bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lipophilic Dye Staining ofCryptococcus neoformansExtracellular Vesicles and Capsule
Authors: Nicola André Moraes , Frases Susana , Casadevall Arturo 
Published: May 2009

ABSTRACTCryptococcus neoformansis an encapsulated yeast that causes systemic mycosis in immunosuppressed individuals. Recent studies have determined that this fungus produces vesicles that are released to the extracellular environment both in vivo and in vitro. These vesicles contain assorted cargo that includes several molecules associated with virulence and implicated in host-pathogen interactions, such as capsular polysaccharides, laccase, urease, and other proteins. To date, visualization of extracellular vesicles has relied on transmission electron microscopy, a time-consuming technique. In this work we report the use of fluorescent membrane tracers to stain lipophilic structures in cryptococcal culture supernatants and capsules. Two dialkylcarbocyanine probes with different spectral characteristics were used to visualize purified vesicles by fluorescence microscopy and flow cytometry. Dual staining of vesicles with dialkylcarbocyanine and RNA-selective nucleic acid dyes suggested that a fraction of the vesicle population carried RNA. Use of these dyes to stain whole cells, however, was hampered by their possible direct binding to capsular polysaccharide. A fluorescent phospholipid was used as additional membrane tracer to stain whole cells, revealing punctate structures on the edge of the capsule which are consistent with vesicular trafficking. Lipophilic dyes provide new tools for the study of fungal extracellular vesicles and their content. The finding of hydrophobic regions in the capsule ofC. neoformansadds to the growing evidence for a structurally complex structure composed of polysaccharide and nonpolysaccharide components.
CD8 T Cells in Old Mice Contribute to the Innate Immune Response toMycobacterium tuberculosisvia Interleukin-12p70-Dependent and Antigen-Independent Production of Gamma Interferon
Authors: Vesosky Bridget , Rottinghaus Erin K. , Davis Craig , Turner Joanne 
Published: May 2009

ABSTRACTElderly individuals have increased morbidity and mortality associated with infectious diseases due in part to the progressive age-associated decline in immune function. Despite this, the old mouse model ofMycobacterium tuberculosisinfection has revealed a CD8- and gamma interferon (IFN-γ)-dependent early resistance to infection. In this study, we investigated the mechanism by which CD8 T cells from old mice contributed to the early immune response toM. tuberculosis. Following a low-dose aerosol infection withM. tuberculosis, CD8 T cells were identified as being a dominant source of IFN-γ expression in the lungs of old mice early after infection, before the typical onset of antigen-specific immunity. In addition,M. tuberculosis-induced IFN-γ production by CD8 T cells isolated from naïve old mice was major histocompatibility complex class I independent but was dependent on interleukin-12p70, confirming an innate role of CD8 T cells duringM. tuberculosisinfection. Moreover, the ability of CD8 T cells from old mice to produce increased innate IFN-γ levels in response toM. tuberculosisinfection was defined as a unique function of CD8 T cells from old mice and not the aged lung environment. Finally, we have identified increased expression of SET as being one possible mechanism by which CD8 T cells from old mice produce enhanced levels of IFN-γ. Additional characterizations of the signaling events that lead to enhanced innate IFN-γ production by CD8 T cells in old mice may lead to novel strategies to further enhance or perpetuate beneficial immune responses in the elderly.
Identification and Gene Disruption of Small Noncoding RNAs in
Streptomyces griseus
Authors: Tezuka Takeaki , Hara Hirofumi , Ohnishi Yasuo , Horinouchi Sueharu 
Published: May 2009

ABSTRACT

Small noncoding RNAs (sRNAs) have been shown to control diverse cellular processes in prokaryotes. To identify and characterize novel bacterial sRNAs, a gram-positive, soil-inhabiting, filamentous bacterium,
Streptomyces griseus
, was examined, on the assumption that
Streptomyces
should express sRNAs as important regulators of morphological and physiological differentiation. By bioinformatics investigation, 54 sRNA candidates, which were encoded on intergenic regions of the
S. griseus
chromosome and were highly conserved in those of both
Streptomyces coelicolor
A3(2) and
Streptomyces avermitilis
, were selected. Of these 54 sRNA candidates, 17 transcripts were detected by Northern blot analysis of the total RNAs isolated from cells grown on solid medium. Then, the direction of transcription of each sRNA candidate gene was determined by S1 nuclease mapping, followed by exclusion of four sRNA candidates that were considered riboswitches of their downstream open reading frames (ORFs). Finally, a further sRNA candidate was excluded because it was cotranscribed with the upstream ORF determined by reverse transcription-PCR. Thus, 12 sRNAs ranging in size from 40 to 300 nucleotides were identified in
S. griseus
. Seven of them were apparently transcribed in a growth phase-dependent manner. Furthermore, of the 12 sRNAs, the expression profiles of 7 were significantly influenced by a mutation of
adpA
, which encodes the central transcriptional regulator of the A-factor regulatory cascade involved in both morphological differentiation and secondary metabolism in
S. griseus
. However, disruption of all 12 sRNA genes showed no detectable phenotypic changes; all the disruptants grew and formed aerial mycelium and spores with the same time course as the wild-type strain on various media and produced streptomycin similarly to the wild-type strain.
OpnS, an Outer Membrane Porin ofXenorhabdus nematophila, Confers a Competitive Advantage for Growth in the Insect Host
Authors: van der Hoeven Ransome , Forst Steven 
Published: May 2009

ABSTRACTThe gammaproteobacteriumXenorhabdus nematophilaengages in a mutualistic association with an entomopathogenic nematode and also functions as a pathogen toward different insect hosts. We studied the role of the growth-phase-regulated outer membrane protein OpnS in host interactions. OpnS was shown to be a 16-stranded β-barrel porin.opnSwas expressed during growth in insect hemolymph and expression was elevated as the cell density increased. When wild-type andopnSdeletion strains were coinjected into insects, the wild-type strain was predominantly recovered from the insect cadaver. Similarly, anopnS-complemented strain outcompeted the ΔopnSstrain. Coinjection of the wild-type and ΔopnSstrains together with uncolonized nematodes into insects resulted in nematode progeny that were almost exclusively colonized with the wild-type strain. Likewise, nematode progeny recovered after coinjection of a mixture of nematodes carrying either the wild-type or ΔopnSstrain were colonized by the wild-type strain. In addition, the ΔopnSstrain displayed a competitive growth defect when grown together with the wild-type strain in insect hemolymph but not in defined culture medium. The ΔopnSstrain displayed increased sensitivity to antimicrobial compounds, suggesting that deletion of OpnS affected the integrity of the outer membrane. These findings show that the OpnS porin confers a competitive advantage for the growth and/or the survival ofX. nematophilain the insect host and provides a new model for studying the biological relevance of differential regulation of porins in a natural host environment.
spr1630 Is Responsible for the Lethality ofclpXMutations inStreptococcus pneumoniae
Authors: Piotrowski Andrew , Burghout Peter , Morrison Donald A. 
Published: May 2009

ABSTRACTThe Clp protease ATPase subunit and chaperone ClpX is dispensable in some bacteria, but it is thought to be essential in others, including streptococci and lactococci. We confirm thatclpXis essential in the Rx strain ofStreptococcus pneumoniaebut show that the requirement forclpXcan be relieved by point mutations, frame shifts, or deletion of the gene spr1630, which is found in many isolates ofS. pneumoniae.Homologs occur frequently inStaphylococcus aureusas well as in a few strains ofListeria monocytogenes,Lactobacillus johnsonii, andLactobacillus rhamnosus. In each case, the spr1630 homolog is accompanied by a putative transcriptional regulator with an HTH DNA binding motif. InS. pneumoniae, the spr1630-spr1629 gene pair, accompanied by a RUP element, occurs as an island inserted between thetrpAandcclAgenes in 15 of 22 sequenced genomes.
The Single Substitution I259T, Conserved in the Plasminogen Activator Pla of PandemicYersinia pestisBranches, Enhances Fibrinolytic Activity
Authors: Haiko Johanna , Kukkonen Maini , Ravantti Janne J. , Westerlund-Wikström Benita , Korhonen Timo K. 
Published: May 2009

ABSTRACTThe outer membrane plasminogen activator Pla ofYersinia pestisis a central virulence factor in plague. The primary structure of the Pla β-barrel is conserved inY. pestisbiovars Antiqua, Medievalis, and Orientalis, which are associated with pandemics of plague. The Pla molecule of the ancestralY. pestislineages Microtus and Angola carries the single amino acid change T259I located in surface loop 5 of the β-barrel. RecombinantY. pestisKIM D34 orEscherichia coliXL1 expressing Pla T259I was impaired in fibrinolysis and in plasminogen activation. Lack of detectable generation of the catalytic light chain of plasmin and inactivation of plasmin enzymatic activity by the Pla T259I construct indicated that Microtus Pla cleaved the plasminogen molecule more unspecifically than did common Pla. The isoform pattern of the Pla T259I molecule was different from that of the common Pla molecule. Microtus Pla was more efficient than wild-type Pla in α2-antiplasmin inactivation. Pla ofY. pestisand PgtE ofSalmonella entericahave evolved from the same omptin ancestor, and their comparison showed that PgtE was poor in plasminogen activation but exhibited efficient antiprotease inactivation. The substitution259IIDKT/TIDKN in PgtE, constructed to mimic the L5 region in Pla, altered proteolysis in favor of plasmin formation, whereas the reverse substitution259TIDKN/IIDKT in Pla altered proteolysis in favor of α2-antiplasmin inactivation. The results suggest that Microtus Pla represents an ancestral form of Pla that has evolved into a more efficient plasminogen activator in the pandemicY. pestislineages.
Complete Genome Sequence of
Lactobacillus plantarum
JDM1
Authors: Zhang Zhuo-Yang , Liu Chang , Zhu Yong-Zhang , Zhong Yi , Zhu Yong-Qiang , Zheng Hua-Jun , Zhao Guo-Ping , Wang Sheng-Yue , Guo Xiao-Kui 
Published: May 2009

ABSTRACT

Lactobacillus plantarum
is a lactic acid bacterium (LAB) species commonly used as a probiotic. We have sequenced the genome of
Lactobacillus plantarum
JDM1, which is a Chinese commercial LAB with several probiotic functions, using a GS 20 system. We recommend that each commercial probiotic strain should undergo complete genome sequencing to ensure safety and stability.
HER-2/neu analysis in breast cancer bone metastases
Authors: Zustin J , Boddin K , Tsourlakis M C , Burandt E , Mirlacher M , Jaenicke F , Izbicki J , Ruether W , Rueger J M , Bokemeyer C , Simon R , Sauter G 
Published: May 2009

Background:HER-2 is the target for antibody-based treatment of breast cancer (trastuzumab), which is highly successful in both advanced disease and the adjuvant setting. HER-2 can be analysed by fluorescence in situ hybridisation (FISH) for gene amplification or immunohistochemistry (IHC) for protein overexpression.Aim:As both methods are known to be influenced by previous tissue processing, to analyse the applicability of both FISH and IHC to decalcified bone metastases of breast cancer.Methods:A tissue microarray (TMA) was constructed from 149 breast cancer bone metastases. Consecutive TMA sections were analysed by FISH (PathVysion) and IHC (HercepTest).Results:FISH analysis was interpretable in 113 (85.0%) cases. Amplification was seen in 14 (12.4%) interpretable metastases. HER-2 positivity on IHC analysis was 3+ in 9.8% of cases and 2+ in 11.3%. A comparison of the two techniques revealed high concordance. Of the 14 cases of amplification, 10 (71%) showed 3+ IHC staining, two (14%) showed 2+, one (7%) showed 1+, and one (7%) showed 0+. Three of the four amplified cases that did not show 3+ IHC staining had an equivocal FISH result, with a HER-2/centromere 17 ratio of 1.8–2.2. Of the 13 cases that showed IHC 3+ staining, amplification was present in 10 (77%).Conclusions:HER-2 FISH analysis has an excellent success rate in highly standardised EDTA-decalcified bone metastases, suggesting that this method is easily applicable to decalcified tissues. The high concordance between IHC and FISH suggests that HER-2 IHC may be equally applicable to EDTA-treated tissues as to the usual formalin-fixed tissues.
Circadian Rhythm in Rest and Activity: A Biological Correlate of Quality of Life and a Predictor of Survival in Patients with Metastatic Colorectal Cancer
Authors: Innominato Pasquale F. , Focan Christian , Gorlia Thierry , Moreau Thierry , Garufi Carlo , Waterhouse Jim , Giacchetti Sylvie , Coudert Bruno , Iacobelli Stefano , Genet Dominique , Tampellini Marco , Chollet Philippe , Lentz Marie-Ange , Mormont Marie-Christine , Lévi Francis , Bjarnason Georg A. ,   for the Chronotherapy Group of the European Organization for Research and Treament of Cancer
Published: May 2009

Abstract
The rest-activity circadian rhythm (CircAct) reflects the function of the circadian timing system. In a prior single-institution study, the extent of CircAct perturbation independently predicted for survival and tumor response in 192 patients receiving chemotherapy for metastatic colorectal cancer. Moreover, the main CircAct parameters correlated with several health-related quality of life (HRQoL) scales. In this prospective study, we attempted to extend these results to an independent cohort of chemotherapy-naive metastatic colorectal cancer patients participating in an international randomized phase III trial (European Organisation for Research and Treatment of Cancer 05963). Patients were randomized to receive chronomodulated or conventional infusion of 5-fluorouracil, leucovorin, and oxaliplatin as first-line treatment for metastatic colorectal cancer. Patients from nine institutions completed the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire-C30 and wore a wrist accelerometer (actigraph) for 3 days before chemotherapy delivery. Two validated parameters (I&lt;O and r24) were used to estimate CircAct. Of 130 patients with baseline CircAct assessments, 96 had baseline HRQoL data. I&lt;O was confirmed to correlate with global quality of life, physical functioning, social functioning, fatigue, and appetite loss (r &gt; |0.25|; P &lt; 0.01). I&lt;O further independently predicted for overall survival with a hazard ratio of 0.94 (P &lt; 0.0001). The associations between CircAct parameters, HRQoL, and survival, which were shown in this international study involving previously untreated metastatic colorectal cancer patients, confirm prior single-institution findings in mostly pretreated metastatic colorectal cancer patients. The circadian timing system constitutes a novel therapeutic target. Interventions that normalize circadian timing system dysfunction may affect quality of life and survival in cancer patients. [Cancer Res 2009;69(11):4700–7]
Abrogating Drug Resistance in Malignant Peripheral Nerve Sheath Tumors by Disrupting Hyaluronan-CD44 Interactions with Small Hyaluronan Oligosaccharides
Authors: Slomiany Mark G. , Dai Lu , Bomar Paul A. , Knackstedt Thomas J. , Kranc D. Alex , Tolliver Lauren , Maria Bernard L. , Toole Bryan P. 
Published: May 2009

Abstract
Malignant peripheral nerve sheath tumors (MPNST) develop in ∼10% of neurofibromatosis type-1 patients and are a major contributing factor to neurofibromatosis-1 patient mortality and morbidity. MPNSTs are multidrug resistant, and thus long-term patient survival rates are poor after standard doxorubicin or multiagent chemotherapies. We show that the hyaluronan receptor CD44 forms complexes with multidrug transporters, BCRP (ABCG2) and P-glycoprotein (ABCB1), in the plasma membrane of human MPNST cells. Small hyaluronan oligosaccharides antagonize hyaluronan-CD44–mediated processes and inhibit hyaluronan production. Treatment of MPNST cells with the hyaluronan oligomers causes disassembly of CD44-transporter complexes and induces internalization of CD44, BCRP, and P-glycoprotein. Consequently, the oligomers suppress drug transporter activity and increase sensitivity to doxorubicin treatment in culture. In vivo, systemic administration of hyaluronan oligomers inhibits growth of MPNST xenografts. Moreover, the oligomers and doxorubicin act synergistically in vivo, in that combined suboptimal doses induce tumor regression to a greater extent than the additive effects of each agent alone. These findings indicate that constitutive hyaluronan-CD44 interactions contribute to drug transporter localization and function at the plasma membrane, and that attenuating hyaluronan-CD44 interactions sensitizes MPNSTs to doxorubicin in vitro and in vivo. These results also show the potential efficacy of hyaluronan oligomers, which are nontoxic and nonimmunogenic, as an adjuvant for chemotherapy in MPNST patients. [Cancer Res 2009;69(12):4992–8]
Mechanism of Regulation and Suppression of Melanoma Invasiveness by Novel Retinoic Acid Receptor-γ Target Gene Carbohydrate Sulfotransferase 10
Authors: Zhao Xiansi , Graves Carole , Ames Sarah J. , Fisher David E. , Spanjaard Remco A. 
Published: May 2009

Abstract
Retinoic acid (RA) induces growth arrest and differentiation of S91 murine melanoma cells and serves as a valuable model for this disease. RA acts through activation of RA receptors (RAR), which are members of the nuclear receptor superfamily of ligand-inducible transcription factors. Interestingly, differentiation is mediated by RARγ, but not by RARα or RARβ, suggesting that RARγ possesses unique and uncharacterized molecular properties. To address this question, DNA microarrays in combination with RAR isoform-specific agonists were employed to identify novel RARγ target genes that may play a role in this process. Here, we identified and validated carbohydrate sulfotransferase 10 (CHST10) as a novel RARγ target gene in S91 cells. The RARγ-inducible CHST10 promoter was obtained, and two atypical, independently functioning RA response elements were identified in a 425 bp region. Surprisingly, this fragment is bound by RARγ, but not by RARα or RARβ, thus providing a mechanism for the observed RARγ-specific regulation. CHST10 is a sulfotransferase that forms HNK-1 glycan on neural cell adhesion proteins and glycolipids, and HNK-1 is thought to modulate cell adhesion and possibly metastasis. We show that CHST10 is also regulated by RARγ in a significant subset of human melanoma cells, and three-dimensional cell culture migration assays suggest that CHST10 functions as a suppressor of invasiveness, but not proliferation, in these cells. Induction of CHST10 by RARγ-activating retinoids may present a novel therapeutic strategy to inhibit invasiveness in a subset of melanoma patients. [Cancer Res 2009;69(12):5218–25]
Hypermethylated Genes as Biomarkers of Cancer in Women with Pathologic Nipple Discharge
Authors: Fackler Mary Jo , Rivers Aeisha , Teo Wei Wen , Mangat Amrit , Taylor Evangeline , Zhang Zhe , Goodman Steve , Argani Pedram , Nayar Ritu , Susnik Barbara , Sukumar Saraswati , Khan Seema A. 
Published: May 2009

Abstract
Purpose: In a pilot study of women with pathologic nipple discharge (PND) undergoing ductoscopy, we tested quantitative assessment of gene promoter hypermethylation using quantitative multiplex methylation–specific PCR (QM-MSP) to enhance detection of duct carcinoma in situ (DCIS).
Experimental Design: Women with PND underwent ductoscopy; ducts with significant lesions were surgically resected (36 ducts in 33 women) and those with minimal findings were not (28 ducts in 16 women). QM-MSP was done on ductoscopy cell samples. Results were compared with cytology and tissue histology.
Results: Cells from ducts with significant lesions on ductoscopy had significantly higher levels of methylation than those with minimal findings. Furthermore, cells from ducts with DCIS displayed higher levels of methylation than those with benign lesions such as papilloma (P = 0.006); or ducts with minimal findings on ductoscopy (P = 0.0001). Cumulative RASSF1A, TWIST1, and HIN1 gene methylation accurately distinguished ducts with cancerous versus benign lesions (100% sensitivity, 72% specificity, and area under the curve of 0.91 according to receiving operating characteristic analyses). QM-MSP analysis was more informative than cytology (100% versus 29% sensitivity, respectively), for detecting DCIS. In a validation set of paraffin-embedded DCIS and papilloma samples from women presenting with PND, QM-MSP was significantly higher in DNA from DCIS than papilloma sections (P = 0.002).
Conclusion: The positive predictive value of ductoscopy was more than doubled (19% versus 47%) with the addition of QM-MSP, demonstrating the benefit of targeting ducts having both high methylation and significant abnormalities on ductoscopy for surgical excision. Future large-scale studies to validate this approach are needed.
Decitabine Effect on Tumor Global DNA Methylation and Other Parameters in a Phase I Trial in Refractory Solid Tumors and Lymphomas
Authors: Stewart David J. , Issa Jean-Pierre , Kurzrock Razelle , Nunez Maria I. , Jelinek Jaroslav , Hong David , Oki Yasuhiro , Guo Zhong , Gupta Sanjay , Wistuba Ignacio I. 
Published: May 2009

AbstractPurpose: By hypomethylating genes, decitabine may up-regulate factors required for chemotherapeutic cytotoxicity. Platinum-resistant cells may have reduced expression of the copper/platinum transporter CTR1.Experimental Design: Thirty-one patients with refractory malignancies received decitabine 2.5 to 10 mg/m2 on days 1 to 5, and 8 to 12 or 15 to 20 mg/m2 on days 1 to 5. Tumor was assessed for DNA methylation (by LINE assays), apoptosis, necrosis, mitoses, Ki67, DNA methyltransferase (DNMT1), CTR1, and p16.Results: Febrile neutropenia was dose limiting. One thymoma patient responded. Decitabine decreased tumor DNA methylation (from median 51.2% predecitabine to 43.7% postdecitabine; P = 0.01, with effects at all doses) and in peripheral blood mononuclear cells (from 65.3-56.0%). There was no correlation between tumor and peripheral blood mononuclear cells. Patients starting decitabine ≤3 versus &gt;3 months after last prior cytotoxic or targeted therapy had lower predecitabine tumor CTR1 scores (P = 0.02), higher p16 (P = 0.04), and trends (P = 0.07) toward higher tumor methylation and apoptosis. Decitabine decreased tumor DNMT1 for scores initially &gt;0 (P = 0.04). Decitabine increased tumor apoptosis (P &lt; 0.05), mitoses (if initially low, P = 0.02), and CTR1 (if initially low, P = 0.025, or if ≤3 months from last prior therapy, P = 0.04). Tumor CTR1 scores correlated inversely with methylation (r = −0.41, P = 0.005), but CTR1 promoter was not hypermethylated. Only three patients had tumor p16 promoter hypermethylation. P16 scores did not increase. Higher blood pressure correlated with lower tumor necrosis (P = 0.03) and a trend toward greater DNA demethylation (P = 0.10).Conclusions: Exposure to various cytotoxic and targeted agents might generate broad pleiotropic resistance by reducing CTR1 and other transporters. Decitabine decreases DNA methylation and augments CTR1 expression through methylation-independent mechanisms.