bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carbohydrate Catabolism in Phaeobacter inhibens DSM 17395, a Member of the Marine Roseobacter Clade
Authors: Wiegmann Katharina , Hensler Michael , Wöhlbrand Lars , Ulbrich Marcus , Schomburg Dietmar , Rabus Ralf 
Published: May 2014

ABSTRACT

Since genome analysis did not allow unambiguous reconstruction of transport, catabolism, and substrate-specific regulation for several important carbohydrates in
Phaeobacter inhibens
DSM 17395, proteomic and metabolomic analyses of
N
-acetylglucosamine-, mannitol-, sucrose-, glucose-, and xylose-grown cells were carried out to close this knowledge gap. These carbohydrates can pass through the outer membrane via porins identified in the outer membrane fraction. For transport across the cytoplasmic membrane, carbohydrate-specific ABC transport systems were identified. Their coding genes mostly colocalize with the respective “catabolic” and “regulatory” genes. The degradation of
N
-acetylglucosamine proceeds via
N
-acetylglucosamine-6-phosphate and glucosamine-6-phosphate directly to fructose-6-phosphate; two of the three enzymes involved were newly predicted and identified. Mannitol is catabolized via fructose, sucrose via fructose and glucose, glucose via glucose-6-phosphate, and xylose via xylulose-5-phosphate. Of the 30 proteins predicted to be involved in uptake, regulation, and degradation, 28 were identified by proteomics and 19 were assigned to their respective functions for the first time. The peripheral degradation pathways feed into the Entner-Doudoroff (ED) pathway, which is connected to the lower branch of the Embden-Meyerhof-Parnas (EMP) pathway. The enzyme constituents of these pathways displayed higher abundances in
P. inhibens
DSM 17395 cells grown with any of the five carbohydrates tested than in succinate-grown cells. Conversely, gluconeogenesis is turned on during succinate utilization. While tricarboxylic acid (TCA) cycle proteins remained mainly unchanged, the abundance profiles of their metabolites reflected the differing growth rates achieved with the different substrates tested. Homologs of the 74 genes involved in the reconstructed catabolic pathways and central metabolism are present in various
Roseobacter
clade members.
Fusion of Self-Assembling Amphipathic Oligopeptides with Cyclodextrin Glycosyltransferase Improves 2-
O
-
d
-Glucopyranosyl-
l
-Ascorbic Acid Synthesis with Soluble Starch as the Glycosyl Donor
Authors: Han Ruizhi , Li Jianghua , Shin Hyun-dong , Chen Rachel R. , Liu Long , Du Guocheng , Chen Jian 
Published: May 2014

ABSTRACT

In this study, we fused six self-assembling amphipathic peptides (SAPs) with cyclodextrin glycosyltransferase (CGTase) from
Paenibacillus macerans
to catalyze 2-
O
-
d
-glucopyranosyl-
l
-ascorbic acid (AA-2G) production with cheap substrates, including maltose, maltodextrin, and soluble starch as glycosyl donors. The results showed that two fusion enzymes, SAP5-CGTase and SAP6-CGTase, increased AA-2G yields to 2.33- and 3.36-fold that of wild-type CGTase when soluble starch was used as a substrate. The cyclization activities of these enzymes decreased, while disproportionation activities increased. Enzymatic characterization of the two fusion enzymes was performed, and kinetics analysis of AA-2G synthesis confirmed the enhanced soluble starch specificity of SAP5-CGTase and SAP6-CGTase compared to that in the wild-type CGTase. As revealed by structure modeling of the fusion and wild-type CGTases, enhanced substrate-binding capacity may result from the increased number of hydrogen bonds present after fusion. This study demonstrates an effective protein fusion approach to improving the substrate specificity of CGTase for AA-2G synthesis. Fusion enzymes, especially SAP6-CGTase, are promising starting points for further development through protein engineering.
Characterization of the Chloroquine Resistance Transporter Homologue in Toxoplasma gondii
Authors: Warring Sally D. , Dou Zhicheng , Carruthers Vern B. , McFadden Geoffrey I. , van Dooren Giel G. 
Published: May 2014

ABSTRACT

Mutations in the
Plasmodium falciparum
chloroquine resistance transporter (
Pf
CRT) protein confer resistance to the antimalarial drug chloroquine.
Pf
CRT localizes to the parasite digestive vacuole, the site of chloroquine action, where it mediates resistance by transporting chloroquine out of the digestive vacuole.
Pf
CRT belongs to a family of transporter proteins called the chloroquine resistance transporter family. CRT family proteins are found throughout the Apicomplexa, in some protists, and in plants. Despite the importance of
Pf
CRT in drug resistance, little is known about the evolution or native function of CRT proteins. The apicomplexan parasite
Toxoplasma gondii
contains one CRT family protein. We demonstrate that
T. gondii
CRT (
Tg
CRT) colocalizes with markers for the vacuolar (VAC) compartment in these parasites. The
Tg
CRT-containing VAC is a highly dynamic organelle, changing its morphology and protein composition between intracellular and extracellular forms of the parasite. Regulated knockdown of
Tg
CRT expression resulted in modest reduction in parasite fitness and swelling of the VAC, indicating that
Tg
CRT contributes to parasite growth and VAC physiology. Together, our findings provide new information on the role of CRT family proteins in apicomplexan parasites.
Influence of the AgrC-AgrA Complex on the Response Time of Staphylococcus aureus Quorum Sensing
Authors: Srivastava Sandeep K. , Rajasree Kalagiri , Fasim Aneesa , Arakere Gayathri , Gopal Balasubramanian 
Published: May 2014

ABSTRACT

The
Staphylococcus aureus
agr
quorum-sensing system plays a major role in the transition from the persistent to the virulent phenotype.
S. aureus
agr
type I to IV strains are characterized by mutations in the sensor domain of the histidine kinase AgrC and differences in the sequences of the secreted autoinducing peptides (AIP). Here we demonstrate that interactions between the cytosolic domain of AgrC (AgrC
Cyto
) and the response regulator domain of AgrA (AgrA
RR
) dictate the spontaneity of the cellular response to AIP stimuli. The crystal structure of AgrC
Cyto
provided a basis for a mechanistic model of AgrC-AgrA interactions. This model enabled an analysis of the biochemical and biophysical parameters of AgrC-AgrA interactions in the context of the conformational features of the AgrC-AgrA complex. This analysis revealed distinct sequence and conformational features that determine the affinity, specificity, and kinetics of the phosphotransfer reaction. This step, which governs the response time for transcriptional reengineering triggered by an AIP stimulus, is independent of the
agr
type and similar for agonist and antagonist stimuli. These experimental data could serve as a basis on which to validate simulations of the quorum-sensing response and for strategies that employ the
agr
quorum-sensing system to combat biofilm formation in
S. aureus
infections.
Genetic Requirements for Sensitivity of Bacteriophage T7 to Dideoxythymidine
Authors: Tran Ngoc Q. , Tabor Stanley , Richardson Charles C. 
Published: May 2014

ABSTRACT

We previously reported that the presence of dideoxythymidine (ddT) in the growth medium selectively inhibits the ability of bacteriophage T7 to infect
Escherichia coli
by inhibiting phage DNA synthese (N. Q. Tran, L. F. Rezende, U. Qimron, C. C. Richardson, and S. Tabor, Proc. Natl. Acad. Sci. U. S. A. 105:9373–9378, 2008, doi:10.1073/pnas.0804164105). In the presence of T7 gene 1.7 protein, ddT is taken up into the
E. coli
cell and converted to ddTTP. ddTTP is incorporated into DNA as ddTMP by the T7 DNA polymerase, resulting in chain termination. We have identified the pathway by which exogenous ddT is converted to ddTTP. The pathway consists of ddT transport by host nucleoside permeases and phosphorylation to ddTMP by the host thymidine kinase. T7 gene 1.7 protein phosphorylates ddTMP and ddTDP, resulting in ddTTP. A 74-residue peptide of the gene 1.7 protein confers ddT sensitivity to the same extent as the 196-residue wild-type gene 1.7 protein. We also show that cleavage of thymidine to thymine and deoxyribose-1-phosphate by the host thymidine phosphorylase greatly increases the sensitivity of phage T7 to ddT. Finally, a mutation in T7 DNA polymerase that leads to discrimination against the incorporation of ddTMP eliminates ddT sensitivity.
Towards tailoring of self-management for patients with chronic heart failure or chronic obstructive pulmonary disease: a protocol for an individual patient data meta-analysis
Authors: Jonkman Nini H , Westland Heleen , Trappenburg Jaap C A , Groenwold Rolf H H , Effing-Tijdhof Tanja W , Troosters Thierry , van der Palen Job , Bourbeau Jean , Jaarsma Tiny , Hoes Arno W , Schuurmans Marieke J 
Published: May 2014

IntroductionSelf-management interventions in patients with chronic conditions have received increasing attention over the past few years, yet the meta-analyses encountered considerable heterogeneity in results. This suggests that the effectiveness of self-management interventions must be assessed in the context of which components are responsible for eliciting the effect and in which subgroups of patients the intervention works best. The aim of the present study is to identify condition-transcending determinants of success of self-management interventions in two parallel individual patient data meta-analyses of self-management trials in patients with congestive heart failure (CHF) and in patients with chronic obstructive pulmonary disease (COPD).Methods and analysisInvestigators of 53 randomised trials (32 in CHF and 21 in COPD) will be requested to share their de-identified individual patient data. Data will be analysed using random effects models, taking clustering within studies into account. Effect modification by age, sex, disease severity, symptom status, comorbid conditions and level of education will be assessed. Sensitivity analyses will be conducted to assess the robustness of the findings.Ethics and disseminationThe de-identified individual patient data are used only for the purpose for which they were originally collected and for which ethical approval has been obtained by the original investigators. Knowledge on the effective ingredients of self-management programmes and identification of subgroups of patients in which those interventions are most effective will guide the development of evidence-based personalised self-management interventions for patients with CHF and COPD as well as with other chronic diseases.Trial registration numberPROSPERO: CRD42013004698.
The development and exploratory analysis of the Back Pain Attitudes Questionnaire (Back-PAQ)
Authors: Darlow Ben , Perry Meredith , Mathieson Fiona , Stanley James , Melloh Markus , Marsh Reginald , Baxter G David , Dowell Anthony 
Published: May 2014

ObjectivesTo develop an instrument to assess attitudes and underlying beliefs about back pain, and subsequently investigate its internal consistency and underlying structures.DesignThe instrument was developed by a multidisciplinary team of clinicians and researchers based on analysis of qualitative interviews with people experiencing acute and chronic back pain. Exploratory analysis was conducted using data from a population-based cross-sectional survey.SettingQualitative interviews with community-based participants and subsequent postal survey.ParticipantsInstrument development informed by interviews with 12 participants with acute back pain and 11 participants with chronic back pain. Data for exploratory analysis collected from New Zealand residents and citizens aged 18 years and above. 1000 participants were randomly selected from the New Zealand Electoral Roll. 602 valid responses were received.MeasuresThe 34-item Back Pain Attitudes Questionnaire (Back-PAQ) was developed. Internal consistency was evaluated by the Cronbach α coefficient. Exploratory analysis investigated the structure of the data using Principal Component Analysis.ResultsThe 34-item long form of the scale had acceptable internal consistency (α=0.70; 95% CI 0.66 to 0.73). Exploratory analysis identified five two-item principal components which accounted for 74% of the variance in the reduced data set: ‘vulnerability of the back’; ‘relationship between back pain and injury’; ‘activity participation while experiencing back pain’; ‘prognosis of back pain’ and ‘psychological influences on recovery’. Internal consistency was acceptable for the reduced 10-item scale (α=0.61; 95% CI 0.56 to 0.66) and the identified components (α between 0.50 and 0.78).ConclusionsThe 34-item long form of the scale may be appropriate for use in future cross-sectional studies. The 10-item short form may be appropriate for use as a screening tool, or an outcome assessment instrument. Further testing of the 10-item Back-PAQ's construct validity, reliability, responsiveness to change and predictive ability needs to be conducted.
Preterm nutritional intake and MRI phenotype at term age: a prospective observational study
Authors: Vasu Vimal , Durighel Giuliana , Thomas Louise , Malamateniou Christina , Bell Jimmy D , Rutherford Mary A , Modi Neena 
Published: May 2014

ObjectiveTo describe (1) the relationship between nutrition and the preterm-at-term infant phenotype, (2) phenotypic differences between preterm-at-term infants and healthy term born infants and (3) relationships between somatic and brain MRI outcomes.DesignProspective observational study.SettingUK tertiary neonatal unit.ParticipantsPreterm infants (<32 weeks gestation) (n=22) and healthy term infants (n=39)Main outcome measuresPreterm nutrient intake; total and regional adipose tissue (AT) depot volumes; brain volume and proximal cerebral arterial vessel tortuosity (CAVT) in preterm infants and in term infants.ResultsPreterm nutrition was deficient in protein and high in carbohydrate and fat. Preterm nutrition was not related to AT volumes, brain volume or proximal CAVT score; a positive association was noted between human milk intake and proximal CAVT score (r=0.44, p=0.05). In comparison to term infants, preterm infants had increased total adiposity, comparable brain volumes and reduced proximal CAVT scores. There was a significant negative correlation between deep subcutaneous abdominal AT volume and brain volume in preterm infants (r=−0.58, p=0.01).ConclusionsThough there are significant phenotypic differences between preterm infants at term and term infants, preterm macronutrient intake does not appear to be a determinant. Our preliminary data suggest that (1) human milk may exert a beneficial effect on cerebral arterial vessel tortuosity and (2) there is a negative correlation between adiposity and brain volume in preterm infants at term. Further work is warranted to see if our findings can be replicated and to understand the causal mechanisms.
Trends in family planning and counselling for women with sickle cell disease in the UK over two decades
Authors: Eissa Asma A , Tuck Susan M , Rantell Khadija , Stott Daniel 
Published: May 2014

BackgroundPregnancies in women with sickle cell disease (SCD) are known to have high rates of maternal and fetal mortality and morbidity. Given these pregnancy-associated problems for women with SCD, advice both about pregnancy planning and about effective contraception are of paramount importance. This study sought to discover the contraception methods used by women with SCD, what complications women with SCD encounter with contraception, and their experiences of pre-pregnancy counselling and pregnancy planning, and how such issues may have changed over the past two decades.MethodThe study was a multicentre, interview-based, cross-sectional study. Interviews were carried out with 102 women with SCD, in north and central London during 2010, concerning their current and previous contraceptive use, their pregnancy history, their menstrual history, and the advice they received concerning pregnancy planning and contraception. Patient information was anonymised and ethical approval was obtained. These data were compared with data from a similar study undertaken in 1993.ResultsThere were significant differences in a number of key areas: the number of unplanned pregnancies decreased from 64% in 1993 to 53% in 2010. The number of women with SCD who were advised not to become pregnant also fell, from 36% to 15%. The use of combined oral contraceptive pills declined, from 45% of the women in 1993 to 31% in 2010. Conversely the use of depot medroxyprogesterone acetate contraception (DMPA) and the levonorgestrel intrauterine system (LNG-IUS) both increased.ConclusionsSignificant changes in the contraceptive methods used by women with SCD are demonstrated in the London population. LNG-IUS use in SCD has not been investigated before. There has been an encouraging decrease in the number of women with SCD who are advised not to become pregnant, perhaps reflecting an improvement in their overall health. Although the number of unplanned pregnancies has fallen, it remains high – emphasising the continuing need for women with SCD to have access to informed advice about pregnancy-associated issues and contraception.
Salivary Auto-Antibodies as Noninvasive Diagnostic Markers of Oral Cavity Squamous Cell Carcinoma
Authors: Wu Chih-Ching , Chang Ya-Ting , Chang Kai-Ping , Liu Yu-Ling , Liu Hao-Ping , Lee I-Ling , Yu Jau-Song , Chiang Wei-Fan 
Published: May 2014

Abstract
Background: Oral cavity squamous cell carcinoma (OSCC) is one of the most common cancers worldwide, and its incidence is still increasing. Approximately 50% of patients with OSCC die within 5 years after diagnosis, mostly ascribed to the fact that the majority of patients present advanced stages of OSCC at the time of diagnosis.
Methods: To discover salivary biomarkers for ameliorating the detection of OSCC, herein, we developed a multiplexed bead-based platform to simultaneously detect auto-antibodies (auto-Abs) in salivary samples.
Results: Compared with healthy individuals, the salivary levels of anti-p53, anti-survivin, anti-Hsp60, and anti-RPLP0 were significantly elevated in patients with OSCC. Noteworthily, the elevated levels of anti-p53, anti-survivin, and anti-Hsp60 were already observed in individuals with oral potentially malignant disorder. Moreover, the salivary levels of anti-p53, anti-survivin, anti-Hsp60, anti-RPLP0, and anti-CK8 were significantly elevated in patients with early-stage OSCC compared with those in healthy individuals. Most importantly, the use of a combined panel of salivary anti-p53, anti-survivin, anti-Hsp60, and anti-RPLP0 largely improves the detection of OSCC.
Conclusion: Collectively, our results reveal that the salivary auto-Abs are effective OSCC biomarkers and the four-auto-Ab panel provides a novel and practicable approach for OSCC screening.
Impact: This study provides the first evidence for the potential clinical application of salivary auto-Abs in OSCC diagnosis. Cancer Epidemiol Biomarkers Prev; 23(8); 1569–78. ©2014 AACR.
Effects of Physical Activity on Melatonin Levels in Previously Sedentary Men and Women
Authors: Thrift Aaron P. , Xiao Liren , Patel Sanjay R. , Tworoger Shelley S. , McTiernan Anne , Duggan Catherine 
Published: May 2014

Abstract
Background: The inverse association between physical activity and cancer risk may be mediated by higher melatonin levels. However, few studies have examined the effect of increased physical activity on melatonin levels.
Methods: The parent study was a randomized controlled trial that randomized 51 men and 49 women to a 12-month moderate-to-vigorous aerobic exercise intervention (“exercisers”) and 51 men and 51 women to a stretching control (“controls”). Participants were of ages 40 to 75 years, and previously sedentary. Levels of the principal urinary metabolite of melatonin, 6-sulfatoxymelatonin (aMT6s), corrected for creatinine levels, were measured in spot morning urine samples by immunoassay at baseline and 12 months. Changes in levels between exercisers and controls were compared using generalized estimating equations for linear regression.
Results: We observed no statistically significant difference in the change in aMT6s levels from baseline to 12 months in exercisers compared with controls (change in aMT6s levels: exercisers, +6.5%; controls, +13%; P = 0.66). There was no evidence of effect modification by age, sex, or body mass index.
Conclusions: A 12-month moderate-intensity exercise intervention did not affect levels of aMT6s.
Impact: Further research needs to focus on other potential mechanisms through which physical activity may reduce the risk of cancer. Cancer Epidemiol Biomarkers Prev; 23(8); 1696–9. ©2014 AACR.
FGFR1/3 Tyrosine Kinase Fusions Define a Unique Molecular Subtype of Non–Small Cell Lung Cancer
Authors: Wang Rui , Wang Lei , Li Yuan , Hu Haichuan , Shen Lei , Shen Xuxia , Pan Yunjian , Ye Ting , Zhang Yang , Luo Xiaoyang , Zhang Yiliang , Pan Bin , Li Bin , Li Hang , Zhang Jie , Pao William , Ji Hongbin , Sun Yihua , Chen Haiquan 
Published: May 2014

Abstract
Purpose: The fibroblast growth factor receptor (FGFR)-3 fusion genes have been recently demonstrated in a subset of non–small cell lung cancer (NSCLC). To aid in identification and treatment of these patients, we examined the frequency, clinicopathologic characteristics, and treatment outcomes of patients who had NSCLC with or without FGFR fusions.
Experimental Design: Fourteen known FGFR fusion variants, including FGFR1, FGFR2, and FGFR3, were detected by RT-PCR and verified by direct sequencing in 1,328 patients with NSCLC. All patients were also analyzed for mutations in EGFR, KRAS, HER2, BRAF, ALK, RET, and ROS1. Clinical characteristics, including age, sex, smoking status, stage, subtypes of lung adenocarcinoma, relapse-free survival, and overall survival, were collected.
Results: Of 1,328 tumors screened, two (0.2%) were BAG4-FGFR1 fusion and 15 (1.1%) were FGFR3-TACC3 fusion. Six of 1,016 patients with lung adenocarcinoma were FGFR3-TACC3 fusions and 11 of 312 lung squamous cell carcinoma harbored BAG4-FGFR1 or FGFR3-TACC3 fusions. Compared with the FGFR fusion-negative group, patients with FGFR fusions were more likely to be smokers (94.1%, 16 of 17 patients, P &lt; 0.001), significantly associated with larger tumor (&gt;3 cm; 88.2%, 15 of 17 patients, P &lt; 0.001) and with a tendency to be more poorly differentiated (53.9%, nine of 17 patients, P = 0.095).
Conclusions: FGFR fusions define a molecular subset of NSCLC with distinct clinical characteristics. FGFR is a druggable target and patients with FGFR fusions may benefit from FGFR-targeted therapy, which needs further clinical investigation. Clin Cancer Res; 20(15); 4107–14. ©2014 AACR.