bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biogenesis of
Salmonella enterica
Serovar Typhimurium Membrane Vesicles Provoked by Induction of PagC
Authors: Kitagawa Ryo , Takaya Akiko , Ohya Mai , Mizunoe Yoshimitsu , Takade Akemi , Yoshida Shin-ichi , Isogai Emiko , Yamamoto Tomoko 
Published: August 2010

ABSTRACT

Gram-negative bacteria ubiquitously release membrane vesicles (MVs) into the extracellular milieu. Although MVs are the product of growing bacteria, not of cell lysis or death, the regulatory mechanisms underlying MV formation remained unknown. We have found that MV biogenesis is provoked by the induction of PagC, a
Salmonella
-specific protein whose expression is activated by conditions that mimic acidified macrophage phagosomes. PagC is a major constituent of
Salmonella
MVs, and increased expression accelerates vesiculation. Expression of PagC is regulated at the posttranscriptional and/or posttranslational level in a sigmaS (RpoS)-dependent manner. Serial quantitative analysis has demonstrated that MV formation can accelerate when the quantity of the MV constituents, OmpX and PagC, rises. Overproduction of PagC dramatically impacts the difference in the relative amount of vesiculation, but the corresponding overproduction of OmpX was less pronounced. Quantitative examination of the ratios of PagC and OmpX in the periplasm, outer membrane, and MVs demonstrates that PagC is preferentially enriched in MVs released from
Salmonella
cells. This suggests that specific protein sorting mechanisms operate when MVs are formed. The possible role(s) of PagC-MV in host cells is discussed.
A Novel Six-Rhodopsin System in a Single Archaeon
Authors: Fu Hsu-Yuan , Lin Yu-Cheng , Chang Yung-Ning , Tseng Hsiaochu , Huang Ching-Che , Liu Kang-Cheng , Huang Ching-Shin , Su Che-Wei , Weng Rueyhung Roc , Lee Yin-Yu , Ng Wailap Victor , Yang Chii-Shen 
Published: August 2010

ABSTRACT

Microbial rhodopsins, a diverse group of photoactive proteins found in
Archaea
,
Bacteria
, and
Eukarya
, function in photosensing and photoenergy harvesting and may have been present in the resource-limited early global environment. Four different physiological functions have been identified and characterized for nearly 5,000 retinal-binding photoreceptors, these being ion transporters that transport proton or chloride and sensory rhodopsins that mediate light-attractant and/or -repellent responses. The greatest number of rhodopsins previously observed in a single archaeon had been four. Here, we report a newly discovered six-rhodopsin system in a single archaeon,
Haloarcula marismortui
, which shows a more diverse absorbance spectral distribution than any previously known rhodopsin system, and, for the first time, two light-driven proton transporters that respond to the same wavelength. All six rhodopsins, the greatest number ever identified in a single archaeon, were first shown to be expressed in
H. marismortui
, and these were then overexpressed in
Escherichia coli
. The proteins were purified for absorption spectra and photocycle determination, followed by measurement of ion transportation and phototaxis. The results clearly indicate the existence of a proton transporter system with two isochromatic rhodopsins and a new type of sensory rhodopsin-like transducer in
H. marismortui
.
The Elemental Sulfur-Responsive Protein (SipA) from the Hyperthermophilic Archaeon
Pyrococcus furiosus
Is Regulated by Sulfide in an Iron-Dependent Manner
Authors: Clarkson Sonya M. , Newcomer Elizabeth C. , Young Everett G. , Adams Michael W. W. 
Published: August 2010

ABSTRACT

The gene (
sipA
) encoding the sulfur-induced protein A (PF2025) is highly upregulated during growth of
Pyrococcus furiosus
on elemental sulfur (S
0
). Expression of
sipA
is regulated by sulfide, the product of S
0
reduction, but in an iron-dependent manner. SipA is proposed to play a role in intracellular iron sulfide detoxification.
AglJ Adds the First Sugar of the N-Linked Pentasaccharide Decorating the
Haloferax volcanii
S-Layer Glycoprotein
Authors: Kaminski Lina , Abu-Qarn Mehtap , Guan Ziqiang , Naparstek Shai , Ventura Valeria V. , Raetz Christian R. H. , Hitchen Paul G. , Dell Anne , Eichler Jerry 
Published: August 2010

ABSTRACT

Like the
Eukarya
and
Bacteria
, the
Archaea
also perform N glycosylation. Using the haloarchaeon
Haloferax volcanii
as a model system, a series of Agl proteins involved in the archaeal version of this posttranslational modification has been identified. In the present study, the participation of HVO_1517 in N glycosylation was considered, given its homology to a known component of the eukaryal N-glycosylation pathway and because of the genomic proximity of
HVO
_
1517
to
agl
genes encoding known elements of the
H. volcanii
N-glycosylation process. By combining the deletion of
HVO
_
1517
with mass spectrometric analysis of both dolichol phosphate monosaccharide-charged carriers and the S-layer glycoprotein, evidence was obtained showing the participation of HVO_1517, renamed AglJ, in adding the first hexose of the N-linked pentasaccharide decorating this reporter glycoprotein. The deletion of
aglJ
, however, did not fully prevent the attachment of a hexose residue to the S-layer glycoprotein. Moreover, in the absence of AglJ, the level of only one of the three monosaccharide-charged dolichol phosphate carriers detected in the cell was reduced. Nonetheless, in cells lacking AglJ, no further sugar subunits were added to the remaining monosaccharide-charged dolichol phosphate carriers or to the monosaccharide-modified S-layer glycoprotein, pointing to the importance of the sugar added through the actions of AglJ for proper N glycosylation. Finally, while
aglJ
can be deleted,
H. volcanii
surface layer integrity is compromised in the absence of the encoded protein.
A Commensal Gone Bad: Complete Genome Sequence of the Prototypical Enterotoxigenic
Escherichia coli
Strain H10407
Authors: Crossman Lisa C. , Chaudhuri Roy R. , Beatson Scott A. , Wells Timothy J. , Desvaux Mickael , Cunningham Adam F. , Petty Nicola K. , Mahon Vivienne , Brinkley Carl , Hobman Jon L. , Savarino Stephen J. , Turner Susan M. , Pallen Mark J. , Penn Charles W. , Parkhill Julian , Turner A. Keith , Johnson Timothy J. , Thomson Nicholas R. , Smith Stephen G. J. , Henderson Ian R. 
Published: August 2010

ABSTRACT

In most cases,
Escherichia coli
exists as a harmless commensal organism, but it may on occasion cause intestinal and/or extraintestinal disease. Enterotoxigenic
E. coli
(ETEC) is the predominant cause of
E. coli
-mediated diarrhea in the developing world and is responsible for a significant portion of pediatric deaths. In this study, we determined the complete genomic sequence of
E. coli
H10407, a prototypical strain of enterotoxigenic
E. coli
, which reproducibly elicits diarrhea in human volunteer studies. We performed genomic and phylogenetic comparisons with other
E. coli
strains, revealing that the chromosome is closely related to that of the nonpathogenic commensal strain
E. coli
HS and to those of the laboratory strains
E. coli
K-12 and C. Furthermore, these analyses demonstrated that there were no chromosomally encoded factors unique to any sequenced ETEC strains. Comparison of the
E. coli
H10407 plasmids with those from several ETEC strains revealed that the plasmids had a mosaic structure but that several loci were conserved among ETEC strains. This study provides a genetic context for the vast amount of experimental and epidemiological data that have been published.
Biosynthetic Pathway for γ-Cyclic Sarcinaxanthin in
Micrococcus luteus
: Heterologous Expression and Evidence for Diverse and Multiple Catalytic Functions of C
50
Carotenoid Cyclases
Authors: Netzer Roman , Stafsnes Marit H. , Andreassen Trygve , Goksøyr Audun , Bruheim Per , Brautaset Trygve 
Published: August 2010

ABSTRACT

We report the cloning and characterization of the biosynthetic gene cluster (
crtE
,
crtB
,
crtI
,
crtE2
,
crtYg
,
crtYh
, and
crtX
) of the γ-cyclic C
50
carotenoid sarcinaxanthin in
Micrococcus luteus
NCTC2665. Expression of the complete and partial gene cluster in
Escherichia coli
hosts revealed that sarcinaxanthin biosynthesis from the precursor molecule farnesyl pyrophosphate (FPP) proceeds via C
40
lycopene, C
45
nonaflavuxanthin, C
50
flavuxanthin, and C
50
sarcinaxanthin. Glucosylation of sarcinaxanthin was accomplished by the
crtX
gene product. This is the first report describing the biosynthetic pathway of a γ-cyclic C
50
carotenoid. Expression of the corresponding genes from the marine
M. luteus
isolate Otnes7 in a lycopene-producing
E. coli
host resulted in the production of up to 2.5 mg/g cell dry weight sarcinaxanthin in shake flasks. In an attempt to experimentally understand the specific difference between the biosynthetic pathways of sarcinaxanthin and the structurally related ε-cyclic decaprenoxanthin, we constructed a hybrid gene cluster with the γ-cyclic C
50
carotenoid cyclase genes
crtYg
and
crtYh
from
M. luteus
replaced with the analogous ε-cyclic C
50
carotenoid cyclase genes
crtYe
and
crtYf
from the natural decaprenoxanthin producer
Corynebacterium glutamicum
. Surprisingly, expression of this hybrid gene cluster in an
E. coli
host resulted in accumulation of not only decaprenoxanthin, but also sarcinaxanthin and the asymmetric ε- and γ-cyclic C
50
carotenoid sarprenoxanthin, described for the first time in this work. Together, these data contributed to new insight into the diverse and multiple functions of bacterial C
50
carotenoid cyclases as key catalysts for the synthesis of structurally different carotenoids.
Radiation Desiccation Response Motif-Like Sequences Are Involved in Transcriptional Activation of the Deinococcal
ssb
Gene by Ionizing Radiation but Not by Desiccation
Authors: Ujaoney Aman Kumar , Potnis Akhilesh A. , Kane Pratiksha , Mukhopadhyaya Rita , Apte Shree Kumar 
Published: August 2010

ABSTRACT

Single-stranded-DNA binding protein (SSB) levels during poststress recovery of
Deinococcus radiodurans
were significantly enhanced by
60
Co gamma rays or mitomycin C treatment but not by exposure to UV rays, hydrogen peroxide (H
2
O
2
), or desiccation. Addition of rifampin prior to postirradiation recovery blocked such induction.
In silico
analysis of the
ssb
promoter region revealed a 17-bp palindromic radiation/desiccation response motif (RDRM1) at bp −114 to −98 and a somewhat similar sequence (RDRM2) at bp −213 to −197, upstream of the
ssb
open reading frame. Involvement of these
cis
elements in radiation-responsive
ssb
gene expression was assessed by constructing transcriptional fusions of edited versions of the
ssb
promoter region with a nonspecific acid phosphatase encoding reporter gene,
phoN
. Recombinant
D. radiodurans
strains carrying such constructs clearly revealed (i) transcriptional induction of the
ssb
promoter upon irradiation and mitomycin C treatment but not upon UV or H
2
O
2
treatment and (ii) involvement of both RDRM-like sequences in such activation of SSB expression, in an additive manner.
Draft Genome Sequences of
Actinobacillus pleuropneumoniae
Serotypes 2 and 6
Authors: Zhan Bujie , Angen Øystein , Hedegaard Jakob , Bendixen Christian , Panitz Frank 
Published: August 2010

ABSTRACT

Actinobacillus pleuropneumoniae
is a bacterial pathogen that causes highly contagious respiratory infection in pigs and has a serious impact on the production economy and animal welfare. As clear differences in virulence between serotypes have been observed, the genetic basis should be investigated at the genomic level. Here, we present the draft genome sequences of the
A. pleuropneumoniae
serotypes 2 (strain 4226) and 6 (strain Femo).
Complete Genome Sequence of
Staphylococcus aureus
Strain JKD6008, an ST239 Clone of Methicillin-Resistant
Staphylococcus aureus
with Intermediate-Level Vancomycin Resistance
Authors: Howden Benjamin P. , Seemann Torsten , Harrison Paul F. , McEvoy Chris R. , Stanton Jo-Ann L. , Rand Christy J. , Mason Chris W. , Jensen Slade O. , Firth Neville , Davies John K. , Johnson Paul D. R. , Stinear Timothy P. 
Published: August 2010

ABSTRACT

We report here the complete 2.92-Mb genome sequence of a clinical isolate of methicillin-resistant
Staphylococcus aureus
subsp.
aureus
that demonstrates intermediate-level vancomycin resistance. The strain, named JKD6008, belongs to multilocus sequence type 239 and was isolated from the bloodstream of a patient in New Zealand in 2003.
Radiation-Guided Drug Delivery to Mouse Models of Lung Cancer
Authors: Hariri Ghazal , Yan Heping , Wang Hailun , Han Zhaozhong , Hallahan Dennis E. 
Published: August 2010

Abstract
Purpose: The purpose of this study was to achieve improved cancer-specific delivery and bioavailability of radiation-sensitizing chemotherapy using radiation-guided drug delivery.
Experimental Design: Phage display technology was used to isolate a recombinant peptide (HVGGSSV) that binds to a radiation-inducible receptor in irradiated tumors. This peptide was used to target nab-paclitaxel to irradiated tumors, achieving tumor-specificity and enhanced bioavailability of paclitaxel.
Results: Optical imaging studies showed that HVGGSSV-guided nab-paclitaxel selectively targeted irradiated tumors and showed 1.48 ± 1.66 photons/s/cm2/sr greater radiance compared with SGVSGHV-nab-paclitaxel, and 1.49 ± 1.36 photons/s/cm2/sr greater than nab-paclitaxel alone (P &lt; 0.05). Biodistribution studies showed &gt;5-fold increase in paclitaxel levels within irradiated tumors in HVGGSSV-nab-paclitaxel–treated groups as compared with either nab-paclitaxel or SGVSGHV-nab-paclitaxel at 72 hours. Both Lewis lung carcinoma and H460 lung carcinoma murine models showed significant tumor growth delay for HVGGSSV-nab-paclitaxel as compared with nab-paclitaxel, SGVSGHV-nab-paclitaxel,and saline controls. HVGGSSV-nab-paclitaxel treatment induced a significantly greater loss in vasculature in irradiated tumors compared with unirradiated tumors, nab-paclitaxel, SGVSGHV-nab-paclitaxel, and untreated controls.
Conclusions: HVGGSSV-nab-paclitaxel was found to bind specifically to the tax-interacting protein-1 (TIP-1) receptor expressed in irradiated tumors, enhance bioavailability of paclitaxel, and significantly increase tumor growth delay as compared with controls in mouse models of lung cancer. Here we show that targeting nab-paclitaxel to radiation-inducible TIP-1 results in increased tumor-specific drug delivery and enhanced biological efficacy in the treatment of cancer. Clin Cancer Res; 16(20); 4968–77. ©2010 AACR.
A Marker of Homologous Recombination Predicts Pathologic Complete Response to Neoadjuvant Chemotherapy in Primary Breast Cancer
Authors: Graeser Monika , McCarthy Afshan , Lord Christopher J. , Savage Kay , Hills Margaret , Salter Janine , Orr Nicholas , Parton Marina , Smith Ian E. , Reis-Filho Jorge S. , Dowsett Mitch , Ashworth Alan , Turner Nicholas C. 
Published: August 2010

Abstract
Purpose: To assess the prevalence of defective homologous recombination (HR)-based DNA repair in sporadic primary breast cancers, examine the clincopathologic features that correlate with defective HR and the relationship with neoadjuvant chemotherapy response.
Experimental Design: We examined a cohort of 68 patients with sporadic primary breast cancer who received neoadjuvant anthracylcine-based chemotherapy, with core biopsies taken 24 hours after the first cycle of chemotherapy. We assessed RAD51 focus formation, a marker of HR competence, by immunofluorescence in postchemotherapy biopsies along with geminin as a marker of proliferative cells. We assessed the RAD51 score as the proportion of proliferative cells with RAD51 foci.
Results: A low RAD51 score was present in 26% of cases (15/57, 95% CI: 15%–40%). Low RAD51 score correlated with high histologic grade (P = 0.031) and high baseline Ki67 (P = 0.005). Low RAD51 score was more frequent in triple-negative breast cancers than in ER- and/or HER2-positive breast cancer (67% vs. 19% respectively; P = 0.0036). Low RAD51 score was strongly predictive of pathologic complete response (pathCR) to chemotherapy, with 33% low RAD51 score cancers achieving pathCR compared with 3% of other cancers (P = 0.011).
Conclusions: Our results suggest that defective HR, as indicated by low RAD51 score, may be one of the factors that underlie sensitivity to anthracycline-based chemotherapy. Defective HR is frequent in triple-negative breast cancer, but it is also present in a subset of other subtypes, identifying breast cancers that may benefit from therapies that target defective HR such as PARP inhibitors. Clin Cancer Res; 16(24); 6159–68. ©2010 AACR.
The role of religiosity, coping strategies, self-efficacy and personality dimensions in the prediction of Iranian undergraduate rehabilitation interns’ satisfaction with their clinical experience
Authors: Mirsaleh YR , Rezai H. , Kivi SR , Ghorbani R. 
Published: August 2010

Objective: To investigate the relationship between religiosity, coping styles, self-efficacy and personality dimensions as predictors of satisfaction with clinical experience in rehabilitation interns during transition from academic study to clinical internship. Design: A cross-sectional survey design. Setting: Five rehabilitation faculties. Participants: Three hundred and eighteen undergraduate rehabilitation interns, including physical therapy, occupational therapy and speech and language pathology students. Main outcome measures: Islamic Religiosity Scale, Ways of Coping Questionnaire, General Self-efficacy Scale, NEO Five Factor Inventory, and Satisfaction with Clinical Experiences Questionnaire. Results: Religiosity, problem-focused coping and general self-efficacy had significant positive correlation with satisfaction with clinical internship in rehabilitation students. Among personality dimensions, openness, agreement and consciousness had significant positive correlation with satisfaction with clinical experience and neuroticism had significant negative correlation with satisfaction with clinical experience. The results of regression analysis demonstrated that religiosity and self-efficacy had important roles in the prediction of satisfaction with clinical experience in all the rehabilitation intern students of three disciplines (physical therapy, occupational therapy, and speech and language pathology). Conclusion: Religiosity, problem-focused coping and general self-efficacy seem to be good predictors of satisfaction with clinical internship in rehabilitation students.
A quasi-experimental feasibility study to determine the effect of a systematic treatment programme on the scores of the Nottingham Adjustment Scale of individuals with visual field deficits following stroke
Authors: Taylor Lisa , Poland Fiona , Harrison Peter , Stephenson Richard 
Published: August 2010

Objective: To evaluate a systematic treatment programme developed by the researcher that targeted aspects of visual functioning affected by visual field deficits following stroke. Design: The study design was a non-equivalent control (conventional) group pretest–posttest quasi-experimental feasibility design, using multisite data collection methods at specified stages. Setting: The study was undertaken within three acute hospital settings as outpatient follow-up sessions. Subjects: Individuals who had visual field deficits three months post stroke were studied. Interventions: A treatment group received routine occupational therapy and an experimental group received, in addition, a systematic treatment programme. The treatment phase of both groups lasted six weeks. Main measures: The Nottingham Adjustment Scale, a measure developed specifically for visual impairment, was used as the primary outcome measure. Results: The change in Nottingham Adjustment Scale score was compared between the experimental ( n = 7) and conventional ( n = 8) treatment groups using the Wilcoxon signed ranks test. The result of Z =  −2.028 ( P =  0.043) showed that there was a statistically significant difference between the change in Nottingham Adjustment Scale score between both groups. Conclusions: The introduction of the systematic treatment programme resulted in a statistically significant change in the scores of the Nottingham Adjustment Scale.
Less-Invasive Reconstruction of Chronic Achilles Tendon Ruptures Using a Peroneus Brevis Tendon Transfer
Authors: Maffulli Nicola , Spiezia Filippo , Longo Umile Giuseppe , Denaro Vincenzo 
Published: August 2010

Background A less-invasive technique to reconstruct chronic Achilles tendon rupture with transfer of the tendon of peroneus brevis is suitable in patients with a tendon gap less than 6 cm. Purpose To report the results of a longitudinal study on reconstruction of chronic Achilles tendon rupture using a less-invasive peroneus brevis repair through 2 paramidline incisions. Study Design Case series; Level of evidence, 4. Methods Thirty-two patients underwent surgery for chronic Achilles tendon rupture with a tendon gap during surgery less than 6 cm, occurring between 60 days and 9 months preoperatively. All participants were prospectively followed for 5 to 8 years; final review was performed at 48.4 ± 13.5 months from the operation. Clinical and functional assessment (anthropometric measurements, isometric strength, postoperative Achilles tendon total rupture score) was performed. Results All patients were able to walk on tiptoes, and no patient used a heel lift or walked with a visible limp. No patient developed a clinically evident deep vein thrombosis or sustained a rerupture. Five patients were managed nonoperatively after a superficial infection of one of the surgical wounds. At final review, the maximum calf circumference remained significantly decreased in the operated leg (39.2 ± 6.2 cm [side with rupture] vs 40.9 ± 7.0 cm [uninjured side]; P = .04). The operated limb was significantly less strong than the nonoperated one (231.2 ± 132.4 N vs 275.3 ± 150.2 N; P = .033). The Achilles tendon total rupture score at final follow-up was 92.5 ± 14.2. Conclusion The management of chronic Achilles tendon tears by a less-invasive peroneus brevis repair is technically demanding but safe. It allows good recovery, even in patients with a chronic rupture of 9 months’ duration. These patients should be warned that they are at risk for postoperative complications and that their ankle plantar flexion strength is likely to be reduced.