produced by Serratia sp. is known to involve separate pathways for the production of the monopyrrole, 2‐methyl‐3‐n‐amyl‐pyrrole (MAP) and the bipyrrole, 4‐methoxy‐2,2′‐bipyrrole‐5‐carbaldehyde (MBC) which are then coupled in the final condensation step. We have previously reported the cloning, sequencing and heterologous expression of the pig cluster responsible for prodigiosin biosynthesis in two Serratia sp. In this article we report the creation of in‐frame deletions or insertions in every biosynthetic gene in the cluster from Serratia sp. ATCC 39006. The biosynthetic intermediates accumulating in each mutant have been analysed by LC‐MS, cross‐feeding and genetic complementation studies. Based on these results we assign specific roles in the biosynthesis of MBC to the following Pig proteins: PigI, PigG, PigA, PigJ, PigH, PigM, PigF and PigN. We report a novel pathway for the biosynthesis of MAP, involving PigD, PigE and PigB. We also report a new chemical synthesis of MAP and one of its precursors, 3‐acetyloctanal. Finally, we identify the condensing enzyme as PigC. We reassess the existing literature and discuss the significance of the results for the biosynthesis of undecylprodigiosin by the Red cluster in Streptomyces coelicolor A3(2).
Candida albicans Cell‐Wall Fraction Exacerbates Collagen‐Induced Arthritis in Mice
Authors: Yordanov M. , Tchorbanov A. , Ivanovska N. 
Published: April 2005

AbstractThe immune system generates a specific response against most pathogens, while developing tolerance to self‐antigens. Commensal micro‐organisms can express molecular structures that mimic self‐epitopes. During acute infection, such pathogen may activate self‐reactive T‐cell clones promoting autoimmunity. In the present study, a β‐mercaptoethanol cell‐wall fraction (MF) from Candida albicans was injected into the paw of naïve ICR and BALB/c mice and into the paw of ICR mice with bovine collagen type II‐induced arthritis (CIA). Development of inflammation was monitored for 6 weeks. MF provoked a stable swelling and histopathologic changes in the injected joint, with a predominance of T‐helper 1 cytokines in ICR mice. In BALB/c strain, a swelling was observed only in the early period, with no evidence of joint pathology. Injection of the MF fraction exacerbated the disease in ICR mice with CIA, and this was associated with the elevation of interferon‐gamma and anti‐bovine type II collagen (bCII) immunoglobulin G2a antibodies. These results indicate that component(s) in the MF fraction cross‐react with bCII‐specific cells.
Reduced Release of Intact and Cleaved Urokinase Receptor in Stimulated Whole‐Blood Cultures from Human Immunodeficiency Virus‐1‐Infected Patients
Authors: Ostrowski S. R. , Piironen T. , Høyer‐Hansen G. , Gerstoft J. , Pedersen B. K. , Ullum H. 
Published: April 2005

AbstractThe blood levels of the soluble forms of the urokinase receptor (suPAR) are increased in human immunodeficiency virus (HIV)‐1‐infected patients. This study investigated whether the release of urokinase‐type plasminogen activator receptor (uPAR) in whole‐blood cultures was affected by HIV infection. The release of different uPAR forms in whole‐blood cultures incubated 24 h with or without phytohemagglutinin and lipopolysaccharide was analysed in 47 HIV patients and 19 controls. suPAR was measured by enzyme‐linked immunosorbent assay (ELISA) (bulk‐suPAR) and three different time‐resolved fluorescence immunoassays measuring three‐domain suPAR [suPAR(I–III)], three‐ and two‐domain suPAR [suPAR(I–III) + suPAR(II–III)] and one‐domain suPAR [suPAR(I)]. The uPAR release was correlated to leucocyte subpopulations and plasma levels of suPAR. The stimulated net whole‐blood culture release of bulk‐uPAR, uPAR(I–III), uPAR(II–III) and uPAR(I) was reduced in HIV patients (all P < 0.01), whereas the spontaneous bulk‐uPAR and uPAR(I–III) release was increased in HIV patients (both P < 0.05). The stimulated uPAR release in whole‐blood cultures correlated well to leucocytes and circulating suPAR levels in controls, whereas the correlation was weaker to leucocytes and nonexisting to circulating suPAR levels in HIV patients. These findings demonstrate that HIV infection affects stimulated and spontaneous uPAR release in whole‐blood cultures. Given that high blood levels of suPAR in HIV patients are linked to immune activation, the perturbations in uPAR release in whole‐blood cultures from HIV patients may also reflect immune activation.
Association of Interferon‐gamma +874(T/A) Single Nucleotide Polymorphism with the Rate of Tryptophan Catabolism in Healthy Individuals
Authors: Raitala A. , Pertovaara M. , Karjalainen J. , Oja S. S. , Hurme M. 
Published: April 2005

AbstractMechanisms induced by tryptophan (trp) catabolism are important in the regulation of both normal and pathogenetic immune responses. The key enzyme is indoleamine‐pyrrole 2,3‐dioxygenase (EC 1.13.11.42) (IDO) which converts trp to kynurenine (kyn), the main toxic metabolite. It is known that interferon‐gamma (IFN‐γ) is able to activate IDO. We wanted to analyse whether the strength of this mechanism would be under genetic control. To this end, we analysed the IFN‐γ+874(T/A) genotypes, which are known to have an effect on IFN‐γ production, of 309 healthy blood donors and correlated these to the levels of trp and kyn in their blood. The data obtained demonstrate that the presence of the high producer T allele was associated with increased IDO activity (i.e. elevated kyn and kyn/trp levels), but this effect was observed only in females. These data show that trp catabolism is genetically controlled by the IFN‐γ gene and may thus be operative in those disease conditions associated with the polymorphisms of the IFN‐γ gene.
A Sero‐Epidemiological Survey of Gelatin Sensitization in Young Japanese Children During the 1979–1996 Period
Authors: Saito A. , Kumagai T. , Kojima H. , Terai I. , Yamanaka T. , Wataya Y. , Umetsu M. , Umetsu A. , Yano S. 
Published: April 2005

AbstractRecently, an increasing number of adverse reactions in children inoculated with live attenuated virus vaccines containing gelatin have been reported. However, the distribution, magnitude and rate of gelatin sensitization in the Japanese population have not been established. Here, the purpose was to investigate the distribution of children with positive gelatin immunoglobulin G (IgG) and/or IgE in Japan and to ascertain whether the incidence of positive antigelatin antibody cases among the general population, as reflected in the sample employed here, has been increasing during the period in question. The presence of IgE and IgG antibodies were measured against gelatin in 1600 panel sera collected from different age groups of Japanese children in Hokkaido/Sapporo from 1979 through 1996. Among the subjects, 39 had gelatin IgG‐ and/or IgE‐positive sera, and these were correlated with the time of obtaining the sera as well as with the age of the subjects. The older the subject and the later the period, the higher the sero‐incidence. Japanese children have become increasingly sensitized to gelatin, especially since the mid‐1990s.
PRETREATMENT WITH INTRAVENOUS ASCORBIC ACID PRESERVES ENDOTHELIAL FUNCTION DURING ACUTE HYPERGLYCAEMIA (R1)
Authors: Mullan Brian A , Ennis Ciaran N , Fee Howard JP , Young Ian S , McCance David R 
Published: April 2005

SUMMARY1. Acute hyperglycaemia may impair endothelial function. Ascorbic acid (AA), administered intra‐arterially, has been reported to improve endothelium‐dependent vasodilatation during a forearm hyperglycaemic clamp. Using a randomized, double‐blind, placebo‐controlled, cross‐over study, we investigated the potential for intravenous ascorbic acid to modify the endothelial response to acute systemic hyperglycaemia in humans.2. Nine healthy male volunteers were recruited from the hospital staff. Endothelial function was determined by measuring the forearm blood flow responses to intrabrachial infusions of endothelium‐dependent (ED) and endothelium‐independent (EID) vasodilators. The endothelial function index (EFI) was derived from the ratio of ED and EID vasodilatation. Haemodynamic and endothelial function measurements were performed at baseline and then repeated 2 h after a systemic hyperglycaemic clamp (14 mmol/L). The subjects, studied on two separate occasions, were randomized to placebo or 2 g intravenous ascorbic acid prior to the initiation of hyperglycaemia.3. After systemic hyperglycaemia with placebo pretreatment, the EFI fell from 1.08 ± 0.21 to 0.74 ± 0.13 (difference (95% confidence interval): 0.34 (0.20, 0.47); P < 0.001). When subjects were pretreated with ascorbic acid, the EFI was not affected by hyperglycaemia (1.11 ± 0.21 to 1.12 ± 0.17; P = 0.938). This difference between placebo and ascorbic acid was significant (P < 0.001). Plasma ascorbate concentrations decreased during hyperglycaemia and correlated directly with the reduction in the EFI (r = 0.798; P < 0.001).4. Pretreatment with an intravenous bolus of ascorbic acid can prevent endothelial dysfunction during acute systemic hyperglycaemia. Therefore, ascorbic acid may have potential therapeutic use in clinical situations where acute hyperglycaemia may be a complication.
MUTATED G‐PROTEIN‐COUPLED RECEPTOR GPR10 IS RESPONSIBLE FOR THE HYPERPHAGIA/DYSLIPIDAEMIA/OBESITY LOCUS OF Dmo1 IN THE OLETF RAT
Authors: Watanabe Takeshi K , Suzuki Mikio , Yamasaki Yuki , Okuno Shiro , Hishigaki Haretsugu , Ono Toshihide , Oga Keiko , Mizoguchi‐Miyakita Ayako , Tsuji Atsushi , Kanemoto Naohide , Wakitani Shigeyuki , Takagi Toshihisa , Nakamura Yusuke , Tanigami Akira 
Published: April 2005

SUMMARY1. We have confirmed the Diabetes Mellitus OLETF type I (Dmo1) effect on hyperphagia, dyslipidaemia and obesity in the Otsuka Long‐Evans Tokushima Fatty (OLETF) strain. The critical interval was narrowed down to 570 kb between D1Got258 to p162CA1 by segregation analyses using congenic lines.2. Within the critical 570 kb region of the Dmo1 locus, we identified the G‐protein‐coupled receptor gene GPR10 as the causative gene mutated in the OLETF strain. The ATG translation initiation codon of GPR10 is changed into ATA in this strain and, so, is unavailable for the initiation of translation.3. The GPR10 protein has a cognate ligand, namely prolactin‐releasing peptide (PrRP). Centrally administered PrRP suppressed the food intake of congenic rats that have a Brown Norway derived Dmo1 region (i.e. with wild‐type GPR10), but did not suppress that of the OLETF strain, indicating that GPR10 is without function and could explain hyperphagia in the OLETF strain.4. Moreover, when restricted in food volume to the same level consumed by the congenic strain, OLETF rats showed few differences in the parameters of dyslipidaemia and obesity compared with congenic strains.5. Taken together, these results demonstrate that the mutated GPR10 receptor is responsible for the hyperphagia leading to obesity and dyslipidaemia in the obese diabetic strain rat.
HYPOTHESIS: SET‐POINTS and LONG‐TERM CONTROL OF ARTERIAL PRESSURE. A THEORETICAL ARGUMENT FOR A LONG‐TERM ARTERIAL PRESSURE CONTROL SYSTEM IN THE BRAIN RATHER THAN THE KIDNEY
Authors: Osborn John W 
Published: April 2005

SUMMARY1. It has been hypothesised that the ‘set‐point’ for the long‐term control of mean arterial (MAP) resides within the kidney. In this model, the set‐point of the ‘chronic renal function curve’ establishes the steady state relationship between renal perfusion pressure and urinary excretion of sodium and water, which, in turn, affects blood volume and cardiac output. The ‘renal–MAP set‐point’ theory predicts that the kidney controls MAP to maintain its own excretory function and that long‐term regulation of blood volume and cardiac output are paramount to the regulation of arterial pressure.2. An alternative hypothesis is proposed in which the ‘set‐point’ for the long‐term control of MAP resides within the central nervous system (CNS) rather than the kidney. In contrast with the ‘renal–MAP set‐point’ model, the ‘CNS‐MAP set‐point’ model dictates that the brain controls MAP to maintain cerebral blood flow and CNS function.3. The ‘CNS‐MAP set‐point hypothesis’ predicts that long‐term regulation of MAP is paramount to the regulation of blood volume and cardiac output. It is proposed that the ‘CNS‐MAP set‐point’ system operates independently of the arterial baroreceptor reflex, which is a short‐term controller of MAP.4. The precise mechanisms by which the CNS ‘senses’ MAP are complex and remain to be discovered. The MAP ‘sensor’ likely involves integration of hormone levels linked to body fluid homeostasis and osmoreceptor and baroreceptor inputs. It is also proposed that an as yet undiscovered ‘central baroreceptor’ exists within the brain itself.5. The ‘CNS‐MAP set‐point hypothesis’ predicts that many forms of experimental and essential hypertension are due to a primary shift in the CNS‐MAP set‐point.
THE ‘BODY FLUID PRESSURE CONTROL SYSTEM’ RELIES ON THE RENIN–ANGIOTENSIN–ALDOSTERONE SYSTEM: BALANCE STUDIES IN FREELY MOVING DOGS
Authors: Seeliger Erdmann , Wronski Thomas , Ladwig Mechthild , Rebeschke Till , Persson Pontus B , Reinhardt H Wolfgang 
Published: April 2005

SUMMARY1. The physiological role of the ‘renal body fluid pressure control system’, including the intrarenal mechanism of ‘pressure natriuresis’, is uncertain.2. Balance studies in freely moving dogs address the following questions: (i) what is the physiological contribution of pressure natriuresis to the control of total body sodium (TBS); (ii) to what extent is long‐term mean arterial blood pressure (MABP) determined by TBS and total body water (TBW); and (iii) during Na accumulation, is Na stored in an osmotically inactive form?3. Diurnal time‐courses of Na excretion (UNaV) and MABP reveal no correlation. Spontaneous MABP changes do not affect UNaV. The long‐term 20% reduction of renal perfusion pressure (RPP) results in Na retention via pressure‐dependent stimulation of the renin–angiotensin–aldosterone system (RAAS), not via a pressure natriuresis mechanism. Prevention of pressure natriuresis does not result in ongoing Na retention when the RAAS is operative. The long‐term 20% elevation of RPP induced by sustained TBS elevation facilitates Na excretion via pressure natriuresis, but does not restore TBS to normal.4. Changes in TBW correlate well with changes in TBS (r2 = 0.79). This correlation is even closer when concomitant changes in total body potassium are also considered (r2 = 0.91).5. With normal or elevated TBW, long‐term MABP changes correlate well with TBW changes (r2 = 0.69). At lowered TBW, no correlation is found.6. In conclusion, the physiological role of pressure natriuresis is limited. Pressure natriuresis does not appear to be operative when RPP is changed from −20 to +10% and neurohumoral control of UNaV is unimpeded. Within this range, pressure‐dependent changes in the RAAS mediate the effects of changes in RPP on UNaV. Pressure natriuresis may constitute a compensating mechanism under pathophysiological conditions of substantial elevation of RPP. A large portion of the long‐term changes in MABP are attributable to changes in TBW. The notion of osmotically inactive Na storage during Na accumulation appears to be invalid.