bluuebunny/crossref_metadata_2025_split huggingface dataset:
Response of Pseudomonas putida KT2440 to Increased NADH and ATP Demand
Authors: Ebert Birgitta E. , Kurth Felix , Grund Marcel , Blank Lars M. , Schmid Andreas 
Published: July 2011

ABSTRACTAdenosine phosphate and NAD cofactors play a vital role in the operation of cell metabolism, and their levels and ratios are carefully regulated in tight ranges. Perturbations of the consumption of these metabolites might have a great impact on cell metabolism and physiology. Here, we investigated the impact of increased ATP hydrolysis and NADH oxidation rates on the metabolism ofPseudomonas putidaKT2440 by titration of 2,4-dinitrophenol (DNP) and overproduction of a water-forming NADH oxidase, respectively. Both perturbations resulted in a reduction of the biomass yield and, as a consequence of the uncoupling of catabolic and anabolic activities, in an amplification of the net NADH regeneration rate. However, a stimulation of the specific carbon uptake rate was observed only whenP. putidawas challenged with very high 2,4-dinitrophenol concentrations and was comparatively unaffected by recombinant NADH oxidase activity. This behavior contrasts with the comparably sensitive performance described, for example, forEscherichia coliorSaccharomyces cerevisiae. The apparent robustness ofP. putidametabolism indicates that it possesses a certain buffering capacity and a high flexibility to adapt to and counteract different stresses without showing a distinct phenotype. These findings are important, e.g., for the development of whole-cell redox biocatalytic processes that impose equivalent burdens on the cell metabolism: stoichiometric consumption of (reduced) redox cofactors and increased energy expenditures, due to the toxicity of the biocatalytic compounds.
Glycosylation of DsbA in Francisella tularensis subsp. tularensis
Authors: Thomas Rebecca M. , Twine Susan M. , Fulton Kelly M. , Tessier Luc , Kilmury Sara L. N. , Ding Wen , Harmer Nicholas , Michell Stephen L. , Oyston Petra C. F. , Titball Richard W. , Prior Joann L. 
Published: July 2011

ABSTRACTInFrancisella tularensissubsp.tularensis, DsbA has been shown to be an essential virulence factor and has been observed to migrate to multiple protein spots on two-dimensional electrophoresis gels. In this work, we show that the protein is modified with a 1,156-Da glycan moiety inO-linkage. The results of mass spectrometry studies suggest that the glycan is a hexasaccharide, comprised ofN-acetylhexosamines, hexoses, and an unknown monosaccharide. Disruption of two genes within theFTT0789-FTT0800putative polysaccharide locus, including agalEhomologue (FTT0791) and a putative glycosyltransferase (FTT0798), resulted in loss of glycan modification of DsbA. TheF. tularensissubsp.tularensisΔFTT0798and ΔFTT0791::Cm mutants remained virulent in the murine model of subcutaneous tularemia. This indicates that glycosylation of DsbA does not play a major role in virulence under these conditions. This is the first report of the detailed characterization of the DsbA glycan and putative role of theFTT0789-FTT0800gene cluster in glycan biosynthesis.
Structure-Based Modification of a Clostridium difficile-Targeting Endolysin Affects Activity and Host Range
Authors: Mayer Melinda J. , Garefalaki Vasiliki , Spoerl Rebecca , Narbad Arjan , Meijers Rob 
Published: July 2011

ABSTRACT

Endolysin CD27L causes cell lysis of the pathogen
Clostridium difficile
, a major cause of nosocomial infection. We report a structural and functional analysis of the catalytic activity of CD27L against
C. difficile
and other bacterial strains. We show that truncation of the endolysin to the N-terminal domain, CD27L
1–179
, gave an increased lytic activity against cells of
C. difficile
, while the C-terminal region, CD27L
180–270
, failed to produce lysis. CD27L
1–179
also has increased activity against other bacterial species that are targeted by the full-length protein and in addition was able to lyse some CD27L-insensitive strains. However, CD27L
1–179
retained a measure of specificity, failing to lyse a wide range of bacteria. The use of green fluorescent protein (GFP)-labeled proteins demonstrated that both CD27L and CD27L
1–179
bound to
C. difficile
cell walls. The crystal structure of CD27L
1–179
confirms that the enzyme is a zinc-dependent
N
-acetylmuramoyl-
l
-alanine amidase. A structure-based sequence analysis allowed us to identify four catalytic residues, a proton relay cascade, and a substrate binding pocket. A BLAST search shows that the closest-related amidases almost exclusively target
Clostridia
. This implied that the catalytic domain alone contained features that target a specific bacterial species. To test this hypothesis, we modified Leu 98 to a Trp residue which is found in an endolysin from a bacteriophage of
Listeria monocytogenes
(PlyPSA). This mutation in CD27L resulted in an increased activity against selected serotypes of
L. monocytogenes
, demonstrating the potential to tune the species specificity of the catalytic domain of an endolysin.
Stepwise Activity of ClpY (HslU) Mutants in the Processive Degradation of Escherichia coli ClpYQ (HslUV) Protease Substrates
Authors: Hsieh Fan-Ching , Chen Chien-Teh , Weng Yu-Ting , Peng Sheng-Shiang , Chen Yu-Chun , Huang Ling-Yi , Hu Hui-Ting , Wu Yew-Long , Lin Nai-Chun , Wu Whei-Fen 
Published: July 2011

ABSTRACT

In
Escherichia coli
, ClpYQ (HslUV) is a two-component ATP-dependent protease composed of ClpY (HslU), an ATPase with unfolding activity, and ClpQ (HslV), a peptidase. In the ClpYQ proteolytic complex, the hexameric rings of ClpY (HslU) are responsible for protein recognition, unfolding, and translocation into the proteolytic inner chamber of the dodecameric ClpQ (HslV). Each of the three domains, N, I, and C, in ClpY has its own distinct activity. The double loops (amino acids [aa] 137 to 150 and 175 to 209) in domain I of ClpY are necessary for initial recognition/tethering of natural substrates such as SulA, a cell division inhibitor protein. The highly conserved sequence GYVG (aa 90 to 93) pore I site, along with the GESSG pore II site (aa 265 to 269), contribute to the central pore of ClpY in domain N. These two central loops of ClpY are in the center of its hexameric ring in which the energy of ATP hydrolysis allows substrate translocation and then degradation by ClpQ. However, no data have been obtained to determine the effect of the central loops on substrate binding or as part of the processivity of the ClpYQ complex. Thus, we probed the features of ClpY important for substrate engagement and protease processivity via random PCR or site-specific mutagenesis. In yeast two-hybrid analysis and pulldown assays, using isolated ClpY mutants and the pore I or pore II site of ClpY, each was examined for its influence on the adjoining structural regions of the substrates. The pore I site is essential for the translocation of the engaged substrates. Our
in vivo
study of the ClpY mutants also revealed that an ATP-binding site in domain N, separate from its role in polypeptide (ClpY) oligomerization, is required for complex formation with ClpQ. Additionally, we found that the tyrosine residue at position 408 in ClpY is critical for stabilization of hexamer formation between subunits. Therefore, our studies suggest that stepwise activities of the ClpYQ protease are necessary to facilitate the processive degradation of its natural substrates.
The Metalloprotease of Listeria monocytogenes Is Regulated by pH
Authors: Forster Brian M. , Bitar Alan Pavinski , Slepkov Emily R. , Kota Karthik J. , Sondermann Holger , Marquis Hélène 
Published: July 2011

ABSTRACTListeria monocytogenesis an intracytosolic bacterial pathogen. Among the factors contributing to escape from vacuoles are a phosphatidylcholine phospholipase C (PC-PLC) and a metalloprotease (Mpl). Both enzymes are translocated across the bacterial membrane as inactive proproteins, whose propeptides serve in part to maintain them in association with the bacterium. We have shown that PC-PLC maturation is regulated by Mpl and pH and that Mpl maturation occurs by autocatalysis. In this study, we tested the hypothesis that Mpl activity is pH regulated. To synchronize the effect of pH on bacteria, the cytosolic pH of infected cells was manipulated immediately after radiolabelingde novo-synthesized bacterial proteins. Immunoprecipitation of secreted Mpl from host cell lysates revealed the presence of the propeptide and catalytic domain in samples treated at pH 6.5 but not at pH 7.3. The zymogen was present in small amounts under all conditions. Since proteases often remain associated with their respective propeptide following autocatalysis, we aimed at determining whether pH regulates autocatalysis or secretion of the processed enzyme. For this purpose, we used an Mpl construct that contains a Flag tag at the N terminus of its catalytic domain and antibodies that can distinguish N-terminal and non-N-terminal Flag. By fluorescence microscopy, we observed the Mpl zymogen associated with the bacterium at physiological pH but not following acidification. Mature Mpl was not detected in association with the bacterium at either pH. Using purified proteins, we determined that processing of the PC-PLC propeptide by mature Mpl is also pH sensitive. These results indicate that pH regulates the activity of Mpl on itself and on PC-PLC.
Quantitative Proteomic Analysis Reveals Formation of an EscL-EscQ-EscN Type III Complex in Enteropathogenic Escherichia coli
Authors: Biemans-Oldehinkel Esther , Sal-Man Neta , Deng Wanyin , Foster Leonard J. , Finlay B. Brett 
Published: July 2011

ABSTRACT

We characterized Orf5 and SepQ, two type III secretion (T3S) system proteins in enteropathogenic
Escherichia coli
, and showed that they are essential for T3S, associated with the bacterial membrane, and interact with EscN. Our findings suggest that Orf5 and SepQ are homologs of YscL and YscQ from
Yersinia
, respectively.
RNase Y in Bacillus subtilis: a Natively Disordered Protein That Is the Functional Equivalent of RNase E from Escherichia coli
Authors: Lehnik-Habrink Martin , Newman Joseph , Rothe Fabian M. , Solovyova Alexandra S. , Rodrigues Cecilia , Herzberg Christina , Commichau Fabian M. , Lewis Richard J. , Stülke Jörg 
Published: July 2011

ABSTRACTThe control of mRNA stability is an important component of regulation in bacteria. Processing and degradation of mRNAs are initiated by an endonucleolytic attack, and the cleavage products are processively degraded by exoribonucleases. In many bacteria, these RNases, as well as RNA helicases and other proteins, are organized in a protein complex called the RNA degradosome. InEscherichia coli, the RNA degradosome is assembled around the essential endoribonuclease E. InBacillus subtilis, the recently discovered essential endoribonuclease RNase Y is involved in the initiation of RNA degradation. Moreover, RNase Y interacts with other RNases, the RNA helicase CshA, and the glycolytic enzymes enolase and phosphofructokinase in a degradosome-like complex. In this work, we have studied the domain organization of RNase Y and the contribution of the domains to protein-protein interactions. We provide evidence for the physical interaction between RNase Y and the degradosome partnersin vivo. We present experimental and bioinformatic data which indicate that the RNase Y contains significant regions of intrinsic disorder and discuss the possible functional implications of this finding. The localization of RNase Y in the membrane is essential both for the viability ofB. subtilisand for all interactions that involve RNase Y. The results presented in this study provide novel evidence for the idea that RNase Y is the functional equivalent of RNase E, even though the two enzymes do not share any sequence similarity.
Assessment of Tissue Autofluorescence and Reflectance for Oral Cavity Cancer Screening
Authors: Sweeny Larissa , Dean Nichole R. , Magnuson J. Scott , Carroll William R. , Clemons Lisa , Rosenthal Eben L. 
Published: July 2011

ObjectiveAlthough approved by the US Food and Drug Administration for clinical use, the utility of handheld tissue reflectance and autofluorescence devices for screening head and neck cancer patients is poorly defined. There is limited published evidence regarding the efficacy of these devices. The authors investigated the sensitivity and specificity of these modalities compared with standard examination.Study DesignProspective, cross‐sectional analysis.SettingTertiary care medical center.Subjects and MethodsPatients who were treated previously for head and neck cancer (n = 88) between 2009 and 2010 were included. Patients were screened using white light visualization (standard of care) and compared with tissue reflectance and autofluorescence visualization. Screening results were compared with biopsy or long‐term follow‐up.ResultsAutofluorescence visualization had a specificity of 81% and a sensitivity of 50% for detecting oral cavity cancer, whereas white light visualization had a specificity of 98% and a sensitivity of 50%. Tissue reflectance visualization had low sensitivity (0%) and good specificity (86%). The power of this study was insufficient to compare the positive and negative predictive values of standard white light examination (50% and 98%, respectively) to tissue autofluorescence (11% and 97%) or reflectance (0% and 95%). In addition, stratification by previous radiation therapy found no statistically significant difference in screening results.ConclusionStandard clinical lighting has a higher specificity than tissue reflectance and autofluorescence visualization for detection of disease in patients with a history of head and neck cancer. This study does not support the added costs associated with these devices.
Severe unilateral headache caused by skull bone infarction with epidural haematoma in a patient with sickle cell disease
Authors: Arends Samuel , Coebergh Jan Adriaan , Kerkhoffs Jean Louis , van Gils Adrianus , Koppen Hille 
Published: July 2011

Background: The clinical manifestations of sickle cell disease (SCD) vary, but may be attributed to vaso-occlusion, chronic hemolytic anemia, and infections as a result of functional asplenia. We report a case of a man who presented with severe headache caused by an uncommon complication of SCD. Case: A 19-year-old Surinamer man presented to the emergency department with severe headache. The progressive headache started one day previously. The headache was located frontotemporally on the right side. It was pulsating with paroxysms of fierce pain. There was no nausea or vomiting. The medical history reported sickle cell disease of the HbSC type. The physical and neurological examination was normal. He was afebrile with a blood pressure of 118/72 mmHg. Blood tests and CSF investigation showed no abnormalities. CT-scan of the head was normal. The headache disappeared after two days. Eight days later he presented again, with a relapsing severe headache. Physical, neurological examination and blood investigations were normal. MRI now showed infarction located in the parietal skull bone, with a small adjacent epidural hematoma. The headache disappeared gradually over 8 days. Repeat MRI one month later showed complete disappearance of the epidural hematoma. The first headache episode was thought to be due to the initial skull bone infarction as no epidural hematoma had been present initially. The second headache episode was thought to be due to the development of the epidural hematoma. Discussion: A skull bone infarction is an uncommon complication of SCD, as typically these are located in the long bones. Even more uncommon is a epidural hematoma which was probably the result of the altered bone and vesselwall structure following the skull bone infarction. To our knowledge this is the first case reporting a skull-bone infarction with adjacent spontaneous epidural hematoma in an adult with sickle cell disease of the HbSC type. Our case emphasizes the need to recognize skull infarction and a concomitant spontaneous epidural hematoma as a possible complication of SCD.
Migraine and mortality: A systematic review and meta-analysis
Authors: Schürks Markus , Rist Pamela M , Shapiro Robert E , Kurth Tobias 
Published: July 2011

Objective: To evaluate the evidence on the association between migraine and mortality. Methods: Systematic review and meta-analysis of studies investigating the association between any migraine (all forms of migraine collectively) or migraine subtypes (e.g. migraine with aura) and mortality published until March 2011. Results: We identified ten cohort studies. Studies differed regarding the types of mortality investigated and only four presented aura-stratified results, limiting pooled analyses with regard to migraine subtypes and with regard to cause-specific mortality. For any migraine pooled analyses do not suggest an association with all-cause mortality (five studies; pooled relative risk (RR) = 0.90, 95% confidence interval (CI) 0.71–1.16), cardiovascular disease mortality (CVD; six studies; pooled RR = 1.09, 95% CI 0.89–1.32), or coronary heart disease mortality (CHD; three studies; pooled RR = 0.95, 95% CI 0.57–1.60). Heterogeneity among studies is moderate to high. Two studies suggest that migraine with aura increases risk for CVD and CHD mortality. Conclusion: This meta-analysis does not suggest that any migraine is associated with increased risk of mortality from all causes, CVD, or CHD. However, there is heterogeneity among studies and suggestion that migraine with aura increases CVD and CHD mortality. Given the high prevalence of migraine in the general population a definitive answer to the question of whether migraine or a subtype alters risk for mortality is of high public health importance and further targeted research implicated.
Arthroscopic Second-Generation Autologous Chondrocyte Implantation
Authors: Filardo Giuseppe , Kon Elizaveta , Di Martino Alessandro , Iacono Francesco , Marcacci Maurilio 
Published: July 2011

Background: Regenerative techniques, such as autologous chondrocyte implantation (ACI), have emerged as a potential therapeutic option for the treatment of chondral lesions, aiming to recreate a hyaline-like tissue in the damaged articular surface. The clinical application of the regenerative approach is well documented for different types of scaffold but mostly with an evaluation of the clinical outcome at short-term follow-up. Purpose: This study was conducted to analyze the clinical outcome obtained with arthroscopic second-generation ACI up to 7 years’ follow-up, to assess the durability of the results, and understand its real potential over time. Study Design: Case series; Level of evidence, 4. Methods: Sixty-two consecutive patients, 48 men and 14 women with a mean age of 28.1 ± 11.4 years, affected by chondral lesions of the femoral condyles were enrolled and treated with arthroscopic implantation of the bioengineered tissue Hyalograft C. The average size of the defects was 2.5 ± 1.0 cm2. Patients were evaluated with International Knee Documentation Committee (IKDC), EuroQol visual analog scale (EQ-VAS), and Tegner scores every year for 7 years, and a magnetic resonance imaging evaluation was performed. Results: A statistically significant improvement was observed in all scores from the basal evaluation to the 84 months’ follow-up. The IKDC subjective score increased from 39.6 ± 15.0 to 73.6 ± 18.8 at 12 months; a further slight improvement was observed at 24 months’ follow-up (76.5 ± 20.7), and then the results were stable and reached a final 7-year value of 77.3 ± 21.5. Seven cases (11%) failed. A better outcome was obtained in young active men, whereas the worst results were found in degenerative lesions or when previous surgery had been performed. Postoperative magnetic resonance imaging studies in 42 cases revealed a complete filling of the cartilage defect in 57% of the lesions, complete integration of the graft in 62% of cases, intact repair tissue surface in 50%, homogeneous repair tissue structure in 43%, and a graft signal-intensity score that was isointense with the adjacent native cartilage in 43% and 48% of the cases in dual T2–fast spin echo and 3-dimensional gradient echo with fat suppression sequences, respectively. Conclusion: The analysis of this group of homogeneous patients, prospectively evaluated every year for 7 years, shows that this bioengineered approach with the proper indications may offer good and stable clinical results over time.
Arthroscopic-Assisted Broström-Gould for Chronic Ankle Instability
Authors: Nery Caio , Raduan Fernando , Del Buono Angelo , Asaumi Inacio Diogo , Cohen Moises , Maffulli Nicola 
Published: July 2011

Background: Lateral ankle sprains account for 85% of ankle lesions. Hypothesis: Combined open and arthroscopic procedures could improve the diagnosis and management of intra-articular lesions and allow surgeons to perform minimally invasive anatomic reconstruction of the lateral ligament complex. Study Design: Case series; Level of evidence, 4. Methods: Forty consecutive patients underwent ankle arthroscopy for recurrent (2 or more episodes) lateral ankle instability unresponsive to nonoperative measures. The clinical diagnosis of mechanical instability was confirmed at imaging (plain radiographs and magnetic resonance imaging [MRI]) and arthroscopic assessment. All patients underwent arthroscopic Broström-Gould repair for management of lateral ankle instability; secondary lesions were also managed. Postoperatively, the American Orthopaedic Foot & Ankle Society (AOFAS) score was administered to assess the functional status; clinical examination and conventional radiographs were performed in all patients. Results: Thirty-eight patients were reviewed at an average postoperative follow-up of 9.8 years. The mean AOFAS score was 90 (range, 44-100) at the last follow-up. No significantly different outcomes were found in patients who had undergone microfractures for management of grade III to IV cartilage lesions compared with patients with no cartilage lesions. Postoperative AOFAS scores were graded as excellent and good in almost all patients (94.7%). Concerning failure rate, 2 patients (5.3%) reported a low AOFAS score: one patient underwent soft tissue removal for anterior impingement, and one received simultaneous medial ankle instability repair. Conclusion: The arthroscopic Broström-Gould–assisted technique could be a viable alternative to the gold-standard Broström-Gould procedure for anatomic repair of chronic lateral ankle instability and management of intra-articular lesions. Prospective randomized controlled trials are needed.
Globalization from Below: Labor Activists Challenging the AFL-CIO Foreign Policy Program
Authors: Scipes Kim 
Published: July 2011

Building on Alberto Melucci’s argument that to understand a social movement, we must look at the period before emergence as a social movement, this article examines labor activists’ efforts to reform the foreign policy program of the AFL-CIO: has sufficient groundwork been laid that a serious possibility of an alternative globalization movement can emerge from within US Labor? This article discusses general efforts to challenge the AFL-CIO’s foreign policy program. It examines the work of US Labor Against the War (USLAW) since its founding in 2003, the California State AFL-CIO’s formal repudiation of the AFL-CIO foreign policy program in 2004, and then efforts at the 2005 National AFL-CIO Convention to keep California’s ‘Build Unity and Trust With Workers Worldwide’ resolution from being fairly discussed at the Convention. Based on evidence presented, it then evaluates whether there is an alternative globalization movement emerging within US Labor or not.