bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coactivation of Vibrio vulnificus putAP operon by cAMP receptor protein and PutR through cooperative binding to overlapping sites
Authors: Lee Jeong Hyun , Choi Sang Ho 
Published: March 2006

SummaryThe cAMP receptor protein (CRP) positively regulates the expression of Vibrio vulnificus putAP genes encoding a proline dehydrogenase and a proline permease. In the present study, an open reading frame encoding PutR was identified downstream of the putAP genes and a mutational analysis revealed that the PutR protein was also involved in regulating the putAP transcription by activating Pput promoter. Although CRP acts as a primary activator and the influence of PutR on Pput is mediated by CRP, the level of Pput activity observed when PutR and CRP functioned together was greater than the sum of Pput activities achieved by each activator alone. Western blot analyses demonstrated that the cellular levels of PutR and CRP were not significantly affected by each other, indicating that PutR and CRP coactivate Pput rather than function sequentially in a regulatory cascade. Two adjacent binding sites for PutR mapped by in vitro DNase I protection assays were found to overlap the CRP binding sites and were centred −91.5 (PCBI) and −133.5 bp (PCBII) upstream of the transcription start site of Pput respectively. PutR and CRP bind to the sites cooperatively and a dissection of the role of the binding sites revealed that CRP at PCBI plays the most crucial role in the activation of Pput. Accordingly, the present results revealed that PutR and CRP coactivate the expression of Pput and exert their effect by cooperatively binding to the promoter.
Candida albicans SET1 encodes a histone 3 lysine 4 methyltransferase that contributes to the pathogenesis of invasive candidiasis
Authors: Raman Suresh Babu , Nguyen M. Hong , Zhang Zongde , Cheng Shaoji , Jia Hong Yan , Weisner Nghe , Iczkowski Kenneth , Clancy Cornelius J. 
Published: March 2006

Summary Candida albicans causes diverse mucosal and systemic diseases. Although this versatility likely depends upon carefully co‐ordinated gene expression, epigenetic regulation in C. albicans remains poorly characterized. Screening a genomic expression library, we identified C. albicans Set1p as an immunogenic protein with homology to a lysine histone methyltransferase of Saccharomyces cerevisiae. In this study, we demonstrated that total immunoglobulin, IgG and IgM titers against a unique Set1p N‐terminal fragment were significantly higher among patients with disseminated candidiasis (DC) or oropharyngeal candidiasis than controls. Disruption of SET1 resulted in complete loss of methylation of histone 3 at lysine residue 4, hyperfilamentous growth under embedded conditions, less negative cell surface charges and diminished adherence to epithelial cells, effects that were reversed upon gene re‐insertion at a disrupted locus. During murine DC, the null mutant was associated with prolonged survival and lower tissue burdens. Taken together, our findings suggest that SET1 regulates multiple processes important to the pathogenesis of candidiasis. The Set1p N‐terminal fragment does not exhibit significant homology to eukaryotic or microbial proteins, and might represent a novel therapeutic, preventive or diagnostic target.
Hierarchical involvement of various GGDEF domain proteins in rdar morphotype development of Salmonella enterica serovar Typhimurium
Authors: Kader Abdul , Simm Roger , Gerstel Ulrich , Morr Michael , Römling Ute 
Published: March 2006

SummaryGGDEF and EAL domain proteins are involved in the turnover of the novel secondary messenger cyclic‐di(3′→5′)‐guanylic acid (c‐di‐GMP) in many bacteria. In this work the role of the 12 GGDEF domain proteins encoded by the Salmonella enterica serovar Typhimurium (S. Typhimurium) chromosome in rdar morphotype development was investigated. Previously, it was shown that the GGDEF domain protein AdrA activated the biosynthesis of cellulose by production of c‐di‐GMP. Enhancement of the c‐di‐GMP levels by overexpression of the GGDEF domain protein AdrA did lead to the activation of curli fimbriae biosynthesis through the elevated expression of CsgD and CsgA. Although knock‐out of the chromosomal copy of adrA influenced CsgA expression, CsgD expression was not altered, although more than half of the total cellular c‐di‐GMP was produced by AdrA at 16 h of growth. On the other hand, chromosomally encoded GGDEF–EAL domain proteins STM2123 and STM3388 were required to additively activate CsgD expression on a transcriptional and post‐transcriptional level. Enhanced c‐di‐GMP levels did overcome temperature regulation of rdar morphotype expression by activation of curli fimbriae as well as cellulose biosynthesis through CsgD expression. Thus in the regulatory cascade leading to rdar morphotype expression c‐di‐GMP activates several subsequent steps in the network.
What is life? The paradigm of DNA and protein cooperation at high local concentrations
Authors: Müller‐Hill Benno 
Published: March 2006

SummaryMany chemical reactions need high concentrations of the molecules involved in order to work efficiently. It is usually impossible for the cell to achieve the necessary high concentrations of all relevant molecules in unconfined solutions but this becomes possible if the high concentration is restricted around a relevant molecule. High local concentrations of interacting molecules have been observed many times in many different biological systems. The examples of Lac and Lambda repressors of Escherichia coli are presented and discussed here as useful paradigms of mechanisms for achieving high local concentrations of interacting protein protomers.
Flk prevents premature secretion of the anti‐σ factor FlgM into the periplasm
Authors: Aldridge Phillip , Karlinsey Joyce E. , Becker Eric , Chevance Fabienne F.V. , Hughes Kelly T. 
Published: March 2006

SummaryThe flk locus of Salmonella typhimurium was identified as a regulator of flagellar gene expression in strains defective in P‐ and l‐ring formation. Flk acts as a regulator of flagellar gene expression by modulating the protein levels of the anti‐σ28 factor FlgM. Evidence is presented which suggests that Flk is a cytoplasmic‐facing protein anchored to the inner membrane by a single, C‐terminal transmembrane‐spanning domain (TMS). The specific amino acid sequence of the TMS is not essential for Flk activity, but membrane anchoring is essential. Membrane fractionation and visualization of protein fusions of green fluorescent protein derivatives to Flk suggested that the Flk protein is present in the membrane as punctate spots in number that are much greater than the number of flagellar basal structures. The turnover of the anti‐σ28 factor FlgM was increased in flk mutant strains. Using FlgM–β‐lactamase fusions we show the increased turnover of FlgM in flk null mutations is due to FlgM secretion into the periplasm where it is degraded. Our data suggest that Flk inhibits FlgM secretion by acting as a braking system for the flagellar‐associated type III secretion system. A model is presented to explain a role for Flk in flagellar assembly and gene regulatory processes.
In vitro‐Generated Viral Double‐Stranded RNA in Contrast to Polyinosinic : Polycytidylic Acid Induces Interferon‐α in Human Plasmacytoid Dendritic Cells
Authors: Löseke S. , Grage‐Griebenow E. , Heine H. , Wagner A. , Akira S. , Bauer S. , Bufe A. 
Published: March 2006

AbstractDouble‐stranded RNA (dsRNA) arises in the cytoplasm during viral replication and was shown to participate in the interferon (IFN)‐α induction process. Besides the intracellular recognition, released dsRNA from dying, infected cells can function as a pathogen‐associated molecular pattern (PAMP) for the innate immune system. In the present study, in vitro‐generated dsRNA fragments of genomic sequences of Newcastle disease virus were used to induce IFN‐α release in human peripheral blood mononuclear cells (PBMC), in immature myeloid dendritic cells (mDC) and in immature plasmacytoid DC (pDC). The extracellular administration of dsRNA fragments but not the application of the corresponding single‐stranded RNA (ssRNA) strands led to an IFN‐α production in PBMC. The synthetic dsRNA analogue polyinosinic acid : polycytidylic acid [Poly(I : C)] could only stimulate IFN‐α production in enriched mDC but not in pDC. In contrast, dsRNA fragments induced IFN‐α only in pDC. Complexation of dsRNA fragments with transfection reagents increased the efficiency of IFN‐α induction and commuted ssRNA molecules into IFN‐α inducers. However, stimulation of in vitro‐generated murine Toll‐like receptor 7 (TLR7) knockout DC and human TLR‐transfected HEK293 cells with dsRNA fragments gave no evidences for the involvement of pDC‐specific TLR7 or TLR9 in the observed IFN‐α induction.
Modelling the long‐term fluvial erosion of the River Somme during the last million years
Authors: Gargani J. , Stab O. , Cojan I. , Brulhet J. 
Published: March 2006

AbstractA process‐based model that simulates fluvial erosion in the River Somme Valley over the last million years is presented here. The model takes into account lithology and climatic influences and allows the simulating of undercapacity and overcapacity sediment transport behaviour. The model has been calibrated to a family of terraces within the River Somme Valley. When matched to this field data, simulation trials suggest that bedrock incision occurred principally from 120 to 60–40 kyr during the last climatic cycle and before the last glaciation. The impact of a progressive tectonic uplift (c. 60 m over c. 1 million years) on the River Somme has also been studied here. Extended over a longer period of time, the simulations suggest that 1 million years ago the profile of the River Somme had a lower slope gradient than today, with little relief throughout the Paris Basin.
Multiple causes of Earth's earliest global glaciation
Authors: Melezhik Victor A. 
Published: March 2006

AbstractIn the context of Earth System evolution, the causal factors driving the Palaeoproterozoic Huronian global glaciations occupy a central position. The rise of O2 at 2320 Ma, which eliminated most of the methane, was not apparently a single cause triggering the glaciation. At c. 2450 Ma mantle‐plume‐driven continental uplifts led to the emplacement of voluminous continental flood‐basalts in low latitudes that were subsequently dissected by rifting. Major topographical features and continental drainage patterns were most likely similar to those in younger continental flood‐basalt provinces and would have enabled deep weathering and erosion of extensive basalt‐covered continental areas. Intense consumption of atmospheric CO2 by silicate weathering of fresh basaltic surfaces would have been further amplified by a constant organic carbon burial rate. These factors, similar to those of younger glacial periods, in combination with the diminished CH4 greenhouse led to an onset of global cooling at the million‐year timescale.
The Arabidopsis co‐expression tool (act): a WWW‐based tool and database for microarray‐based gene expression analysis
Authors: Jen Chih‐Hung , Manfield Iain W. , Michalopoulos Ioannis , Pinney John W. , Willats William G.T. , Gilmartin Philip M. , Westhead David R. 
Published: March 2006

SummaryWe present a new WWW‐based tool for plant gene analysis, the Arabidopsis Co‐Expression Tool (act), based on a large Arabidopsis thaliana microarray data set obtained from the Nottingham Arabidopsis Stock Centre. The co‐expression analysis tool allows users to identify genes whose expression patterns are correlated across selected experiments or the complete data set. Results are accompanied by estimates of the statistical significance of the correlation relationships, expressed as probability (P) and expectation (E) values. Additionally, highly ranked genes on a correlation list can be examined using the novel clique finder tool to determine the sets of genes most likely to be regulated in a similar manner. In combination, these tools offer three levels of analysis: creation of correlation lists of co‐expressed genes, refinement of these lists using two‐dimensional scatter plots, and dissection into cliques of co‐regulated genes. We illustrate the applications of the software by analysing genes encoding functionally related proteins, as well as pathways involved in plant responses to environmental stimuli. These analyses demonstrate novel biological relationships underlying the observed gene co‐expression patterns. To demonstrate the ability of the software to develop testable hypotheses on gene function within a defined biological process we have used the example of cell wall biosynthesis genes. The resource is freely available at http://www.arabidopsis.leeds.ac.uk/ACT/
A spatiotemporal analysis of enzymatic activities associated with carbon metabolism in wild‐type and mutant embryos of Arabidopsis using in situ histochemistry
Authors: Baud Sébastien , Graham Ian A. 
Published: March 2006

SummaryArabidopsis as a molecular genetic model offers many advantages for the study of seed development, but these do not extend to biochemical and enzymatic studies, which are often compromised by the limited amount of material available from the small developing embryos. A set of assays based on the coupling of an enzymatic reaction to the reduction of NAD, NADP or FAD, and subsequent reduction and precipitation of a tetrazolium salt, have been adapted to investigate 18 enzyme activities associated with carbon metabolism in developing Arabidopsis embryos. The use of organelle‐specific marker enzymes demonstrates the utility of the method for detection of activities in mitochondria, plastids and peroxisomes as well as the cytosol. The temporal staining patterns obtained allow classification of the activities into three main categories based on whether they peak in the early, intermediate or late stages of maturation. An interesting switch from ATP to pyrophosphate consuming pathways occurs at the onset of the maturation phase, which involves key steps in primary carbon metabolism such as phosphofructokinase. This spatiotemporal characterization of carbon metabolism has also been applied to various mutants disrupted in embryo development including gnom (gn), acetyl‐CoA carboxylase1 (acc1), schlepperless (slp), and wrinkled1 (wri1). The data obtained demonstrate that the extent to which carbon metabolism is affected in mutants is not necessarily correlated to the severity of the mutation considered. Through the advanced characterization of trehalose‐6‐P synthase1 (tps1) embryos, this approach finally provides new insight into the regulatory role played by trehalose metabolism in embryo development.
CYP707A3, a major ABA 8′‐hydroxylase involved in dehydration and rehydration response in Arabidopsis thaliana
Authors: Umezawa Taishi , Okamoto Masanori , Kushiro Tetsuo , Nambara Eiji , Oono Youko , Seki Motoaki , Kobayashi Masatomo , Koshiba Tomokazu , Kamiya Yuji , Shinozaki Kazuo 
Published: March 2006

SummaryAbscisic acid (ABA) catabolism is one of the determinants of endogenous ABA levels affecting numerous aspects of plant growth and abiotic stress responses. The major ABA catabolic pathway is triggered by ABA 8′‐hydroxylation catalysed by the cytochrome P450 CYP707A family. Among four members of Arabidopsis CYP707As, the expression of CYP707A3 was most highly induced in response to both dehydration and subsequent rehydration. A T‐DNA insertional cyp707a3‐1 mutant contained higher ABA levels in turgid plants, which showed a reduced transpiration rate and hypersensitivity to exogenous ABA during early seedling growth. On dehydration, the cyp707a3‐1 mutant accumulated a higher amount of stress‐induced ABA than the wild type, an event that occurred relatively later and was coincident with slow drought induction of CYP707A3. The cyp707a3 mutant plants exhibited both exaggerated ABA‐inducible gene expression and enhanced drought tolerance. Conversely, constitutive expression of CYP707A3 relieved growth retardation by ABA, increased transpiration, and a reduction of endogenous ABA in both turgid and dehydrated plants. Taken together, our results indicate that CYP707A3 plays an important role in determining threshold levels of ABA during dehydration and after rehydration.
HLA‐E and immunobiology of pregnancy
Authors: Tripathi P. , Naik S. , Agrawal S. 
Published: March 2006

AbstractRecently, it has been suggested that non‐classical antigens such as human leukocyte antigen (HLA)‐G and HLA‐E may interact with KIR receptors of NK cells which results into downregulation of immune response and helps in the maintenance of pregnancy. In the present study, we have investigated HLA‐E polymorphism in normal fertile women and recurrent spontaneous aborters to assess the effect of HLA‐E alleles on the success of pregnancy. Allele E*0101 was found to be significantly higher in patients with recurrent spontaneous abortion (χ2 = 4.097 and P = 0.0430). Differential expression, peptide affinity, and stability of E*0101 may be one of the reasons.
Antigen‐presenting cells expressing glutamate decarboxylase 67 were identified as epithelial cells in glutamate decarboxylase 67‐GFP knock‐in mouse thymus
Authors: Maemura K. , Yanagawa Y. , Obata K. , Dohi T. , Egashira Y. , Shibayama Y. , Watanabe M. 
Published: March 2006

AbstractGlutamate decarboxylase (GAD), which has two isoforms, GAD65, and GAD67, is responsible for synthesis of the major inhibitory neurotransmitter, γ‐aminobutyric acid. GAD is expressed predominantly in the central nervous system; recent reports suggest that GAD is also expressed in non‐neuronal organs including the pancreas. In the pancreatic islets, GAD serves as one of the autoantigens in type I diabetes mellitus. Recent flow cytometric analyses have shown that a variety of self‐antigens, including GAD, are ectopically transcribed and expressed in particular cell populations of the thymus, although consensus concerning the cellular phenotype has not been obtained. The aim of this study was to clarify the localization and cellular phenotype of GAD67‐expressing cells in the thymus at a cellular level with a novel approach using GAD67‐green fluorescent protein (GFP) knock‐in mice, in which GFP is expressed specifically in GAD67‐positive cells. GFP‐positive cells were detected in the thymic medulla and were identified as epithelial cells by immunohistochemistry. Almost all GFP‐positive cells were positive for major histocompatibility complex (MHC) class II antigen staining and were positive for both cytokeratin and Ulex Europaeus Agglutinin I, markers of medullary thymic epithelial cells, but were negative for CD11c, Gr‐1, and CD45, markers of dendritic cells, macrophages, and B‐lymphocytes, respectively.
HLA‐B27 testing in Thai patients using the PCR‐SSP technique
Authors: Nathalang O. , Tantimavanich S. , Nillakupt K. , Arnutti P. , Jaruchaimontree C. 
Published: March 2006

AbstractWe develop the HLA‐B27 test kit using the PCR‐SSP technique. Five hundred forty blood samples were tested for HLA‐B27 by microlymphocytotoxicity test (LCT) and PCR‐SSP. It was found that 127 (23.5%) and 134 (24.8%) of these samples were positive for HLA‐B27 by LCT and PCR‐SSP, respectively. The sensitivity and specificity of the PCR‐SSP were 94.8 and 100%, respectively, when using LCT as the standard method. The PCR‐SSP positive predictive value was 100%, negative predictive value was 98.3%, and a concordance rate of 98.7%. This study shows that the PCR‐SSP is simple, convenient, and a more cost‐effective in‐house test kit.
Regulation of MHC class II expression, a unique regulatory system identified by the study of a primary immunodeficiency disease
Authors: Krawczyk M. , Reith W. 
Published: March 2006

AbstractMajor histocompatibility complex class II (MHC‐II) molecules are of central importance for adaptive immunity. Defective MHC‐II expression causes a severe immunodeficiency disease called bare lymphocyte syndrome (BLS). Studies of the molecular defects underlying BLS have been pivotal for characterization of the regulatory system controlling the transcription of MHC‐II genes. The precisely controlled pattern of MHC‐II gene expression is achieved by a very peculiar and highly specialized molecular machinery that involves the interplay between ubiquitous DNA‐binding transcription factors and a highly unusual, tightly regulated, non‐DNA‐binding coactivator called the MHC class II transactivator (CIITA). CIITA single handedly coordinates practically all aspects of MHC‐II gene regulation and has therefore been dubbed the master controller of MHC‐II expression. Several of the unusual features of the MHC‐II regulatory system may be a consequence of the fact that CIITA originated from an ancient family of cytoplasmic proteins involved in inflammation and innate immunity. The function of CIITA in transcriptional regulation of MHC‐II genes could thus be a recent acquisition by an ancestral protein having a role in an unrelated system.
Aetiological factors related to a positive direct antiglobulin test result in human immunodeficiency virus‐infected patients
Authors: Lai M. , D’Onofrio G. , Visconti E. , Tamburrini E. , Cauda R. , Leone G. 
Published: March 2006

Background and Objectives The aim of this study was to examine the clinical importance and causes of a positive result in the direct antiglobulin test (DAT) in human immunodeficiency virus‐infected (HIV+) patients. We therefore studied haematological parameters in outpatient samples, and also analysed the impact of highly active anti‐retroviral therapy (HAART) on the DAT results.Study Design and Methods Haematological parameters, clinical stages, chemo‐antibiotic treatments and HAART treatment were studied to determine any relationships with DAT results in 115 consecutive HIV+patients.Results Significantly lower haemoglobin (Hb) levels were detected in patients with HIV who had a positive DAT result. Hepatitis C virus (HCV) co‐infection (odds ratio 2·529) and trimethoprim‐suphamethoxazfole (TMP‐SMX) prophylaxis (odds ratio 3·751) had a significant association with DAT positivity. Patients receiving HAART were less likely to have a positive DAT [odds ratio (OR) 0·383;P = 0·035]. Among the patients treated with TMP‐SMX, those with a positive DAT had lower Hb levels (11·9 g/dl) than those with a negative DAT (14·2 g/dl;P = 0·04). HCV antibody positivity and TMP‐SMX prophylaxis showed a cumulative effect on positive DATs (OR 4·533). The surface exploratory analysis indicated the distribution of the positive DATs in relationship with the CD4+count and Hb levels.Conclusions Significantly lower Hb levels were detected in DAT‐positive HIV+patients. HCV co‐infection and TMP‐SMX prophylaxis appear to confer an increased risk of DAT positivity. The presence of red blood cell autoantibodies may be associated with anaemia in HIV disease in the absence of overt haemolysis.