bluuebunny/crossref_metadata_2025_split huggingface dataset:
Organotin Decomposition by Pyochelin, Secreted by
Pseudomonas aeruginosa
Even in an Iron-Sufficient Environment
Authors: Sun Guo-Xin , Zhou Wen-Qiang , Zhong Jian-Jiang 
Published: September 2006

ABSTRACT

A triphenyltin (TPT)-decomposing strain,
Pseudomonas aeruginosa
CGMCC 1.860, was screened out. It secreted an unknown TPT-decomposing factor into the medium, later shown to be pyochelin, even in the presence of 100 μM iron. To our knowledge, this is the first report of organotin decomposition by pyochelin.
Effects of Chloromethanes on Growth of and Deletion of the
pce
Gene Cluster in Dehalorespiring
Desulfitobacterium hafniense
Strain Y51
Authors: Futagami Taiki , Yamaguchi Takehito , Nakayama Shun-ichi , Goto Masatoshi , Furukawa Kensuke 
Published: September 2006

ABSTRACT

The dehalorespiring
Desulfitobacterium hafniense
strain Y51 efficiently dechlorinates tetrachloroethene (PCE) to
cis
-1,2-dichloroethene (
cis
-DCE) via trichloroethene by PceA reductive dehalogenase encoded by the
pceA
gene. In a previous study, we found that the significant growth inhibition of strain Y51 occurred in the presence of commercial
cis
-DCE. In this study, it turned out that the growth inhibition was caused by chloroform (CF) contamination of
cis
-DCE. Interestingly, CF did not affect the growth of PCE-nondechlorinating SD (small deletion) and LD (large deletion) variants, where the former fails to transcribe the
pceABC
genes caused by a deletion of the promoter and the latter lost the entire
pceABCT
gene cluster. Therefore, PCE-nondechlorinating variants, mostly LD variant, became predominant, and dechlorination activity was significantly reduced in the presence of CF. Moreover, such a growth inhibitory effect was also observed in the presence of carbon tetrachloride at 1 μM, but not carbon dichloride even at 1 mM.
Multiple Contributions of Peroxisomal Metabolic Function to Fungal Pathogenicity in
Colletotrichum lagenarium
Authors: Asakura Makoto , Okuno Tetsuro , Takano Yoshitaka 
Published: September 2006

ABSTRACT

In
Colletotrichum lagenarium
, which is the causal agent of cucumber anthracnose,
PEX6
is required for peroxisome biogenesis and appressorium-mediated infection. To verify the roles of peroxisome-associated metabolism in fungal pathogenicity, we isolated and functionally characterized
ICL1
of
C. lagenarium
, which encodes isocitrate lyase involved in the glyoxylate cycle in peroxisomes. The
icl1
mutants failed to utilize fatty acids and acetate for growth. Although Icl1 has no typical peroxisomal targeting signals, expression analysis of the GFP-Icl1 fusion protein indicated that Icl1 localizes in peroxisomes. These results indicate that the glyoxylate cycle that occurs inside the peroxisome is required for fatty acid and acetate metabolism for growth. Importantly, in contrast with the
pex6
mutants that form nonmelanized appressoria, the
icl1
mutants formed appressoria that were highly pigmented with melanin, suggesting that the glyoxylate cycle is not essential for melanin biosynthesis in appressoria. However, the
icl1
mutants exhibited a severe reduction in virulence. Appressoria of the
icl1
mutants failed to develop penetration hyphae in the host plant, suggesting that
ICL1
is involved in host invasion. The addition of glucose partially restored virulence of the
icl1
mutant. Heat shock treatment of the host plant also enabled the
icl1
mutants to develop lesions, implying that the infection defect of the
icl1
mutant is associated with plant defense. Together with the requirement of
PEX6
for appressorial melanization, our findings suggest that peroxisomal metabolic pathways play functional roles in appressorial melanization and subsequent host invasion steps, and the latter step requires the glyoxylate cycle.
Comparison of Two Fingerprinting Techniques, Terminal Restriction Fragment Length Polymorphism and Automated Ribosomal Intergenic Spacer Analysis, for Determination of Bacterial Diversity in Aquatic Environments
Authors: Danovaro R. , Luna G. M. , Dell'Anno A. , Pietrangeli B. 
Published: September 2006

ABSTRACT

We investigated bacterial diversity in different aquatic environments (including marine and lagoon sediments, coastal seawater, and groundwater), and we compared two fingerprinting techniques (terminal restriction fragment length polymorphism [T-RFLP] and automated ribosomal intergenic spacer analysis [ARISA]) which are currently utilized for estimating richness and community composition. Bacterial diversity ranged from 27 to 99 phylotypes (on average, 56) using the T-RFLP approach and from 62 to 101 genotypes (on average, 81) when the same samples were analyzed using ARISA. The total diversity encountered in all matrices analyzed was 144 phylotypes for T-RFLP and 200 genotypes for ARISA. Although the two techniques provided similar results in the analysis of community structure, bacterial richness and diversity estimates were significantly higher using ARISA. These findings suggest that ARISA is more effective than T-RFLP in detecting the presence of bacterial taxa accounting for <5% of total amplified product. ARISA enabled also distinction among aquatic bacterial isolates of
Pseudomonas
spp. which were indistinguishable using T-RFLP analysis. Overall, the results of this study show that ARISA is more accurate than T-RFLP analysis on the 16S rRNA gene for estimating the biodiversity of aquatic bacterial assemblages.
Lack of Evidence for Vertical Transmission of
Campylobacter
spp. in Chickens
Authors: Callicott Kenneth A. , Friðriksdóttir Vala , Reiersen Jarle , Lowman Ruff , Bisaillon Jean-Robert , Gunnarsson Eggert , Berndtson Eva , Hiett Kelli L. , Needleman David S. , Stern Norman J. 
Published: September 2006

ABSTRACT

Campylobacter jejuni
is a major cause of bacterial food-borne infection in the industrial world. There is evidence that
C. jejuni
is present in eggs and hatchery fluff, opening the possibility for vertical transmission from hens to progeny. Poultry operations in Iceland provide an excellent opportunity to study this possibility, since breeding flocks are established solely from eggs imported from grandparent flocks in Sweden. This leaves limited opportunity for grandparents and their progeny to share isolates through horizontal transmission. While
Campylobacter
was not detected in all grandparent flocks, 13 of the 16 egg import lots consisted of eggs gathered from one or more
Campylobacter
-positive grandparent flocks. No evidence of
Campylobacter
was found by PCR in any of the 10 relevant quarantine hatchery fluff samples examined, and no
Campylobacter
was isolated from the parent birds through 8 weeks, while they were still in quarantine rearing facilities. After the birds were moved to less biosecure rearing facilities,
Campylobacter
was isolated, and 29 alleles were observed among the 224 isolates studied. While three alleles were found in both Sweden and Iceland, in no case was the same allele found both in a particular grandparent flock and in its progeny. We could find no evidence for vertical transmission of
Campylobacter
to the approximately 60,000 progeny parent breeders that were hatched from eggs coming from
Campylobacter
-positive grandparent flocks. If vertical transmission is occurring, it is not a significant source for the contamination of chicken flocks with
Campylobacter
spp.
Metabolic-State-Dependent Remodeling of the Transcriptome in Response to Anoxia and Subsequent Reoxygenation in
Saccharomyces cerevisiae
Authors: Lai Liang-Chuan , Kosorukoff Alexander L. , Burke Patricia V. , Kwast Kurt E. 
Published: September 2006

ABSTRACT

We conducted a comprehensive genomic analysis of the temporal response of yeast to anaerobiosis (six generations) and subsequent aerobic recovery (≈2 generations) to reveal metabolic-state (galactose versus glucose)-dependent differences in gene network activity and function. Analysis of variance showed that far fewer genes responded (raw
P
value of ≤10
−8
) to the O
2
shifts in glucose (1,603 genes) than in galactose (2,388 genes). Gene network analysis reveals that this difference is due largely to the failure of “stress”-activated networks controlled by Msn2/4, Fhl1, MCB, SCB, PAC, and RRPE to transiently respond to the shift to anaerobiosis in glucose as they did in galactose. After ≈1 generation of anaerobiosis, the response was similar in both media, beginning with the deactivation of Hap1 and Hap2/3/4/5 networks involved in mitochondrial functions and the concomitant derepression of Rox1-regulated networks for carbohydrate catabolism and redox regulation and ending (≥2 generations) with the activation of Upc2- and Mot3-regulated networks involved in sterol and cell wall homeostasis. The response to reoxygenation was rapid (<5 min) and similar in both media, dominated by Yap1 networks involved in oxidative stress/redox regulation and the concomitant activation of heme-regulated ones. Our analyses revealed extensive networks of genes subject to combinatorial regulation by both heme-dependent (e.g., Hap1, Hap2/3/4/5, Rox1, Mot3, and Upc2) and heme-independent (e.g., Yap1, Skn7, and Puf3) factors under these conditions. We also uncover novel functions for several
cis
-regulatory sites and
trans
-acting factors and define functional regulons involved in the physiological acclimatization to changes in oxygen availability.
A Eukaryote without Catalase-Containing Microbodies:
Neurosporacrassa
Exhibits a Unique Cellular Distributionof Its Four Catalases
Authors: Schliebs Wolfgang , Würtz Christian , Kunau Wolf-Hubert , Veenhuis Marten , Rottensteiner Hanspeter 
Published: September 2006

ABSTRACT

Microbodies usually house catalase to decompose hydrogen peroxide generated within
the organelle by the action of various oxidases. Here we have analyzed
whether peroxisomes (i.e., catalase-containing microbodies) exist in
Neurospora crassa
. Three distinct catalase isoforms were
identified by native catalase activity gels under various
peroxisome-inducing conditions. Subcellular fractionation by density
gradient centrifugation revealed that most of the
spectrophotometrically measured activity was present in the light upper
fractions, with an additional small peak coinciding with the peak
fractions of HEX-1, the marker protein for Woronin bodies, a
compartment related to the microbody family. However, neither in-gel
assays nor monospecific antibodies generated against the three purified
catalases detected the enzymes in any dense organellar fraction.
Furthermore, staining of an
N. crassa
wild-type strain with
3,3′-diaminobenzidine and H
2
O
2
did not
lead to catalase-dependent reaction products within microbodies.
Nonetheless,
N. crassa
does possess a gene (
cat-4
)
whose product is most similar to the peroxisomal type of monofunctional
catalases. This novel protein indeed exhibited catalase activity, but
was not localized to microbodies either. We conclude that
N.
crassa
lacks catalase-containing peroxisomes, a characteristic
that is probably restricted to a few filamentous fungi that produce
little hydrogen peroxide within
microbodies.
The Predicted G-Protein-Coupled Receptor GPR-1 Is Required for Female Sexual Development inthe Multicellular Fungus
Neurospora crassa
Authors: Krystofova Svetlana , Borkovich Katherine A. 
Published: September 2006

ABSTRACT

G-protein-coupled receptors (GPCRs) control important aspects of asexual and sexual
development in eukaryotic organisms. We have identified a predicted
GPCR in the filamentous fungus
Neurospora crassa
with
similarity to cyclic AMP-receptor like GPCRs from
Dictyostelium
discoideum
and GCR1 from
Arabidopsis thaliana
. Expression
of
gpr-1
is highest in female reproductive structures, and
deletion of
gpr-1
leads to defects during sexual development.
Unfertilized female structures (protoperithecia) fromΔ
gpr-1
strains are weakly pigmented, small, and
submerged in the agar. The perithecia produced after fertilization have
deformed beaks that lack ostioles, the openings through which
ascospores are discharged. Localization studies using a GPR-1-green
fluorescent protein fusion protein showed that GPR-1 is targeted to
female reproductive structures. Genetic epistasis experiments with the
three Gα genes were inconclusive due to the early block in
mating exhibited by Δ
gna-1
strains. Phenotypic
analysis of mutants from a high-throughput
N. crassa
knockout
project allowed identification of BEK-1, a homeodomain transcription
factor that is a potential target of GPR-1. The perithecial defects ofΔ
bek-1
strains are similar to those of theΔ
gpr-1
strain, and epistasis analysis indicates that
bek-1
could function downstream of
gpr-1
during
postfertilization events. The effect must be posttranscriptional, as
bek-1
transcript levels are not affected inΔ
gpr-1
strains. The lack of ostioles inΔ
gpr-1
and Δ
bek-1
mutants has an
undesirable effect on the ability to spread progeny (ascospores) by the
normal ejection mechanism and would severely compromise the fitness of
these strains in
nature.
Neutrophil-derived APRIL concentrated in tumor lesions by proteoglycans correlates with human B-cell lymphoma aggressiveness
Authors: Schwaller Juerg , Schneider Pascal , Mhawech-Fauceglia Paulette , McKee Thomas , Myit Samir , Matthes Thomas , Tschopp Jurg , Donze Olivier , Le Gal Frederique-Anne , Huard Bertrand 
Published: September 2006

AbstractA PRoliferation-Inducing TNF Ligand (APRIL) costimulates B-cell activation. When overexpressed in mice, APRIL induces B-cell neoplasia, reminiscent of human B-cell chronic lymphoid leukemia (B-CLL). We analyzed APRIL expression in situ in human non-Hodgkin lymphomas. APRIL up-regulation was only observed in high-grade B-cell lymphomas, diffuse large B-cell lymphoma (DLBCL), and Burkitt lymphoma (BL). Up-regulation was seen in 46% and 20% of DLBCL and BL, respectively. In DLBCL, neutrophils, constitutively producing APRIL and infiltrating the tumor tissue, were the main cellular source of APRIL. Rare DLBCL cases showed a predominance of histiocytes or mesenchymal cells as APRIL source. APRIL secreted by neutrophils accumulated on tumor cells via proteoglycan binding. In addition to proteoglycans, DLBCL tumor cells expressed the APRIL signaling receptor, TACI and/or BCMA, indicating that these tumor cells are fully equipped to respond to APRIL. A retrospective clinical analysis revealed a significant correlation between high expression of APRIL in tumor lesions and decreased overall patient survival rate. Hence, APRIL produced by inflammatory cells infiltrating lymphoma lesions may increase tumor aggressiveness and affect disease outcome.
KLF4 suppresses transformation of pre-B cells by ABL oncogenes
Authors: Kharas Michael G. , Yusuf Isharat , Scarfone Vanessa M. , Yang Vincent W. , Segre Julia A. , Huettner Claudia S. , Fruman David A. 
Published: September 2006

AbstractGenes that are strongly repressed after B-cell activation are candidates for being inactivated, mutated, or repressed in B-cell malignancies. Krüppel-like factor 4 (Klf4), a gene down-regulated in activated murine B cells, is expressed at low levels in several types of human B-cell lineage lymphomas and leukemias. The human KLF4 gene has been identified as a tumor suppressor gene in colon and gastric cancer; in concordance with this, overexpression of KLF4 can suppress proliferation in several epithelial cell types. Here we investigate the effects of KLF4 on pro/pre–B-cell transformation by v-Abl and BCR-ABL, oncogenes that cause leukemia in mice and humans. We show that overexpression of KLF4 induces arrest and apoptosis in the G1 phase of the cell cycle. KLF4-mediated death, but not cell-cycle arrest, can be rescued by Bcl-XL overexpression. Transformed pro/pre-B cells expressing KLF4 display increased expression of p21CIP and decreased expression of c-Myc and cyclin D2. Tetracycline-inducible expression of KLF4 in B-cell progenitors of transgenic mice blocks transformation by BCR-ABL and depletes leukemic pre-B cells in vivo. Collectively, our work identifies KLF4 as a putative tumor suppressor in B-cell malignancies.
CD26 inhibition enhances allogeneic donor-cell homing and engraftment after in utero hematopoietic-cell transplantation
Authors: Peranteau William H. , Endo Masayuki , Adibe Obinna O. , Merchant Aziz , Zoltick Philip W. , Flake Alan W. 
Published: September 2006

AbstractIn utero hematopoietic-cell transplantation (IUHCT) can induce donor-specific tolerance to facilitate postnatal transplantation. Induction of tolerance requires a threshold level of mixed hematopoietic chimerism. CD26 is a peptidase whose inhibition increases homing and engraftment of hematopoietic cells in postnatal transplantation. We hypothesized that CD26 inhibition would increase donor-cell homing to the fetal liver (FL) and improve allogeneic engraftment following IUHCT. To evaluate this hypothesis, B6GFP bone marrow (BM) or enriched hematopoietic stem cells (HSCs) were transplanted into allogeneic fetal mice with or without CD26 inhibition. Recipients were analyzed for FL homing and peripheral-blood chimerism from 4 to 28 weeks of life. We found that CD26 inhibition of donor cells results in (1) increased homing of allogeneic BM and HSCs to the FL, (2) an increased number of injected animals with evidence of postnatal engraftment, (3) increased donor chimerism levels following IUHCT, and (4) a competitive engraftment advantage over noninhibited congenic donor cells. This study supports CD26 inhibition as a potential method to increase the level of FL homing and engraftment following IUHCT. The resulting increased donor chimerism suggests that CD26 inhibition may in the future be used as a method of increasing donor-specific tolerance following IUHCT.
Human Langerhans-cell activation triggered in vitro by conditionally expressed MKK6 is counterregulated by the downstream effector RelB
Authors: Jörgl Almut , Platzer Barbara , Taschner Sabine , Heinz Leonhard X. , Höcher Bernhard , Reisner Peter M. , Göbel Florian , Strobl Herbert 
Published: September 2006

AbstractEnvironmentally exposed epithelial Langerhans cells (LCs) encounter diverse innate stress signals, which lead to the activation of complex intracellular signaling cascades. Among these, p38 MAPK is consistently phosphorylated. For which aspects of LC activation triggering of p38 signaling is sufficient remains to be elucidated. We show that conditional induction of a dominant active form of MAPK kinase 6 (d.a.MKK6), a direct upstream kinase of p38, in LCs efficiently induces the up-regulation of costimulatory molecules and enhances their T-cell stimulatory capacity. These immediate effects showed no or only a minor requirement for classical NF-κB signaling. Concomitant with LC activation, d.a.MKK6 induced the alternative NF-κB member RelB, whose nuclear localization marks mature DCs. Specific inhibition of nuclear RelB during d.a.MKK6-induced LC activation further enhanced their maturation state. This observation was validated using the p38 activator anisomycin, thus suggesting a novel LC intrinsic control mechanism regulated by RelB.
Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species
Authors: Legault Boris A , Lopez-Lopez Arantxa , Alba-Casado Jose Carlos , Doolittle W Ford , Bolhuis Henk , Rodriguez-Valera Francisco , Papke R Thane 
Published: September 2006

Abstract

Background
Mature saturated brine (crystallizers) communities are largely dominated (>80% of cells) by the square halophilic archaeon "Haloquadratum walsbyi". The recent cultivation of the strain HBSQ001 and thesequencing of its genome allows comparison with the metagenome of this taxonomically simplified environment. Similar studies carried out in other extreme environments have revealed very little diversity in gene content among the cell lineages present.

Results
The metagenome of the microbial community of a crystallizer pond has been analyzed by end sequencing a 2000 clone fosmid library and comparing the sequences obtained with the genome sequence of "Haloquadratum walsbyi". The genome of the sequenced strain was retrieved nearly complete within this environmental DNA library. However, many ORF's that could be ascribed to the "Haloquadratum" metapopulation by common genome characteristics or scaffolding to the strain genome were not present in the specific sequenced isolate. Particularly, three regions of the sequenced genome were associated with multiple rearrangements and the presence of different genes from the metapopulation. Many transposition and phage related genes were found within this pool which, together with the associated atypical GC content in these areas, supports lateral gene transfer mediated by these elements as the most probable genetic cause of this variability. Additionally, these sequences were highly enriched in putative regulatory and signal transduction functions.

Conclusion
These results point to a large pan-genome (total gene repertoire of the genus/species) even in this highly specialized extremophile and at a single geographic location. The extensive gene repertoire is what might be expected of a population that exploits a diverse nutrient pool, resulting from the degradation of biomass produced at lower salinities.
Optimized detection of circulating anti-nuclear envelope autoantibodies by immunofluorescence
Authors: Tsiakalou Vagia , Tsangaridou Elena , Polioudaki Hara , Nifli Artemissia-Phoebe , Koulentaki Meri , Akoumianaki Tonia , Kouroumalis Elias , Castanas Elias , Theodoropoulos Panayiotis A 
Published: September 2006

Abstract

Background
Antinuclear antibodies are useful diagnostic tools in several autoimmune diseases. However, the routine detection of nuclear envelope autoantibodies using immunofluorescence (IF) is not always easy to perform in patients' sera because of the presence of autoantibodies to other nuclear and cytoplasmic components which could mask the characteristic rim-like pattern of nuclear envelope autoantibodies. This is particularly common in sera from patients with primary biliary cirrhosis (PBC), which generaly have high titres of anti-mitochondrial antibodies. Therefore, we have assayed a number of commercial slides and alternative fixation conditions to optimize the detection of anti-nuclear envelope antibodies (ANEA) in PBC sera.

Methods
We have explored the presence of ANEA in 33 sera from patients with established PBC using three different Hep2 commercial slides and home-made slides with HeLa and Hep2 cells fixed with methanol, ethanol, 1% or 4% formaldehyde.

Results
We observed that the IF pattern was related to the cell type used (Hep2 or HeLa), the manufacturer and the cell fixation scheme. When both cell lines were fixed with 1% formaldehyde, the intensity of the cytoplasmic staining was considerably decreased regardless to the serum sample, whereas the prevalence of cytoplasmic autoantibodies was significantly lowered, as compared to any of the Hep2 commercial slide and fixation used. In addition, the prevalence of ANEA was importantly increased in formaldehyde-fixed cells.

Conclusion
Immunofluorescence using appropriately fixed cells represent an easy, no time-consuming and low cost technique for the routine screening of sera for ANEA. Detection of ANEA is shown to be more efficient using formaldehyde-fixed cells instead of commercially available Hep2 cells.
Open access and beyond
Authors: Mathur Shawn , Schmidt Christian , Das Chhaya , Tucker Philip W 
Published: September 2006

Abstract
Uncensored exchange of scientific results hastens progress. Open Access does not stop at the removal of price and permission barriers; still, censorship and reading disabilities, to name a few, hamper access to information. Here, we invite the scientific community and the public to discuss new methods to distribute, store and manage literature in order to achieve unfettered access to literature.