bluuebunny/crossref_metadata_2025_split huggingface dataset:
Initiation of Heat-Induced Replication Requires DnaA and the L-13-mer of
oriC
Authors: González-Soltero Rocío , Botello Emilia , Jiménez-Sánchez Alfonso 
Published: November 2006

ABSTRACT

An upshift of 10°C or more in the growth temperature of an
Escherichia coli
culture causes induction of extra rounds of chromosome replication. This stress replication initiates at
oriC
but has functional requirements different from those of cyclic replication. We named this phenomenon

h

eat-

i

nduced

r

eplication (HIR). Analysis of HIR in bacterial strains that had complete or partial
oriC
deletions and were suppressed by F integration showed that no sequence outside
oriC
is used for HIR. Analysis of a number of
oriC
mutants showed that deletion of the L-13-mer, which makes
oriC
inactive for cyclic replication, was the only mutation studied that inactivated HIR. The requirement for this sequence was strictly correlated with Benham's theoretical stress-induced DNA duplex destabilization.
oriC
mutations at DnaA, FIS, or IHF binding sites showed normal HIR activation, but DnaA was required for HIR. We suggest that strand opening for HIR initiation occurs due to heat-induced destabilization of the L-13-mer, and the stable oligomeric DnaA-single-stranded
oriC
complex might be required only to load the replicative helicase DnaB.
Characterization of the Carboxysomal Carbonic Anhydrase CsoSCA from
Halothiobacillus neapolitanus
Authors: Heinhorst Sabine , Williams Eric B. , Cai Fei , Murin C. Daniel , Shively Jessup M. , Cannon Gordon C. 
Published: November 2006

ABSTRACT

In cyanobacteria and many chemolithotrophic bacteria, the CO
2
-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is sequestered into polyhedral protein bodies called carboxysomes. The carboxysome is believed to function as a microcompartment that enhances the catalytic efficacy of RubisCO by providing the enzyme with its substrate, CO
2
, through the action of the shell protein CsoSCA, which is a novel carbonic anhydrase. In the work reported here, the biochemical properties of purified, recombinant CsoSCA were studied, and the catalytic characteristics of the carbonic anhydrase for the CO
2
hydration and bicarbonate dehydration reactions were compared with those of intact and ruptured carboxysomes. The low apparent catalytic rates measured for CsoSCA in intact carboxysomes suggest that the protein shell acts as a barrier for the CO
2
that has been produced by CsoSCA through directional dehydration of cytoplasmic bicarbonate. This CO
2
trap provides the sequestered RubisCO with ample substrate for efficient fixation and constitutes a means by which microcompartmentalization enhances the catalytic efficiency of this enzyme.
pH-Dependent Activation of the BarA-UvrY Two-Component System inEscherichia coli
Authors: Mondragón Verónica , Franco Bernardo , Jonas Kristina , Suzuki Kazushi , Romeo Tony , Melefors Öjar , Georgellis Dimitris 
Published: November 2006

ABSTRACTThebarAanduvrYgenes ofEscherichia coliencode a two-component sensor kinase and a response regulator, respectively. Although this system plays a major role in the regulation of central carbon metabolism, motility, and biofilm formation by controlling the expression of the CsrB and CsrC noncoding RNAs, the environmental conditions and the physiological signal(s) to which it responds remain obscure. In this study, we explored the effect of external pH on the activity of BarA/UvrY. Our results indicate that a pH lower than 5.5 provides an environment that does not allow activation of the BarA/UvrY signaling pathway.
Evidence for Recombination inMycobacterium tuberculosis
Authors: Liu Xiaoming , Gutacker Michaela M. , Musser James M. , Fu Yun-Xin 
Published: November 2006

ABSTRACTDue to its mostly isolated living environment,Mycobacterium tuberculosisis generally believed to be highly clonal, and thus recombination between different strains must be rare and is not critical for the survival of the species. To investigate the roles recombination could have possibly played in the evolution ofM. tuberculosis, an analysis was conducted on previously determined genotypes of 36 synonymous single nucleotide polymorphisms (SNPs) in 3,320M. tuberculosisisolates. The results confirmed the predominant clonal structure of theM. tuberculosispopulation. However, recombination between different strains was also suggested. To further resolve the issue, 175 intergenic SNPs and 234 synonymous SNPs were genotyped in 37 selected representative strains. A clear mosaic polymorphic pattern ahead of the MT0105 locus encoding a PPE (Pro-Pro-Glu) protein was obtained, which is most likely a result of recombination hot spot. Given that PPE proteins are thought to be critical in host-pathogen interactions, we hypothesize that recombination has been influential in the history ofM. tuberculosisand possibly a major contributor to the diversity observed ahead of the MT0105 locus.
The Cation-Responsive Protein NhaR of
Escherichia coli
Activates
pgaABCD
Transcription, Required for Production of the Biofilm Adhesin Poly-β-1,6-
N
-Acetyl-
d
-Glucosamine
Authors: Goller Carlos , Wang Xin , Itoh Yoshikane , Romeo Tony 
Published: November 2006

ABSTRACT

The
pgaABCD
operon of
Escherichia coli
is required for production of the biofilm adhesin poly-β-1,6-
N
-acetyl-
d
-glucosamine (PGA). We establish here that NhaR, a DNA-binding protein of the LysR family of transcriptional regulators, activates transcription of this operon. Disruption of the
nhaR
gene decreased biofilm formation without affecting planktonic growth. PGA production was undetectable in an
nhaR
mutant strain. Expression of a
pgaA
′-′
lacZ
translational fusion was induced by NaCl and alkaline pH, but not by CaCl
2
or sucrose, in an
nhaR
-dependent fashion. Primer extension and quantitative real-time reverse transcription-PCR analyses further revealed that NhaR affects the steady-state level of
pga
mRNA. A purified recombinant NhaR protein bound specifically and with high affinity within the
pgaABCD
promoter region; one apparent binding site overlaps the −35 element, and a second site lies immediately upstream of the first. This protein was necessary and sufficient for activation of in vitro transcription from the
pgaA
promoter. These results define a novel mechanism for regulation of biofilm formation in response to environmental conditions and suggest an expanded role for NhaR in promoting bacterial survival.
Wall Teichoic Acid Polymers Are Dispensable for Cell Viability in
Bacillus subtilis
Authors: D'Elia Michael A. , Millar Kathryn E. , Beveridge Terry J. , Brown Eric D. 
Published: November 2006

ABSTRACT

An extensive literature has established that the synthesis of wall teichoic acid in
Bacillus subtilis
is essential for cell viability. Paradoxically, we have recently shown that wall teichoic acid biogenesis is dispensable in
Staphylococcus aureus
(M. A. D'Elia, M. P. Pereira, Y. S. Chung, W. Zhao, A. Chau, T. J. Kenney, M. C. Sulavik, T. A. Black, and E. D. Brown, J. Bacteriol. 188:4183-4189, 2006). A complex pattern of teichoic acid gene dispensability was seen in
S. aureus
where the first gene (
tarO
) was dispensable and later acting genes showed an indispensable phenotype. Here we show, for the first time, that wall teichoic acid synthesis is also dispensable in
B. subtilis
and that a similar gene dispensability pattern is seen where later acting enzymes display an essential phenotype, while the gene
tagO
, whose product catalyzes the first step in the pathway, could be deleted to yield viable mutants devoid of teichoic acid in the cell wall.
Horizontal Gene Transfer in a Polyclonal Outbreak of Carbapenem-ResistantAcinetobacter baumannii
Authors: Valenzuela Jubelle K. , Thomas Lee , Partridge Sally R. , van der Reijden Tanny , Dijkshoorn Lenie , Iredell Jon 
Published: November 2006

ABSTRACTIn the last few years, phenotypically carbapenem resistantAcinetobacterstrains have been identified throughout the world, including in many of the hospitals and intensive care units (ICUs) of Australia. Genotyping of Australian ICU outbreak-associated isolates by pulsed-field gel electrophoresis of whole genomic DNA indicated that different strains were cocirculating within one hospital. The carbapenem-resistant phenotype of these and other Australian isolates was found to be due to carbapenem-hydrolyzing activity associated with the presence of theblaOXA-23gene. In all resistant strains examined, theblaOXA-23gene was adjacent to the insertion sequence ISAba1in a structure that has been found inAcinetobacter baumanniistrains of a similar phenotype from around the world;blaOXA-51-like genes were also found in allA. baumanniistrains but were not consistently associated with ISAba1, which is believed to provide the promoter required for expression of linked antibiotic resistance genes. Most isolates were also found to contain additional antibiotic resistance genes within the cassette arrays of class 1 integrons. The same cassette arrays, in addition to the ISAba1-blaOXA-23structure, were found within unrelated strains, but no common plasmid carrying these accessory genetic elements could be identified. It therefore appears that antibiotic resistance genes are readily exchanged between cocirculating strains in epidemics of phenotypically indistinguishable organisms. Epidemiological investigation of major outbreaks should include whole-genome typing as well as analysis of potentially transmissible resistance genes and their vehicles.
Vaccinia Virus Interactions with the Cell Membrane Studied by New Chromatic Vesicle and Cell Sensor Assays
Authors: Orynbayeva Z. , Kolusheva S. , Groysman N. , Gavrielov N. , Lobel L. , Jelinek R. 
Published: November 2006

ABSTRACT
The potential danger of cross-species viral infection points to the significance of understanding the contributions of nonspecific membrane interactions with the viral envelope compared to receptor-mediated uptake as a factor in virus internalization and infection. We present a detailed investigation of the interactions of vaccinia virus particles with lipid bilayers and with epithelial cell membranes using newly developed chromatic biomimetic membrane assays. This analytical platform comprises vesicular particles containing lipids interspersed within reporter polymer units that emit intense fluorescence following viral interactions with the lipid domains. The chromatic vesicles were employed as membrane models in cell-free solutions and were also incorporated into the membranes of epithelial cells, thereby functioning as localized membrane sensors on the cell surface. These experiments provide important insight into membrane interactions with and fusion of virions and the kinetic profiles of these processes. In particular, the data emphasize the significance of cholesterol/sphingomyelin domains (lipid rafts) as a crucial factor promoting bilayer insertion of the viral particles. Our analysis of virus interactions with polymer-labeled living cells exposed the significant role of the epidermal growth factor receptor in vaccinia virus infectivity; however, the data also demonstrated the existence of additional non-receptor-mediated mechanisms contributing to attachment of the virus to the cell surface and its internalization.
Incorporation of Glycosylphosphatidylinositol-Anchored Granulocyte- MacrophageColony-Stimulating Factor or CD40 Ligand Enhances Immunogenicity of Chimeric Simian Immunodeficiency Virus-Like Particles
Authors: Skountzou Ioanna , Quan Fu-Shi , Gangadhara Sailaja , Ye Ling , Vzorov Andrei , Selvaraj Periasamy , Jacob Joshy , Compans Richard W. , Kang Sang-Moo 
Published: November 2006

ABSTRACTThe rapid worldwide spread of human immunodeficiency virus (HIV) mandates the development of successful vaccination strategies. Since live attenuated HIV is not accepted as a vaccine due to safety concerns, virus-like particles (VLPs) offer an attractive safe alternative because they lack the viral genome yet they are perceived by the immune system as a virus particle. We hypothesized that adding immunostimulatory signals to VLPs would enhance their efficacy. To accomplish this we generated chimeric simian immunodeficiency virus (SIV) VLPs containing either glycosylphosphatidylinositol (GPI)-anchored granulocyte-macrophage colony-stimulating factor (GM-CSF) or CD40 ligand (CD40L) and investigated their biological activity and ability to enhance immune responses in vivo. Immunization of mice with chimeric SIV VLPs containing GM-CSF induced SIV Env-specific antibodies as well as neutralizing activity at significantly higher levels than those induced by standard SIV VLPs, SIV VLPs containing CD40L, or standard VLPs mixed with soluble GM-CSF. In addition, mice immunized with chimeric SIV VLPs containing either GM-CSF or CD40L showed significantly increased CD4+- and CD8+-T-cell responses to SIV Env, compared to standard SIV VLPs. Taken together, these results demonstrate that the incorporation of immunostimulatory molecules enhances humoral and cellular immune responses. We propose that anchoring immunostimulatory molecules into SIV VLPs can be a promising approach to augmenting the efficacy of VLP antigens.
Identification of a Ribonucleoprotein Intermediate of Tomato Mosaic Virus RNA Replication Complex Formation
Authors: Komoda Keisuke , Mawatari Natsuki , Hagiwara-Komoda Yuka , Naito Satoshi , Ishikawa Masayuki 
Published: November 2006

ABSTRACT

The replication of eukaryotic positive-strand RNA virus genomes occurs in the membrane-bound RNA replication complexes. Previously, we found that the extract of evacuolated tobacco BY-2 protoplasts (BYL) is capable of supporting the translation and subsequent replication of the genomic RNAs of plant positive-strand RNA viruses, including
Tomato mosaic virus
(ToMV). Here, to dissect the process that precedes the formation of ToMV RNA replication complexes, we prepared membrane-depleted BYL (mdBYL), in which the membranes were removed by centrifugation. In mdBYL, ToMV RNA was translated to produce the 130-kDa and 180-kDa replication proteins, but the synthesis of any ToMV-related RNAs did not occur. When BYL membranes were added back to the ToMV RNA-translated mdBYL after the termination of translation with puromycin, ToMV RNA was replicated. Using a replication-competent ToMV derivative that encodes the FLAG-tagged 180-kDa replication protein, it was shown by affinity purification that a complex that contained the 130-kDa and 180-kDa proteins and ToMV genomic RNA was formed after translation in mdBYL. When the complex was mixed with BYL membranes, ToMV RNA was replicated, which suggests that this ribonucleoprotein complex is an intermediate of ToMV RNA replication complex formation. We have named this ribonucleoprotein complex the “pre-membrane-targeting complex.” Our data suggest that the formation of the pre-membrane-targeting complex is coupled with the translation of ToMV RNA, while posttranslationally added exogenous 180-kDa protein and replication templates can contribute to replication and can be replicated, respectively. Based on these results, we discuss the mechanisms of ToMV RNA replication complex formation.
Dietary intake, weight gain, and birth outcomes of physically active pregnant women: a pilot study
Authors: Giroux Isabelle , Inglis Stuart D. , Lander Susan , Gerrie Shannon , Mottola Michelle F. 
Published: November 2006

Pregnant women have increased energy and nutrient needs. Exercise also increases energy and glucose demands. This pilot study examined whether women who were physically active during pregnancy met their dietary needs, gained weight adequately, avoided hypoglycemia, and had normal birth outcomes. Based on a convenience sample, 11 active women were studied from 18 weeks gestation to delivery. They exercised for 40 min at 70% VO2 peak, 3–4 times per week. Weekly measures included capillary blood glucose concentrations, body mass, and food records. Birth outcome measures included baby mass, length, and activity, pulse, grimace, appearance, and respiration (APGAR) scores. Our findings suggest that these subjects had lower average energy intake (8680 ± 490 kJ/d) than recommended for the 2nd and 3rd trimesters (13 020 ±185 kJ/d; 13 480 ± 185 kJ/d, respectively, p < 0.0001). Protein requirements for pregnancy were exceeded. Average intakes of iron (19 ± 2 mg/d) and folate (356 ± 33 μg/d) were lower than Recommended Dietary Allowances (RDAs) (27 mg/d and 600 μg/d, respectively) and milk products consumed were less than the recommended daily servings. Four women gained less weight per week than recommended for pregnancy. No hypoglycemia occurred post-exercise. Birth outcome measures were within normal ranges. Comparative studies with a larger number of subjects are required to determine if active pregnant women have adequate nutrient intakes and weight gain.
Effect of fasudil on macrovascular disorder-induced endothelial dysfunction
Authors: Shah Dhvanit I. , Singh Manjeet 
Published: November 2006

The present study has been designed to investigate the effect of fasudil (Rho-kinase inhibitor) in hypercholesterolemia- and hypertension-induced endothelial dysfunction. High fat diet (8 weeks) and desoxycortisone acetate (DOCA) (40 mg·kg–1) were administered (s.c.) to rats to produce hypercholesterolemia and hypertension (mean arterial blood pressure > 120 mmHg), respectively. Endothelial dysfunction was assessed using isolated aortic ring, electron microscopy of thoracic aorta, and serum concentration of nitrite/nitrate. The expression of mRNA for p22phox and eNOS was assessed by using RT-PCR. Serum thiobarbituric acid reactive substances concentration and aortic superoxide anion concentration were estimated to assess oxidative stress. Fasudil (30 mg·kg–1, p.o.) and atorvastatin (30 mg·kg–1, p.o.) treatments markedly prevented hypercholesterolemia- and hypertension-evoked attenuation of acetylcholine-induced endothelium-dependent relaxation, impairment of vascular endothelial lining, decrease in expression of mRNA for eNOS and serum nitrite/nitrate concentration, and an increase in expression of mRNA for p22phox, superoxide anion, and serum thiobarbituric acid reactive substances. The ameliorative effect of fasudil was prevented by L-NAME. In conclusion, fasudil-induced inhibition of Rho-kinase may improve hypercholesterolemia- and hypertension-induced endothelial dysfunction.
The Internalization and Degradation of Human Copper Transporter 1 following Cisplatin Exposure
Authors: Holzer Alison K. , Howell Stephen B. 
Published: November 2006

Abstract
The human copper transporter 1 (hCTR1), the major transporter responsible for copper influx, mediates one component of the cellular accumulation of cisplatin (DDP). Both copper and DDP cause rapid down-regulation of hCTR1 expression in human ovarian carcinoma cells. In this study, we investigated the mechanism of this effect using digital deconvolution microscopy and Western blot analysis of cells stained with antibodies directed at both ends of the protein. Treatment of 2008 cells with DDP in combination with inhibitors of various endosomal pathways (amiloride, cytochalasin D, nystatin, and methyl-β-cyclodextrin) showed that hCTR1 degradation was blocked by amiloride and cytochalasin D, indicating that hCTR1 was internalized primarily by macropinocytosis. Expression of transdominant-negative forms of dynamin I and Rac showed that loss of hCTR1 was not dependent on pathways regulated by either of these proteins. DDP-induced loss of hCTR1 was blocked by the proteasome inhibitors lactacystin, proteasome inhibitor 1, and MG132. This study confirms that DDP triggers the rapid loss of hCTR1 from ovarian carcinoma cells at clinically relevant concentrations. The results indicate that DDP-induced loss of hCTR1 involves internalization from the plasma membrane by macropinocytosis followed by proteasomal degradation. Because hCTR1 is a major determinant of early DDP uptake, prevention of its degradation offers a potential approach to enhancing tumor sensitivity. (Cancer Res 2006; 66(22): 10944-52)
MicroRNA Responses to Cellular Stress
Authors: Marsit Carmen J. , Eddy Karen , Kelsey Karl T. 
Published: November 2006

Abstract
Recent work has begun to explore the instrumental role that small noncoding RNA species, particularly microRNAs (miRNA), have both in classifying human tumors and in directing embryonic development. These studies suggest that developmental programs in essentially all organisms studied are set, in part, by varied expressions of miRNAs and that neoplasia is characterized by altered expression of miRNAs. Reasoning that these observations are linked, we examined whether cellular exposures that induce both developmental anomalies and cancer alter miRNAs. Using microarrays of 385 known human miRNAs, we studied human lymphoblastoid cells grown under various conditions or treatments. Folate deficiency induced a pronounced global increase in miRNA expression. We observed no significant alteration in miRNA expression in cells treated with γ-irradiation, whereas exposure to sodium arsenite led to global increases in miRNA expression. The miRNA hsa-miR-222 was identified from these arrays as significantly overexpressed under folate-deficient conditions, and this finding was confirmed in vivo in human peripheral blood from individuals with low folate intake. Alterations to cellular miRNA expression profiles represent a novel mode of action of folate deprivation and arsenic exposure, and specific alterations in miRNA expression may be a powerful biomarker for these and other toxins with serious effects on human health. (Cancer Res 2006; 66(22): 10843-8)
Functional CXCR4-Expressing Microparticles and SDF-1 Correlate with Circulating Acute Myelogenous Leukemia Cells
Authors: Kalinkovich Alexander , Tavor Sigal , Avigdor Abraham , Kahn Joy , Brill Alexander , Petit Isabelle , Goichberg Polina , Tesio Melania , Netzer Neta , Naparstek Elizabeth , Hardan Izhar , Nagler Arnon , Resnick Igor , Tsimanis Alexander , Lapidot Tsvee 
Published: November 2006

Abstract
Stromal cell–derived factor-1 (SDF-1/CXCL12) and its receptor CXCR4 are implicated in the pathogenesis and prognosis of acute myelogenous leukemia (AML). Cellular microparticles, submicron vesicles shed from the plasma membrane of various cells, are also associated with human pathology. In the present study, we investigated the putative relationships between the SDF-1/CXCR4 axis and microparticles in AML. We detected CXCR4-expressing microparticles (CXCR4+ microparticles) in the peripheral blood and bone marrow plasma samples of normal donors and newly diagnosed adult AML patients. In samples from AML patients, levels of CXCR4+ microparticles and total SDF-1 were elevated compared with normal individuals. The majority of CXCR4+ microparticles in AML patients were CD45+, whereas in normal individuals, they were mostly CD41+. Importantly, we found a strong correlation between the levels of CXCR4+ microparticle and WBC count in the peripheral blood and bone marrow plasma obtained from the AML patients. Of interest, levels of functional, noncleaved SDF-1 were reduced in these patients compared with normal individuals and also strongly correlated with the WBC count. Furthermore, our data indicate NH2-terminal truncation of the CXCR4 molecule in the microparticles of AML patients. However, such microparticles were capable of transferring the CXCR4 molecule to AML-derived HL-60 cells, enhancing their migration to SDF-1 in vitro and increasing their homing to the bone marrow of irradiated NOD/SCID/β2mnull mice. The CXCR4 antagonist AMD3100 reduced these effects. Our findings suggest that functional CXCR4+ microparticles and SDF-1 are involved in the progression of AML. We propose that their levels are potentially valuable as an additional diagnostic AML variable. (Cancer Res 2006; 66(22): 11013-20)