bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of class A, B and C CpG‐oligodeoxynucleotides on in vitro activation of innate immune cells in human immunodeficiency virus‐1 infected individuals
Authors: Martinson Jeffrey A. , Tenorio Allan R. , Montoya Carlos J. , Al‐Harthi Lena , Gichinga Carolyne N. , Krieg Arthur M. , Baum Linda L. , Landay Alan L. 
Published: January 2007

SummaryOligodeoxynucleotides (ODN) with unmethylated deoxycytidyl‐deoxyguanosine dinucleotides (CpG‐ODNs) stimulate Toll‐like receptor 9 (TLR9) in plasmacytoid dendritic cells (pDC) and B cells and activate innate and adaptive immunity. Three classes of synthetic CpG‐ODNs, class A, B and C, activate cells through TLR9; our goal was to evaluate their effect on cells from human immunodeficiency virus (HIV)‐1+ individuals. We compared the frequencies and the unstimulated activation status of immune effector cells in HIV‐1+ and HIV‐1– individuals. Fewer pDC, myeloid dendritic cells (mDC), B cells, natural killer (NK) cells and invariant natural killer T cells (iNKT) were present in HIV‐1+ peripheral blood mononuclear cells (PBMC) and their baseline activation status was higher than HIV‐1– PBMC. Exposure of HIV‐1+ PBMC to all classes of CpG‐ODNs led to activation and maturation of pDC based on CD86, CD80, and CD83 expression similar to that of cells from HIV‐1– individuals. The percentage of CpG‐ODN stimulated pDC that express CD40 was dramatically higher when cells were obtained from HIV‐1+ than from HIV‐1– individuals. B‐lymphocytes were activated similarly in HIV‐1+ and HIV‐1– individuals. mDC, NK and iNKT cell, which lack TLR9, were indirectly activated. Interferon‐α (IFN‐α) and interferon inducible protein 10 (IP‐10) secretion was induced by class A or C but not class B CpG‐ODN, but the concentrations were less than those produced by HIV‐1– PBMC. HIV‐1 infected individuals have fewer innate effector cells that are chronically activated, but these cells can be further activated by CpG‐ODN, which suggests that synthetic CpG‐ODNs could be used to enhance the immune system in HIV‐1 infected individuals.
Efficacy of intracoronal bleaching techniques with different light activation sources
Authors: Carrasco L. D. , Guerisoli D. M. Z. , Rocha M. J. A. , Pécora J. D. , Fröner I. C. 
Published: January 2007

AbstractAim  To evaluate ex vivo the efficacy of 35% hydrogen peroxide for intracoronal bleaching when activated by LEDs, halogen lamp or by the walking bleach technique.Methodology  Forty extracted human maxillary central incisors had their crowns resected 1 mm below the amelo‐cemental junction and were submitted to artificial staining in centrifuged rat haemolysed blood. A 2‐mm thick glass ionomer cervical plug was placed inside the canal, at the level of the amelo‐cemental junction. Samples were divided randomly into five groups: group I received 35% hydrogen peroxide gel activated by LEDs. Group II received 35% hydrogen peroxide gel activated by a halogen lamp‐based light curing unit. Group III received 35% hydrogen peroxide gel followed by the walking bleach technique. Group IV was neither artificially stained nor bleached (positive control) and group V was stained, but not bleached (negative control). The shade of the teeth was assessed visually by three independent and calibrated evaluators, before and after bleaching. The results were analysed using Kruskal–Wallis one‐way analysis of variance and Dunn's post‐test.Results  No statistical differences regarding sample shades were found amongst groups for the tested internal bleaching techniques (P > 0.05).Conclusions  Hydrogen peroxide for intracoronal bleaching when activated either by LEDs, halogen lamp or by the walking bleach technique presented similar efficacy.
In‐frame overlapping genes: the challenges for regulating gene expression
Authors: Yu Jae‐Sung , Kokoska Robert J. , Khemici Vanessa , Steege Deborah A. 
Published: January 2007

SummaryIn‐frame overlapping genes in phage, plasmid and bacterial genomes permit synthesis of more than one form of protein from the same gene. Having one gene entirely within another rather than two separate genes presumably precludes recombination events between the identical sequences. However, studies of such gene pairs indicate that the overlapping arrangement can make regulation of the genes more difficult. Here, we extend studies of in‐frame overlapping genes II and X from filamentous phage f1 to determine if translational controls are required to regulate the gene properly. These genes encode proteins (pII and pX) with essential but opposing roles in phage DNA replication. They must be tightly regulated to maintain production of the proteins at relative steady state levels that permit continuous replication without killing the host. To determine why little or no pX appears to be made on the gene II/X mRNA, gene II translation was lowered by progressively deleting into the gene II initiator region. Increased pX translation resulted, suggesting that elongating ribosomes on the gene II mRNA interfere with internal initiation on the gene X ribosome binding site and limit gene X translation. As judged from systematically lowering the efficiency of suppression at a gene II amber codon upstream from the gene X start, the already modest level of gene II translation would have to be reduced by more than twofold to relieve all interference with internal initiation. Further downregulation of gene X expression proved to be required to maintain pX at levels relative to pII that are tolerated by the cell. Site‐directed mutagenesis and nuclease mapping revealed that the gene X initiation site is sequestered in an extended RNA secondary structure that lowers gene X translation on the two mRNAs encoding it. The more general implications of the results for expression of in‐frame overlapping genes are discussed.
Structural insights on the translation initiation complex: ghosts of a universal initiation complex
Authors: Allen Gregory S. , Frank Joachim 
Published: January 2007

SummaryAll living organisms utilize ribosomes to translate messenger RNA into proteins. Initiation of translation, the process of bringing together mRNA, initiator transfer RNA, and the ribosome, is therefore of critical importance to all living things. Two protein factors, IF1 (a/eIF1A) and IF2 (a/eIF5B), are conserved among all three kingdoms of life and have been called universal initiation factors (Roll‐Mecak et al., 2001). Recent X‐ray, NMR and cryo‐EM structures of the universal factors, alone and in complex with eubacterial ribosomes, point to the structural homology among the initiation factors and initiation complexes. Taken together with genomic and functional evidence, the structural studies allow us to predict some features of eukaryotic and archaeal initiation complexes. Although initiation of translation in eukaryotes and archaea requires more initiation factors than in eubacteria we propose the existence of a common denominator initiation complex with structural and functional homology across all kingdoms of life.
The F plasmid‐encoded TraM protein stimulates relaxosome‐mediated cleavage at oriT through an interaction with TraI
Authors: Ragonese Heather , Haisch Debi , Villareal Ernesto , Choi June‐Hyuk , Matson Steven W. 
Published: January 2007

SummaryConjugative DNA transfer is a highly conserved process for the direct transfer of DNA from a donor to a recipient. The conjugative initiator proteins are key players in the DNA processing reactions that initiate DNA transfer – they introduce a site‐ and strand‐specific break in the DNA backbone via a transesterification that leaves the initiator protein covalently bound on the 5′‐end of the cleaved DNA strand. The action of the initiator protein at the origin of transfer (oriT) is governed by auxiliary proteins that alter the architecture of the DNA molecule, allowing binding of the initiator protein. In the F plasmid system, two auxiliary proteins have roles in establishing the relaxosome: the host‐encoded IHF and the plasmid‐encoded TraY. Together, these proteins direct the loading of TraI which contains the catalytic centre for the transesterification. The F‐oriT sequence includes a binding site for another plasmid‐encoded protein, TraM, which is required for DNA transfer. Here the impact of TraM protein on the formation and activity of the F plasmid relaxosome has been examined. Purified TraM stimulates the formation of relaxed DNA in a reaction that requires the minimal components of the relaxosome, TraI, TraY and IHF. Unlike TraY and IHF, TraM is not essential for the formation of the relaxosome in vitro and TraM cannot substitute for either TraY or IHF in this process. The TraM binding site sbmC, along with both IHF binding sites, is essential for stimulation of the relaxase reaction. In addition, stimulation of transesterification appears to require the C‐terminal domain of TraI suggesting that TraM and TraI may interact through this domain on TraI. Taken together, these results provide additional evidence of a role for TraM as a component of the relaxosome, suggest a previously unknown interaction between TraI and TraM, and allow us to propose a molecular role for the C‐terminal domain of TraI.
Multiple co‐regulatory elements and IHF are necessary for the control of fimB expression in response to sialic acid and N‐acetylglucosamine in Escherichia coli K‐12
Authors: Sohanpal Baljinder K. , Friar Simon , Roobol Joanne , Plumbridge Jacqueline A. , Blomfield Ian C. 
Published: January 2007

SummaryExpression of the FimB recombinase, and hence the OFF‐to‐ON switching of type 1 fimbriation in Escherichia coli, is inhibited by sialic acid (Neu5Ac) and by GlcNAc. NanR (Neu5Ac‐responsive) and NagC (GlcNAc‐6P‐responsive) activate fimB expression by binding to operators (ONR and ONC1 respectively) located more than 600 bp upstream of the fimB promoter within the large (1.4 kb) nanC‐fimB intergenic region. Here it is demonstrated that NagC binding to a second site (ONC2), located 212 bp closer to fimB, also controls fimB expression, and that integration host factor (IHF), which binds midway between ONC1 and ONC2, facilitates NagC binding to its two operator sites. In contrast, IHF does not enhance the ability of NanR to activate fimB expression in the wild‐type background. Neither sequences up to 820 bp upstream of ONR, nor those 270 bp downstream of ONC2, are required for activation by NanR and NagC. However, placing the NanR, IHF and NagC binding sites closer to the fimB promoter enhances the ability of the regulators to activate fimB expression. These results support a refined model for how two potentially key indicators of host inflammation, Neu5Ac and GlcNAc, regulate type 1 fimbriation.
Loss of a conserved 7‐methylguanosine modification in 16S rRNA confers low‐level streptomycin resistance in bacteria
Authors: Okamoto Susumu , Tamaru Aki , Nakajima Chie , Nishimura Kenji , Tanaka Yukinori , Tokuyama Shinji , Suzuki Yasuhiko , Ochi Kozo 
Published: January 2007

SummaryStreptomycin has been an important drug for the treatment of tuberculosis since its discovery in 1944. But numerous strains of Mycobacterium tuberculosis, the bacterial pathogen that causes tuberculosis, are now streptomycin resistant. Although such resistance is often mediated by mutations within rrs, a 16S rRNA gene or rpsL, which encodes the ribosomal protein S12, these mutations are found in a limited proportion of clinically isolated streptomycin‐resistant M. tuberculosis strains. Here we have succeeded in identifying a mutation that confers low‐level streptomycin resistance to bacteria, including M. tuberculosis. We found that mutations within the gene gidB confer low‐level streptomycin resistance and are an important cause of resistance found in 33% of resistant M. tuberculosis isolates. We further clarified that the gidB gene encodes a conserved 7‐methylguanosine (m7G) methyltransferase specific for the 16S rRNA, apparently at position G527 located in the so‐called 530 loop. Thus, we have identified gidB as a new streptomycin‐resistance locus and uncovered a resistance mechanism that is mediated by loss of a conserved m7G modification in 16S rRNA. The clinical significance of M. tuberculosis gidB mutation also is noteworthy, as gidB mutations emerge spontaneously at a high frequency of 10−6 and, once emerged, result in vigorous emergence of high‐level streptomycin‐resistant mutants at a frequency more than 2000 times greater than that seen in wild‐type strains. Further studies on the precise function of GidB may provide a basis for developing strategies to suppress pathogenic bacteria, including M. tuberculosis.
A bHLH regulatory gene in the common morning glory, Ipomoea purpurea, controls anthocyanin biosynthesis in flowers, proanthocyanidin and phytomelanin pigmentation in seeds, and seed trichome formation
Authors: Park Kyeung‐Il , Ishikawa Naoko , Morita Yasumasa , Choi Jeong‐Doo , Hoshino Atsushi , Iida Shigeru 
Published: January 2007

SummaryThe transcriptional regulators for anthocyanin pigmentation include proteins containing R2R3‐MYB domains, bHLH domains and conserved WD40 repeats, and their interactions determine the set of genes to be expressed. Spontaneous ivory seed (ivs) mutants of Ipomoea purpurea displaying pale pigmented flowers and ivory seeds are caused by insertions of DNA transposons into the bHLH2 gene that encodes a bHLH transcriptional regulator. A partial reduction in the expression of all structural genes encoding enzymes for anthocyanin biosynthesis was observed in the young flower buds of these ivs mutants. The DFR‐B and ANS transcripts were completely abolished in the ivs seed coats, whereas the early biosynthetic genes for flavonol biosynthesis remained active. The production and accumulation of both proanthocyanidin and phytomelanin pigments in the ivory seed coats were drastically reduced. Moreover, the unbranched trichomes in the ivory seeds were smaller in size and fewer in number than those in the wild‐type dark‐brown seeds, and the surface of the epidermis without trichomes in the dark‐brown seeds looked rougher, due to the protruding tangential walls, than that in the ivory seeds. Although the I. purpurea bHLH2 gene is the most closely related to the petunia AN1 gene, whose mutation is known to confer white flowers and to be deficient in acidification of their vacuoles, the vacuolar alkalization in the epidermal flower limbs of I. purpurea ivs mutants appears to occur normally. These results are discussed with regard to the function of bHLH transcriptional regulators controlling flower and seed pigmentation as well as other epidermal traits.
Nitrogen deficiency in Arabidopsis affects galactolipid composition and gene expression and results in accumulation of fatty acid phytyl esters
Authors: Gaude Nicole , Bréhélin Claire , Tischendorf Gilbert , Kessler Felix , Dörmann Peter 
Published: January 2007

SummaryNitrogen is an essential nutrient for plants because it represents a major constituent of numerous cellular compounds, including proteins, amino acids, nucleic acids and lipids. While N deprivation is known to have severe consequences for primary carbon metabolism, the effect on chloroplast lipid metabolism has not been analysed in higher plants. Nitrogen limitation in Arabidopsis led to a decrease in the chloroplast galactolipid monogalactosyldiacylglycerol (MGDG) and a concomitant increase in digalactosyldiacylglycerol (DGDG), which correlated with an elevated expression of the DGDG synthase genes DGD1 and DGD2. The amounts of triacylglycerol and free fatty acids increased during N deprivation. Furthermore, phytyl esters accumulated containing medium‐chain fatty acids (12:0, 14:0) and a large amount of hexadecatrienoic acid (16:3). Fatty acid phytyl esters were localized to chloroplasts, in particular to thylakoids and plastoglobules. Different polyunsaturated acyl groups were found in phytyl esters accumulating in Arabidopsis lipid mutants and in other plants, including 16:3 and 18:3 species. Therefore N deficiency in higher plants results in a co‐ordinated breakdown of galactolipids and chlorophyll with deposition of specific fatty acid phytyl esters in thylakoids and plastoglobules of chloroplasts.
The protective effect of rural living against atopy in Mongolia
Authors: Viinanen A. , Munhbayarlah S. , Zevgee T. , Narantsetseg L. , Naidansuren Ts. , Koskenvuo M. , Helenius H. , Terho E. O. 
Published: January 2007

Background:  Farm environment in childhood protects against atopy. We investigated in a population‐based study in Mongolia the effects of rural living and migration from rural to urban areas on the risk of atopy.Methods:  The screening study data of 9453 subjects, aged 10–60 years, were used for taking the sample for the clinical study in which 869 subjects were examined. Asthma, allergic rhinoconjunctivitis and sensitization were clinically defined and their risk factors analysed by logistic regression.Results:  The risks of allergic rhinoconjunctivitis [adjusted odds ratio (OR) 0.43, 95% confidence interval (CI) 0.19–0.98] and allergic sensitization (OR 0.26, 95% CI 0.13–0.55) were the lowest in subjects living in a village from birth and intermediate in subjects who had relocated from a village to a town (OR for rhinoconjunctivitis 0.68, 95% CI 0.36–1.27, OR for sensitization 0.62, 95% CI 0.35–1.12) compared with subjects living in a town from birth. Simultaneous exposure to herd animals and dung heating decreased the risk of atopy. Keeping animals was a risk‐factor for asthma only in Ulaanbaatar city.Conclusions:  Continuing farm exposure after childhood may be important in reducing the risk of atopy.
Seven hundred and fifty‐nine (759) chances to learn: a 3‐year pilot project to analyse transfusion‐related near‐miss events in the Republic of Ireland
Authors: Lundy D. , Laspina S. , Kaplan H. , Rabin Fastman B. , Lawlor E. 
Published: January 2007

Background  The National Haemovigilance Office has collected and analysed reports on errors associated with transfusion since 2000. A 3‐year pilot research project in near‐miss event reporting commenced in November 2002.Materials and Methods  Near‐miss reports from 10 hospital sites were analysed between May 2003 and May 2005. The Medical Event Reporting System for Transfusion Medicine was used to collect and analyse the data. Root cause analysis was used to identify causes of error.Results  A total of 759 near‐miss events were reported. Near misses are occurring 18 times more frequently than adverse events causing harm. Sample collection was found to be the highest risk step in the work process and was the first site of error in 468 (62%) events. Of these, 13 (3%) involved samples taken from the wrong patient. Medical staff were frequently involved in error. The general wards and emergency department were identified as high‐risk clinical areas, in addition, 78 (10%) events occurred within the transfusion laboratory. Three specific human and two system failures were shown to have been associated with the errors identified in this study.Conclusions  This study confirms that near‐miss events occur far more frequently than adverse events causing harm. Collecting near‐miss data is an effective means of highlighting human and system failures associated with transfusion that may otherwise go unnoticed. These data can be used to identify areas where resources need to be targeted in order to prevent future harm to patients, improving the overall safety of transfusion.
Differences in expression and activity of β,β′‐carotene‐15,15′‐ oxygenase in liver and duodenum of cattle with yellow or white fat
Authors: Morales A. , González A. , Varela‐Echavarría A. , Shimada A. , Mora O. 
Published: January 2007

AbstractPasture‐fed cattle show yellow pigmentation of their fat due to β‐carotene stored in this tissue. β,β′‐Carotene‐15,15′‐oxygenase (βCO) is an enzyme expressed in different tissues, and it cleaves β‐carotene into retinal. We compared the expression and activity of βCO in duodenum and liver of cattle with pigmented or non‐pigmented fat. In the duodenum, in situ hybridizations showed expression of βCO in epithelial cells and crypts of the mucosa that was similar in animals from pigmented and non‐pigmented fat; liver showed diffuse signal at lobules, but pigmented animals showed higher signals near the portal space. Analyses by real‐time reverse‐transcription polymerase chain reaction also showed amplification of mRNA for βCO in duodenum and liver, with no difference between pigmented or non‐pigmented animals. Enzyme activity was similar in the duodenum, but pigmented animals had higher enzyme activity (p = 0.004) in liver. Cattle with pigmented fat had higher expression and activity of βCO in liver, but its level was not high enough to prevent the storage of β‐carotene in adipose tissues.
Effects of a dietary application of a yeast cell wall extract on innate and acquired immunity, on oxidative status and growth performance in weanling piglets and on the ileal epithelium in fattened pigs
Authors: Sauerwein H. , Schmitz S. , Hiss S. 
Published: January 2007

SummaryPotential immunomodulatory effects of a cell wall extract from Saccharomyces cerevisiae (Y; Antaferm MG) were tested in pigs: in trial I, 0.03% Y and in trial II 0.3% Y was used. Based on earlier observations that Y may increase feed intake, two treatment groups, Y‐a (fed ad libitum) and Y‐r (fed restrictively) were studied in comparison with a control group (C) in both trials. Y‐r received the amount of feed consumed by C. Immune status was surveyed by determining phagocytic activity and oxidative burst of neutrophils and blood concentrations of haptoglobin (Hp), and immunoglobulin (Ig) G and A. Oxidative stress was monitored by recording reactive oxygen metabolites (ROM) and total antioxidant capacity. In a third trial, fattened pigs were used for morphological and immunohistochemical studies (IgM and IgA as well as CD and CD T cells) in ileal epithelium. Pigs fed 0.03% Y for 2 weeks prior to slaughter were compared with the C group. Feed intake was identical in the Y‐a and Y‐b groups and data subsets were accordingly pooled. Treatment and time as well as treatment × time interactions were detectable for most of the parameters studied, but a distinct immunomodulatory effect of Y was not consistently identifiable and performance did not improve. In trial III, the intestinal parameters investigated were not different between Y and C.
Serological Detection of Grapevine leafroll virus 2 Using an Antiserum Developed against the Recombinant Coat Protein†
Authors: Ling K.‐S. , Zhu H.‐Y. , Petrovic N. , Gonsalves D. 
Published: January 2007

Abstract Grapevine leafroll associated virus 2 (GLRaV 2) is one of the important components in the leafroll disease complex. The coat protein gene of GLRaV 2 was cloned into a protein expression vector pMAL‐c2x and the recombinant protein, consisting of the maltose binding protein (MBP) and GLRaV 2 coat protein (CP), was expressed in Escherichia coli. The recombinant MBP‐CP was used to raise a high quality antiserum. When used in Western blot analysis, the anti‐MBP‐CP antiserum produced specific reaction to the recombinant protein as well as to the viral coat protein of GLRaV 2. In Immunosorbent electron microscopy study, the anti‐MBP‐CP antibodies strongly decorated the GLRaV 2 virions. Using the newly developed antiserum, an indirect plate‐trapped antigen enzyme‐linked immunosorbent assay method was developed and successfully implemented for virus detection. A field survey was conducted to evaluate the virus infection status by GLRaV 2 and GLRaV 3 using antibodies developed against their respective recombinant coat proteins.