bluuebunny/crossref_metadata_2025_split huggingface dataset:
Calcineurin-Responsive Zinc Finger Transcription Factor CRZ1 of
Botrytis cinerea
Is Required for Growth, Development, and Full Virulence on Bean Plants
Authors: Schumacher Julia , de Larrinoa Inigo F. , Tudzynski Bettina 
Published: February 2008

ABSTRACT

Recently, we showed that the α subunit BCG1 of a heterotrimeric G protein is an upstream activator of the Ca
2+
/calmodulin-dependent phosphatase calcineurin in the gray mold fungus
Botrytis cinerea
. To identify the transcription factor acting downstream of BCG1 and calcineurin, we cloned the gene encoding the
B. cinerea
homologue of CRZ1 (“CRaZy,”
c
alcineurin-
r
esponsive
z
inc finger transcription factor), the mediator of calcineurin function in yeast. BcCRZ1 is able to partially complement the corresponding
Saccharomyces cerevisiae
mutant, and the subcellular localization of the green fluorescent protein-BcCRZ1 fusion product in yeast cells depends on the calcium level and calcineurin activity. Bc
crz1
deletion mutants are not able to grow on minimal media and grow slowly on media containing plant extracts. Hyphal morphology, conidiation, and sclerotium formation are impaired. The cell wall and membrane integrity, stress response (extreme pH, H
2
O
2
, Ca
2+
, Li
+
), and ability of the hyphae to penetrate the intact plant surface are affected in the mutants. However, BcCRZ1 is almost dispensable for the conidium-derived infection of bean plants. The addition of Mg
2+
restores the growth rate, conidiation, and penetration and improves the cell wall integrity but has no impact on sclerotium formation or hypersensitivity to Ca
2+
and H
2
O
2
. The expression of a set of recently identified BCG1- and calcineurin-dependent genes is also affected in ΔBc
crz1
mutants, confirming that this transcription factor acts downstream of calcineurin in
B. cinerea
. Since the Bc
crz1
mutants still respond to calcineurin inhibitors, we conclude that BcCRZ1 is not the only target of calcineurin.
Creation of a Chloroplast Microsatellite Reporter for Detection of Replication Slippage in
Chlamydomonas reinhardtii
Authors: GuhaMajumdar Monica , Dawson-Baglien Ethan , Sears Barbara B. 
Published: February 2008

ABSTRACT

Microsatellites are composed of short tandem direct repeats; deletions or duplications of those repeats through the process of replication slippage result in microsatellite instability relative to other genomic loci. Variation in repeat number occurs so frequently that microsatellites can be used for genotyping and forensic analysis. However, an accurate assessment of the rates of change can be difficult because the presence of many repeats makes it difficult to determine whether changes have occurred through single or multiple events. The current study was undertaken to experimentally assess the rates of replication slippage that occur in vivo in the chloroplast DNA of
Chlamydomonas reinhardtii
. A reporter construct was created in which a stretch of AAAG repeats was inserted into a functional gene to allow changes to be observed when they occurred at the synthetic microsatellite. Restoration of the reading frame occurred through replication slippage in 15 of every million viable cells. Since only one-third of the potential insertion/deletion events would restore the reading frame, the frequency of change could be deduced to be 4.5 × 10
−5
. Analysis of the slippage events showed that template slippage was the primary event, resulting in deletions rather than duplications. These findings contrasted with events observed in
Escherichia coli
during maintenance of the plasmid, where duplications were the rule.
Plasmid Transfer via Transduction from
Streptococcus thermophilus
to
Lactococcus lactis
Authors: Ammann Andreas , Neve Horst , Geis Arnold , Heller Knut J. 
Published: February 2008

ABSTRACT

Using
Streptococcus thermophilus
phages, plasmid transduction in
Lactococcus lactis
was demonstrated. The transduction frequencies were 4 orders of magnitude lower in
L. lactis
than in
S. thermophilus
. These results are the first evidence that there is phage-mediated direct transfer of DNA from
S. thermophilus
to
L. lactis
. The implications of these results for phage evolution are discussed.
Altering the Ratio of Phenazines inPseudomonas chlororaphis(aureofaciens) Strain 30-84: Effects on Biofilm Formation and Pathogen Inhibition
Authors: Maddula V. S. R. K. , Pierson E. A. , Pierson L. S. 
Published: February 2008

ABSTRACTPseudomonas chlororaphisstrain 30-84 is a plant-beneficial bacterium that is able to control take-all disease of wheat caused by the fungal pathogenGaeumannomyces graminisvar. tritici. The production of phenazines (PZs) by strain 30-84 is the primary mechanism of pathogen inhibition and contributes to the persistence of strain 30-84 in the rhizosphere. PZ production is regulated in part by the PhzR/PhzI quorum-sensing (QS) system. Previous flow cell analyses demonstrated that QS and PZs are involved in biofilm formation inP. chlororaphis(V. S. R. K. Maddula, Z. Zhang, E. A. Pierson, and L. S. Pierson III, Microb. Ecol. 52:289-301, 2006).P. chlororaphisproduces mainly two PZs, phenazine-1-carboxylic acid (PCA) and 2-hydroxy-PCA (2-OH-PCA). In the present study, we examined the effect of altering the ratio of PZs produced byP. chlororaphison biofilm formation and pathogen inhibition. As part of this study, we generated derivatives of strain 30-84 that produced only PCA or overproduced 2-OH-PCA. Using flow cell assays, we found that these PZ-altered derivatives of strain 30-84 differed from the wild type in initial attachment, mature biofilm architecture, and dispersal from biofilms. For example, increased 2-OH-PCA production promoted initial attachment and altered the three-dimensional structure of the mature biofilm relative to the wild type. Additionally, both alterations promoted thicker biofilm development and lowered dispersal rates compared to the wild type. The PZ-altered derivatives of strain 30-84 also differed in their ability to inhibit the fungal pathogenG. graminisvar. tritici. Loss of 2-OH-PCA resulted in a significant reduction in the inhibition ofG. graminisvar. tritici. Our findings suggest that alterations in the ratios of antibiotic secondary metabolites synthesized by an organism may have complex and wide-ranging effects on its biology.
The HopZ Family ofPseudomonas syringaeType III Effectors Require Myristoylation for Virulence and Avirulence Functions inArabidopsis thaliana
Authors: Lewis Jennifer D. , Abada Wasan , Ma Wenbo , Guttman David S. , Desveaux Darrell 
Published: February 2008

ABSTRACTPseudomonas syringaeutilizes the type III secretion system to translocate effector proteins into plant cells, where they can contribute to the pathogen's ability to infect and cause disease. Recognition of these effectors by resistance proteins induces defense responses that typically include a programmed cell death reaction called the hypersensitive response. The YopJ/HopZ family of type III effector proteins is a common family of effector proteins found in animal- and plant-pathogenic bacteria. The HopZ family inP. syringaeincludes HopZ1aPsyA2, HopZ1bPgyUnB647, HopZ1cPmaE54326, HopZ2Ppi895Aand HopZ3PsyB728a. HopZ1a is predicted to be most similar to the ancestralhopZallele and causes a hypersensitive response in multiple plant species, includingArabidopsis thaliana. Therefore, it has been proposed that host defense responses have driven the diversification of this effector family. In this study, we further characterized the hypersensitive response induced by HopZ1a and demonstrated that it is not dependent on known resistance genes. Further, we identified a novel virulence function for HopZ2 that requires the catalytic cysteine demonstrated to be required for protease activity. Sequence analysis of the HopZ family revealed the presence of a predicted myristoylation sequence in all members except HopZ3. We demonstrated that the myristoylation site is required for membrane localization of this effector family and contributes to the virulence and avirulence activities of HopZ2 and HopZ1a, respectively. This paper provides insight into the selective pressures driving virulence protein evolution by describing a detailed functional characterization of the diverse HopZ family of type III effectors with the model plantArabidopsis.
Identification of a Second Lipopolysaccharide inPorphyromonas gingivalisW50
Authors: Rangarajan Minnie , Aduse-Opoku Joseph , Paramonov Nikolay , Hashim Ahmed , Bostanci Nagihan , Fraser Owen P. , Tarelli Edward , Curtis Michael A. 
Published: February 2008

ABSTRACTWe previously described a cell surface anionic polysaccharide (APS) inPorphyromonas gingivalisthat is required for cell integrity and serum resistance. APS is a phosphorylated branched mannan that shares a common epitope with posttranslational additions to some of the Arg-gingipains. This study aimed to determine the mechanism of anchoring of APS to the surface ofP. gingivalis. APS was purified on concanavalin A affinity columns to minimize the loss of the anchoring system that occurred during chemical extraction.1H nuclear magnetic resonance spectroscopy of the lectin-purified APS confirmed the previous structure but also revealed additional signals that suggested the presence of a lipid A. This was confirmed by fatty acid analysis of the APS and matrix-assisted laser desorption ionization-time of flight mass spectrometry of the lipid A released by treatment with sodium acetate buffer (pH 4.5). Hence,P. gingivalissynthesizes two distinct lipopolysaccharide (LPS) macromolecules containing different glycan repeating units: O-LPS (with O-antigen tetrasaccharide repeating units) and A-LPS (with APS repeating units). Nonphosphorylated penta-acylated and nonphosphorylated tetra-acylated species were detected in lipid A fromP. gingivalistotal LPS and in lipid A from A-LPS. These lipid A species were unique to lipid A derived from A-LPS. Biological assays demonstrated a reduced proinflammatory activity of A-LPS compared to that of total LPS. Inactivation of a putative O-antigen ligase (waaL) at PG1051, which is required for the final step of LPS biosynthesis, abolished the linkage of both the O antigen and APS to the lipid A core of O-LPS and A-LPS, respectively, suggesting that WaaL inP. gingivalishas dual specificity for both O-antigen and APS repeating units.
Genome Sequence of
Thermofilum pendens
Reveals an Exceptional Loss of Biosynthetic Pathways without Genome Reduction
Authors: Anderson Iain , Rodriguez Jason , Susanti Dwi , Porat Iris , Reich Claudia , Ulrich Luke E. , Elkins James G. , Mavromatis Kostas , Lykidis Athanasios , Kim Edwin , Thompson Linda S. , Nolan Matt , Land Miriam , Copeland Alex , Lapidus Alla , Lucas Susan , Detter Chris , Zhulin Igor B. , Olsen Gary J. , Whitman William , Mukhopadhyay Biswarup , Bristow James , Kyrpides Nikos 
Published: February 2008

ABSTRACT

We report the complete genome of
Thermofilum pendens
, a deeply branching, hyperthermophilic member of the order
Thermoproteales
in the archaeal kingdom
Crenarchaeota. T. pendens
is a sulfur-dependent, anaerobic heterotroph isolated from a solfatara in Iceland. It is an extracellular commensal, requiring an extract of
Thermoproteus tenax
for growth, and the genome sequence reveals that biosynthetic pathways for purines, most amino acids, and most cofactors are absent. In fact,
T. pendens
has fewer biosynthetic enzymes than obligate intracellular parasites, although it does not display other features that are common among obligate parasites and thus does not appear to be in the process of becoming a parasite. It appears that
T. pendens
has adapted to life in an environment rich in nutrients.
T. pendens
was known previously to utilize peptides as an energy source, but the genome revealed a substantial ability to grow on carbohydrates.
T. pendens
is the first crenarchaeote and only the second archaeon found to have a transporter of the phosphotransferase system. In addition to fermentation,
T. pendens
may obtain energy from sulfur reduction with hydrogen and formate as electron donors. It may also be capable of sulfur-independent growth on formate with formate hydrogen lyase. Additional novel features are the presence of a monomethylamine:corrinoid methyltransferase, the first time that this enzyme has been found outside the
Methanosarcinales
, and the presence of a presenilin-related protein. The predicted highly expressed proteins do not include proteins encoded by housekeeping genes and instead include ABC transporters for carbohydrates and peptides and clustered regularly interspaced short palindromic repeat-associated proteins.
Digressing with Aristotle: Hieronymus Dandinus' De corpore animato (1610) and the Expansion of Late Aristotelian Philosophy
Authors: Edwards Michael 
Published: February 2008

AbstractEarly modern scholastic and Aristotelian philosophy is now a growing area of study. However, little attention has been paid to the structure and form of late Aristotelian texts, partly because they have often been seen as baroque and excessively intricate in construction. This article examines the role of structural and stylistic issues in the De anima commentary of the Jesuit author Hieronymus Dandinus (1554-1634), focusing particularly on the techniques he used to integrate knowledge from other disciplines and expand the familiar commentary format. It argues that taking these issues seriously has important implications for our understanding of the dynamics of reading Aristotle in the early modern period.
Autoimmune disorders and risk of non-Hodgkin lymphoma subtypes: a pooled analysis within the InterLymph Consortium
Authors: Ekström Smedby Karin , Vajdic Claire M. , Falster Michael , Engels Eric A. , Martínez-Maza Otoniel , Turner Jennifer , Hjalgrim Henrik , Vineis Paolo , Seniori Costantini Adele , Bracci Paige M. , Holly Elizabeth A. , Willett Eleanor , Spinelli John J. , La Vecchia Carlo , Zheng Tongzhang , Becker Nikolaus , De Sanjosé Silvia , Chiu Brian C.-H. , Dal Maso Luigino , Cocco Pierluigi , Maynadié Marc , Foretova Lenka , Staines Anthony , Brennan Paul , Davis Scott , Severson Richard , Cerhan James R. , Breen Elizabeth C. , Birmann Brenda , Grulich Andrew E. , Cozen Wendy 
Published: February 2008

Abstract
Some autoimmune disorders are increasingly recognized as risk factors for non-Hodgkin lymphoma (NHL) overall, but large-scale systematic assessments of risk of NHL subtypes are lacking. We performed a pooled analysis of self-reported autoimmune conditions and risk of NHL and subtypes, including 29 423 participants in 12 case-control studies. We computed pooled odds ratios (OR) and 95% confidence intervals (CI) in a joint fixed-effects model. Sjögren syndrome was associated with a 6.5-fold increased risk of NHL, a 1000-fold increased risk of parotid gland marginal zone lymphoma (OR = 996; 95% CI, 216-4596), and with diffuse large B-cell and follicular lymphomas. Systemic lupus erythematosus was associated with a 2.7-fold increased risk of NHL and with diffuse large B-cell and marginal zone lymphomas. Hemolytic anemia was associated with diffuse large B-cell NHL. T-cell NHL risk was increased for patients with celiac disease and psoriasis. Results for rheumatoid arthritis were heterogeneous between studies. Inflammatory bowel disorders, type 1 diabetes, sarcoidosis, pernicious anemia, and multiple sclerosis were not associated with risk of NHL or subtypes. Thus, specific autoimmune disorders are associated with NHL risk beyond the development of rare NHL subtypes in affected organs. The pattern of associations with NHL subtypes may harbor clues to lymphomagenesis.
Expression of the "stem cell marker" CD133 in pancreas and pancreatic ductal adenocarcinomas
Authors: Immervoll Heike , Hoem Dag , Sakariassen Per Øystein , Steffensen Ole Johnny , Molven Anders 
Published: February 2008

Abstract

Background
It has been suggested that a small population of cells with unique self-renewal properties and malignant potential exists in solid tumors. Such "cancer stem cells" have been isolated by flow cytometry, followed by xenograft studies of their tumor-initiating properties. A frequently used sorting marker in these experiments is the cell surface protein CD133 (prominin-1). The aim of this work was to examine the distribution of CD133 in pancreatic exocrine cancer.

Methods
Fifty-one cases of pancreatic ductal adenocarcinomas were clinically and histopathologically evaluated, and immunohistochemically investigated for expression of CD133, cytokeratin 19 and chromogranin A. The results were interpreted on the background of CD133 expression in normal pancreas and other normal and malignant human tissues.

Results
CD133 positivity could not be related to a specific embryonic layer of organ origin and was seen mainly at the apical/endoluminal surface of non-squamous, glandular epithelia and of malignant cells in ductal arrangement. Cytoplasmic CD133 staining was observed in some non-epithelial malignancies. In the pancreas, we found CD133 expressed on the apical membrane of ductal cells. In a small subset of ductal cells and in cells in centroacinar position, we also observed expression in the cytoplasm. Pancreatic ductal adenocarcinomas showed a varying degree of apical cell surface CD133 expression, and cytoplasmic staining in a few tumor cells was noted. There was no correlation between the level of CD133 expression and patient survival.

Conclusion
Neither in the pancreas nor in the other investigated organs can CD133 membrane expression alone be a criterion for "stemness". However, there was an interesting difference in subcellular localization with a minor cell population in normal and malignant pancreatic tissue showing cytoplasmic expression. Moreover, since CD133 was expressed in shed ductal cells of pancreatic tumors and was found on the surface of tumor cells in vessels, this molecule may have a potential as clinical marker in patients suffering from pancreatic cancer.
Activation of cyclic-AMP response element binding protein contributes to adiponectin-stimulated interleukin-10 expression in raw 264.7 macrophages
Authors: Park Pil-hoon , Huang Honglian , McMullen Megan R , Bryan Kathryn , Nagy Laura E 
Published: February 2008

AbstractAdiponectin, an adipokine predominantly secreted from adipose tissue, has potent anti-inflammatory properties. Although the mechanisms for the anti-inflammatory properties of adiponectin are not well understood, recent evidence suggests that increased production of interleukin-10 (IL-10), a potent immunomodulatory cytokine, is involved in the anti-inflammatory actions of adiponectin. Globular adiponectin (gAcrp) increased IL-10 promoter activity and IL-10 mRNA accumulation in RAW 264.7 macrophages. Deletion of the sequences from −416 and −369 in the IL-10 promoter, containing a cyclic AMP-response element (CRE), decreased gAcrp-induced IL-10 promoter activation. Treatment of RAW 264.7 macrophages with gAcrp increased the phosphorylation of cyclic AMP response element binding protein (CREB) at Ser133, as well as enhanced the DNA binding activity of CREB. Further, overexpression of a dominant negative form of CREB suppressed gAcrp-induced transcriptional activation of IL-10. gAcrp-stimulated CREB phosphorylation was mediated by the activation of both ERK1/2- and cAMP-dependent protein kinase (PKA)-dependent pathways. Inhibition of either ERK1/2 or PKA activity prevented gAcrp-stimulated CREB phosphorylation, as well as gAcrp-stimulated IL-10 promoter activation. Taken together, these data identify gAcrp-stimulated phospho-CREB as a key transcription factor responsible for gAcrp-induced IL-10 promoter activation.
Natural killer cells from protein kinase C θ−/− mice stimulated with interleukin-12 are deficient in production of interferon-γ
Authors: Page Karen M , Chaudhary Divya , Goldman Samuel J , Kasaian Marion T 
Published: February 2008

AbstractProtein kinase C θ (PKCθ) is expressed in NK cells, but its functional role has not been defined. Here, we demonstrate involvement of PKCθ in IL-12-induced NK cell IFN-γ production. NK cells from PKCθ−/− mice produced less IFN-γ in response to IL-12 than those from wild-type (WT) mice. IL-12-induced NK cell cytotoxicity was unaffected, and NK cells from PKCθ−/− mice did not display reduced IFN-γ production in response to IL-18, indicating a specific role for PKCθ in IL-12-induced IFN-γ production. Under the conditions tested, T cells did not produce IFN-γ in response to IL-12 or affect the ability of NK cells to produce the cytokine. PKCθ deficiency did not affect NK cell numbers, granularity, viability, or cytotoxic activity in response to polyinosinic:polycytydylic acid. NK cells from PKCθ−/− mice exhibited normal expression of IL-12Rβ1 and STAT4 proteins and normal induction of STAT4 phosphorylation in response to IL-12. Phosphorylation of threonine 538 within the catalytic domain of PKCθ was detectable in NK cells from WT mice but was not enhanced by IL-12. Transcription of IFN-γ increased similarly in NK cells from WT and PKCθ−/− mice in response to IL-12, and there was no difference in IFN-γ mRNA stability. Taken together, these findings indicate a role for PKCθ in the post-transcriptional regulation of IL-12-induced IFN-γ production.
Quantification of lamivudine-resistant hepatitis B virus mutants by type-specific TaqMan minor groove binder probe assay in patients with chronic hepatitis B
Authors: Yoshida Shigeru , Hige Shuhei , Yoshida Miyuki , Yamashita Naoki , Fujisawa Shin-ichi , Sato Kaori , Kitamura Tadashiro , Nishimura Masaharu , Chuma Makoto , Asaka Masahiro , Chiba Hitoshi 
Published: February 2008

Background Lamivudine (LAM)-resistant hepatitis B virus (HBV) with mutations in the polymerase region frequently appears after long-term use of LAM. Several methods allowing detection of mutant strains (YIDD, YVDD) have been reported, but they have no quantitative characteristics. In this study, we explored a unique approach for quantification of each mutant strain. Methods A method for detection and quantification of wild and mutant strains was developed using realtime polymerase chain reaction and type-specific minor groove binder (MGB) probes, and tested in patients with chronic hepatitis B before and after additive treatment with adefovir dipivoxil (ADV). Results A good correlation was confirmed in HBV DNA quantity obtained between the YMDD-specific MBG probe assay and Amplicor HBV Monitor assay results ( P < 0.001), linear between 3 and 9 log copies/mL serum. Of 109 samples from patients with chronic hepatitis B tested by both these assays and conventional direct sequencing, 90 (88.2%) showed identical results. The assays successfully detected and quantified a single type of mutant in three of four patients with additive ADV treatment, and also two coexisting mutant types (YIDD and YVDD) in the remaining patient. Conclusions Our specific and sensitive method for detection and quantification of HBV DNA with the wild-type YMDD motif and its two mutant forms (YIDD and YVDD) appears to be clinically useful, especially in patients with multiple mutant HBV infections.