bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Death of Human Cancer Cells Following Photodynamic Therapy: Apoptosis Competence is Necessary for Bcl‐2 Protection but not for Induction of Autophagy†
Authors: Xue Liang‐yan , Chiu Song‐mao , Azizuddin Kashif , Joseph Sheeba , Oleinick Nancy L. 
Published: June 2007

AbstractPhotodynamic therapy (PDT) is an efficient inducer of apoptosis in many types of cells, except in cells deficient in one or more of the factors that mediate apoptosis. Recent reports have identified autophagy as a potential alternative cell death process following PDT. Here we investigated the occurrence of autophagy after PDT with the photosensitizer Pc 4 in human cancer cells that are deficient in the pro‐apoptotic factor Bax (human prostate cancer DU145 cells) or the apoptosis mediator caspase‐3 (human breast cancer MCF‐7v cells) and in apoptosis‐competent cells (MCF‐7c3 cells that stably overexpress human pro‐caspase‐3 and Chinese hamster ovary CHO 5A100 cells). Further, each of the cell lines was also studied with and without stably overexpressed Bcl‐2. Autophagy was identified by electron microscopic observation of the presence of double‐membrane‐delineated autophagosomal vesicles in the cytosol and by immunoblot observation of the Pc 4‐PDT dose‐ and time‐dependent increase in the level of LC3‐II, a component of the autophagosomal membrane. Autophagy was observed in all of the cell lines studied, whether or not they were capable of typical apoptosis and whether or not they overexpressed Bcl‐2. The presence of stably overexpressed Bcl‐2 in the cells protected against PDT‐induced apoptosis and loss of clonogenicity in apoptosis‐competent cells (MCF‐7c3 and CHO 5A100 cells). In contrast, Bcl‐2 overexpression did not protect against the development of autophagy in any of the cell lines or against loss of clonogenicity in apoptosis‐deficient cells (MCF‐7v and DU145 cells). Furthermore, 3‐methyladenine and wortmannin, inhibitors of autophagy, provided greater protection against loss of viability to apoptosis‐deficient than to apoptosis‐competent cells. The results show that autophagy occurs during cell death following PDT in human cancer cells competent or not for normal apoptosis. Only the apoptosis‐competent cells are protected by Bcl‐2 against cell death.
Advantages of Using Microbial Technology over Traditional Chemical Technology in Removal of Black Crusts from Stone Surfaces of Historical Monuments
Authors: Cappitelli Francesca , Toniolo Lucia , Sansonetti Antonio , Gulotta Davide , Ranalli Giancarlo , Zanardini Elisabetta , Sorlini Claudia 
Published: June 2007

ABSTRACT

This study compares two cleaning methods, one involving an ammonium carbonate-EDTA mixture and the other involving the sulfate-reducing bacterium
Desulfovibrio vulgaris
subsp.
vulgaris
ATCC 29579, for the removal of black crust (containing gypsum) on marble of the Milan Cathedral (Italy). In contrast to the chemical cleaning method, the biological procedure resulted in more homogeneous removal of the surface deposits and preserved the patina noble under the black crust. Whereas both of the treatments converted gypsum to calcite, allowing consolidation, the chemical treatment also formed undesirable sodium sulfate.
Effects of Different Animal Waste Treatment Technologies on Detection and Viability of Porcine Enteric Viruses
Authors: Costantini Verónica P. , Azevedo Ana C. , Li Xin , Williams Mike C. , Michel Frederick C. , Saif Linda J. 
Published: June 2007

ABSTRACTEnteric pathogens in animal waste that is not properly processed can contaminate the environment and food. The persistence of pathogens in animal waste depends upon the waste treatment technology, but little is known about persistence of porcine viruses. Our objectives were to characterize the porcine enteric viruses (porcine noroviruses [PoNoVs], porcine sapoviruses [PoSaVs], rotavirus A [RV-A], RV-B, and RV-C) in fresh feces or manure and to evaluate the effects of different candidate environmentally superior technologies (ESTs) for animal waste treatment on the detection of these viruses. Untreated manure and samples collected at different stages during and after treatment were obtained from swine farms that used conventional waste management (CWM) and five different candidate ESTs. The RNA from porcine enteric viruses was detected by reverse transcription-PCR and/or seminested PCR; PoSaV and RV-A were also detected by enzyme-linked immunosorbent assay. Cell culture immunofluorescence (CCIF) and experimental inoculation of gnotobiotic (Gn) pigs were used to determine RV-A/C infectivity in posttreatment samples. The PoSaV and RV-A were detected in pretreatment samples from each farm, whereas PoNoV and RV-C were detected in pretreatment feces from three of five and four of five farms using the candidate ESTs, respectively. After treatment, PoSaV RNA was detected only in the samples from the farm using CWM and not from the farms using the candidate ESTs. RV-A and RV-C RNAs were detected in four of five and three of four candidate ESTs, respectively, after treatment, but infectious particles were not detected by CCIF, nor were clinical signs or seroconversion detected in inoculated Gn pigs. These results indicate that only RV-A/C RNA, but no viral infectivity, was detected after treatment. Our findings address a public health concern regarding environmental quality surrounding swine production units.
Labeling of
Bifidobacterium longum
Cells with
13
C-Substituted Leucine for Quantitative Proteomic Analyses
Authors: Couté Yohann , Hernandez Céline , Appel Ron D. , Sanchez Jean-Charles , Margolles Abelardo 
Published: June 2007

ABSTRACT

Stable isotope labeling of amino acids in cell culture was used for
Bifidobacterium longum
. A comprehensive proteomic strategy was developed and validated by designing an appropriate semidefined medium that allows stable replacement of natural leucine by [
13
C
6
]leucine. Using this strategy, proteins having variations of at least 50% in their expression rates can be quantified with great confidence.
Regulation of Phosphoinositide Levels by the Phospholipid Transfer Protein Sec14p Controls Cdc42p/p21-Activated Kinase-Mediated Cell Cycle Progression at Cytokinesis
Authors: Howe Alicia G. , Fairn Gregory D. , MacDonald Kendra , Bankaitis Vytas A. , McMaster Christopher R. 
Published: June 2007

ABSTRACT

Sec14p is an essential phosphatidylcholine/phosphatidylinositol transfer protein with a well-described role in the regulation of Golgi apparatus-derived vesicular transport in yeast. Inactivation of the CDP-choline pathway for phosphatidylcholine synthesis allows cells to survive in the absence of Sec14p function through restoration of Golgi vesicular transport capability. In this study,
Saccharomyces cerevisiae
cells containing a
SEC14
temperature-sensitive allele along with an inactivated CDP-choline pathway were transformed with a high-copy-number yeast genomic library. Genes whose increased expression inhibited cell growth in the absence of Sec14p function were identified. Increasing levels of the Rho GTPase Cdc42p and its direct effector kinases Cla4p and Ste20p prevented the growth of cells lacking Sec14p and CDP-choline pathway function. Growth suppression was accompanied by an increase in large and multiply budded cells. This effect on polarized cell growth did not appear to be due to an inability to establish cell polarity, since both the actin cytoskeleton and localization of the septin Cdc12p were unaffected by increased expression of Cdc42p, Cla4p, or Ste20p. Nuclei were present in both the mother cell and the emerging bud, consistent with Sec14p regulation of the cell cycle subsequent to anaphase but prior to cytokinesis/septum breakdown. Increased expression of phosphatidylinositol 4-kinases and phosphatidylinositol 4-phosphate 5-kinase prevented growth arrest by
CDC42
,
CLA4
, or
STE20
upon inactivation of Sec14p function. Sec14p regulation of phosphoinositide levels affects cytokinesis at the level of the Cdc42p/Cla4p/Ste20p signaling cascade.
Evolutionarily Divergent Type II Protein Arginine Methyltransferase in
Trypanosoma brucei
Authors: Pasternack Deborah A. , Sayegh Joyce , Clarke Steven , Read Laurie K. 
Published: June 2007

ABSTRACT

Protein arginine methylation is a posttranslational modification that impacts cellular functions, such as RNA processing, transcription, DNA repair, and signal transduction. The majority of our knowledge regarding arginine methylation derives from studies of yeast and mammals. Here, we describe a protein arginine
N
-methyltransferase (PRMT), TbPRMT5, from the early-branching eukaryote
Trypanosoma brucei
. TbPRMT5 shares the greatest sequence similarity with PRMT5 and Skb1 type II enzymes from humans and
Schizosaccharomyces pombe
, respectively, although it is significantly divergent at the amino acid level from its mammalian and yeast counterparts. Recombinant TbPRMT5 displays broad substrate specificity in vitro, including methylation of a mitochondrial-gene-regulatory protein, RBP16. TbPRMT5 catalyzes the formation of ω-
N

G

-monomethylarginine and symmetric ω-
N

G

,
N

G
′

-dimethylarginine and does not require trypanosome cofactors for this activity. These data establish that type II PRMTs evolved early in the eukaryotic lineage. In vivo, TbPRMT5 is constitutively expressed in the bloodstream form and procyclic-form (insect host) life stages of the parasite and localizes to the cytoplasm. Genetic disruption via RNA interference in procyclic-form trypanosomes indicates that TbPRMT5 is not essential for growth in this life cycle stage. TbPRMT5-TAP ectopically expressed in procyclic-form trypanosomes is present in high-molecular-weight complexes and associates with an RG domain-containing DEAD box protein related to yeast Ded1 and two kinetoplastid-specific proteins. Thus, TbPRMT5 is likely to be involved in novel methylation-regulated functions in trypanosomes, some of which may include RNA processing and/or translation.
The Acidic Repetitive Domain of the
Magnetospirillum gryphiswaldense
MamJ Protein Displays Hypervariability but Is Not Required for Magnetosome Chain Assembly
Authors: Scheffel André , Schüler Dirk 
Published: June 2007

ABSTRACT

Magnetotactic bacteria navigate along the earth's magnetic field using chains of magnetosomes, which are intracellular organelles comprising membrane-enclosed magnetite crystals. The assembly of highly ordered magnetosome chains is under genetic control and involves several specific proteins. Based on genetic and cryo-electron tomography studies, a model was recently proposed in which the acidic MamJ magnetosome protein attaches magnetosome vesicles to the actin-like cytoskeletal filament formed by MamK, thereby preventing magnetosome chains from collapsing. However, the exact functions as well as the mode of interaction between MamK and MamJ are unknown. Here, we demonstrate that several functional MamJ variants from
Magnetospirillum gryphiswaldense
and other magnetotactic bacteria share an acidic and repetitive central domain, which displays an unusual intra- and interspecies sequence polymorphism, probably caused by homologous recombination between identical copies of Glu- and Pro-rich repeats. Surprisingly,
mamJ
mutant alleles in which the central domain was deleted retained their potential to restore chain formation in a Δ
mamJ
mutant, suggesting that the acidic domain is not essential for MamJ's function. Results of two-hybrid experiments indicate that MamJ physically interacts with MamK, and two distinct sequence regions within MamJ were shown to be involved in binding to MamK. Mutant variants of MamJ lacking either of the binding domains were unable to functionally complement the Δ
mamJ
mutant. In addition, two-hybrid experiments suggest both MamK-binding domains of MamJ confer oligomerization of MamJ. In summary, our data reveal domains required for the functions of the MamJ protein in chain assembly and maintenance and provide the first experimental indications for a direct interaction between MamJ and the cytoskeletal filament protein MamK.
Regulation of the α-Crystallin Geneacr2by the MprAB Two-Component System ofMycobacterium tuberculosis
Authors: Pang Xiuhua , Howard Susan T. 
Published: June 2007

ABSTRACTCoordinated regulation of molecular chaperones is an important feature of the bacterial stress response. The small molecular chaperone geneacr2ofMycobacterium tuberculosisis activated by exposure to several stresses, including heat and the detergent sodium dodecyl sulfate (SDS). In this study, we show thatacr2is directly regulated by the MprAB two-component system, and that MprAB has both positive and negative effects onacr2expression. mRNA analyses showed thatacr2expression levels were lower under SDS stress and control conditions but higher under heat shock in anmprABdeletion mutant than they were in the parental strain. Parental expression patterns were restored in anmprAB-complemented strain. Western blotting using an anti-Acr2 antibody showed that Acr2 protein synthesis correlated with mRNA levels. Primer extension identified one transcriptional start point (TSP) foracr2in all three strains under control and stress conditions. Electrophoresis mobility shift assays revealed multiple MprA binding sites in theacr2promoter, including one downstream and three upstream of theacr2TSP, with one overlapping the binding sites predicted for SigE, SigH, and HspR. DNA footprinting confirmed that MprA protected large sections of theacr2promoter region. Expression of several housekeeping genes under SDS stress also was evaluated, revealing the upregulation of large molecular chaperone genes and, unexpectedly,sigA, with slightly lowersigAmRNA levels detected in themprABdeletion mutant than in the wild type. In contrast to Acr2, SigA protein synthesis did not correlate with mRNA expression. Overall, the data indicated that MprA has complex interactions with theacr2promoter and indirect effects on major housekeeping genes.
Structural and Functional Analyses of the Major Outer Membrane Protein ofChlamydia trachomatis
Authors: Sun Guifeng , Pal Sukumar , Sarcon Annahita K. , Kim Soyoun , Sugawara Etsuko , Nikaido Hiroshi , Cocco Melanie J. , Peterson Ellena M. , de la Maza Luis M. 
Published: June 2007

ABSTRACTChlamydia trachomatisis a major pathogen throughout the world, and preventive measures have focused on the production of a vaccine using the major outer membrane protein (MOMP). Here, in elementary bodies and in preparations of the outer membrane, we identified native trimers of the MOMP. The trimers were stable under reducing conditions, although disulfide bonds appear to be present between the monomers of a trimer and between trimers. Cross-linking of the outer membrane complex demonstrated that the MOMP is most likely not in a close spatial relationship with the 60- and 12-kDa cysteine-rich proteins. Extraction of the MOMP fromChlamydiaisolates under nondenaturing conditions yielded the trimeric conformation of this protein as shown by cross-linking and analysis by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis with different concentrations of acrylamide. Using circular dichroism spectroscopy, we determined that the trimers were formed mainly of β-pleated sheet structures in detergent micelles. Using a liposomal swelling assay, the MOMP was found to have porin activity, and the size of the pore was estimated to be approximately 2 nm in diameter. The trimers were found to be stable in SDS at temperatures ranging from 4 to 37°C and over a pH range of 5.0 to 8.0. In addition, the trimers of MOMP were found to be resistant to digestion with trypsin. In conclusion, these results show that the native conformation of the MOMP ofC. trachomatisis a trimer with predominantly a β-sheet structure and porin function.
Proteomic and Transcriptomic Analysis of Extracellular Proteins and mRNA Levels inThermobifida fuscaGrown on Cellobiose and Glucose
Authors: Chen Shaolin , Wilson David B. 
Published: June 2007

ABSTRACTThermobifida fuscasecretes proteins that carry out plant cell wall degradation. Using two-dimensional electrophoresis, the extracellular proteome ofT. fuscagrown on cellobiose was compared to that of cells grown on glucose. Extracellular proteins, the expression of which is induced by cellobiose, mainly are cellulases and cellulose-binding proteins. Other major extracellular proteins induced by cellobiose include a xylanase (Xyl10A) and two unknown proteins, the C-terminal regions of which are homologous to a lytic transglycosylase goose egg white lysozyme domain and an NLPC_P60 domain (which defines a family of cell wall peptidases), respectively. Transcriptional analysis of genes encoding cellobiose-induced proteins suggests that their expression is controlled at the transcriptional level and that their expression also is induced by cellulose. Some other major extracellular proteins produced byT. fuscagrown on both cellobiose and glucose include Lam81A and three unknown proteins that are homologous to aminopeptidases and xylanases or that contain a putative NLPC_P60 domain.
Escherichia coli
K1-Specific Bacteriophage CUS-3 Distribution and Function in Phase-Variable Capsular Polysialic Acid O Acetylation
Authors: King Michael R. , Vimr Ross P. , Steenbergen Susan M. , Spanjaard Lodewijk , Plunkett Guy , Blattner Frederick R. , Vimr Eric R. 
Published: June 2007

ABSTRACT

Escherichia coli
K1 is the leading cause of human neonatal sepsis and meningitis and is important in other clinical syndromes of both humans and domestic animals; in this strain the polysialic acid capsule (K1 antigen) functions by inhibiting innate immunity. Recent discovery of the phase-variable capsular O acetylation mechanism indicated that the O-acetyltransferase gene,
neuO
, is carried on a putative K1-specific prophage designated CUS-3 (E. L.
Deszo, S. M. Steenbergen, D. I. Freedberg, and E. R. Vimr
, Proc. Natl. Acad. Sci. USA
102:
5564-5569, 2005). Here we describe the isolation and characterization of a CUS-3 derivative (CUS-3a), demonstrating its morphology, lysogenization of a sensitive host, and the distribution of CUS-3 among a collection of 111 different K1 strains. The 40,207-bp CUS-3 genome was annotated from the strain RS218 genomic DNA sequence, indicating that most of the 63 phage open reading frames have their closest homologues in one of seven different lambdoid phages. Translational fusion of a reporter
lacZ
fragment to the hypervariable poly-Ψ domain facilitated measurement of phase variation frequencies, indicating no significant differences between switch rates or effects on rates of the methyl-directed mismatch repair system. PCR analysis of poly-Ψ domain length indicated preferential loss or gain of single 5′-AAGACTC-3′ nucleotide repeats. Analysis of a K1 strain previously reported as “locked on” indicated a poly-Ψ region with the least number of heptad repeats compatible with in-frame
neuO
expression. The combined results establish CUS-3 as an active mobile contingency locus in
E. coli
K1, indicating its capacity to mediate population-wide capsule variation.
Function of Periplasmic Hydrogenases in the Sulfate-Reducing Bacterium
Desulfovibrio vulgaris
Hildenborough
Authors: Caffrey Sean M. , Park Hyung-Soo , Voordouw Johanna K. , He Zhili , Zhou Jizhong , Voordouw Gerrit 
Published: June 2007

ABSTRACT

The sulfate-reducing bacterium
Desulfovibrio vulgaris
Hildenborough possesses four periplasmic hydrogenases to facilitate the oxidation of molecular hydrogen. These include an [Fe] hydrogenase, an [NiFeSe] hydrogenase, and two [NiFe] hydrogenases encoded by the
hyd
,
hys
,
hyn1
, and
hyn2
genes, respectively. In order to understand their cellular functions, we have compared the growth rates of existing (
hyd
and
hyn1
) and newly constructed (
hys
and
hyn-1 hyd
) mutants to those of the wild type in defined media in which lactate or hydrogen at either 5 or 50% (vol/vol) was used as the sole electron donor for sulfate reduction. Only strains missing the [Fe] hydrogenase were significantly affected during growth with lactate or with 50% (vol/vol) hydrogen as the sole electron donor. When the cells were grown at low (5% [vol/vol]) hydrogen concentrations, those missing the [NiFeSe] hydrogenase suffered the greatest impairment. The growth rate data correlated strongly with gene expression results obtained from microarray hybridizations and real-time PCR using mRNA extracted from cells grown under the three conditions. Expression of the
hys
genes followed the order 5% hydrogen > 50% hydrogen > lactate, whereas expression of the
hyd
genes followed the reverse order. These results suggest that growth with lactate and 50% hydrogen is associated with high intracellular hydrogen concentrations, which are best captured by the higher activity, lower affinity [Fe] hydrogenase. In contrast, growth with 5% hydrogen is associated with a low intracellular hydrogen concentration, requiring the lower activity, higher affinity [NiFeSe] hydrogenase.
Regulation of
pyr
Gene Expression in
Mycobacterium smegmatis
by PyrR-Dependent Translational Repression
Authors: Fields Christopher J. , Switzer Robert L. 
Published: June 2007

ABSTRACT

Regulation of pyrimidine biosynthetic (
pyr
) genes by a transcription attenuation mechanism that is mediated by the PyrR mRNA-binding regulatory protein has been demonstrated for numerous gram-positive bacteria. Mycobacterial genomes specify
pyrR
genes and contain obvious PyrR-binding sequences in the initially transcribed regions of their
pyr
operons, but transcription antiterminator and attenuation terminator sequences are absent from their
pyr
5′ leader regions. This work demonstrates that repression of
pyr
operon expression in
Mycobacterium smegmatis
by exogenous uracil requires the
pyrR
gene and the
pyr
leader RNA sequence for binding of PyrR. Plasmids containing the
M. smegmatis pyr
promoter-leader region translationally fused to
lacZ
also displayed
pyrR
-dependent repression, but transcriptional fusions of the same sequences to a
lacZ
gene that retained the
lacZ
ribosome-binding site were not regulated by PyrR plus uracil. We propose that PyrR regulates
pyr
expression in
M. smegmatis
, other mycobacteria, and probably in numerous other bacteria by a translational repression mechanism in which nucleotide-regulated binding of PyrR occludes the first ribosome-binding site of the
pyr
operon.
Metabolic equivalents during the 10-m shuttle walking test for post-myocardial infarction patients
Authors: Woolf-May K , Ferrett D 
Published: June 2007

Objective:Comorbidities are found to affect metabolic equivalents (METs). Therefore the main objective of this study was to compare METs (1 MET: oxygen uptake (Vo2) 3.5 ml/kg/min) during an incremental shuttle walking test (SWT) between non-cardiac and post-myocardial infarction (MI) men, and secondly to determine any differences in Vo2(ml/kg/min) between flat treadmill walking and the turning during the shuttle walking in non-cardiac subjects.Design:Comparative study.Subjects:Thirty one post-MI (mean (SD) age 63.5 (6.5), range 53–77 years) from phase IV cardiac rehabilitation and 19 non-cardiac (64.6 (7.5), range 51–76 years) men participated.Methods:All subjects performed an SWT, and non-cardiac subjects a treadmill test of similar protocol. Throughout both, the subject’s Vo2was measured.Results:Analysis comparing lines of regression showed METs at 1.12 to 4.16 mph were higher (p<0.001) for post-MIs versus non-cardiac subjects. For non-cardiac subjects, there were no differences between the treadmill test and SWT (p>0.9) and LoA showed acceptable agreement in METs between treadmill vs SWT, mean difference −1.1 (8.8) (1.96SD).Conclusion:It would appear that for asymptomatic individuals it is appropriate to apply established METs for flat walking to the SWT. However, the significantly higher METs for the post-MI compared with the non-cardiac subjects indicates the need for caution when using METs derived from healthy subjects in the prescription of exercise for myocardial patients.