bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photoautotrophic Polyhydroxybutyrate Granule Formation Is Regulated by Cyanobacterial Phasin PhaP in Synechocystis sp. Strain PCC 6803
Authors: Hauf Waldemar , Watzer Björn , Roos Nora , Klotz Alexander , Forchhammer Karl 
Published: April 2015

ABSTRACT

Cyanobacteria are photoautotrophic microorganisms which fix atmospheric carbon dioxide via the Calvin-Benson cycle to produce carbon backbones for primary metabolism. Fixed carbon can also be stored as intracellular glycogen, and in some cyanobacterial species like
Synechocystis
sp. strain PCC 6803, polyhydroxybutyrate (PHB) accumulates when major nutrients like phosphorus or nitrogen are absent. So far only three enzymes which participate in PHB metabolism have been identified in this organism, namely, PhaA, PhaB, and the heterodimeric PHB synthase PhaEC. In this work, we describe the cyanobacterial PHA surface-coating protein (phasin), which we term PhaP, encoded by
ssl2501
. Translational fusion of Ssl2501 with enhanced green fluorescent protein (eGFP) showed a clear colocalization to PHB granules. A deletion of
ssl2501
reduced the number of PHB granules per cell, whereas the mean PHB granule size increased as expected for a typical phasin. Although deletion of
ssl2501
had almost no effect on the amount of PHB, the biosynthetic activity of PHB synthase was negatively affected. Secondary-structure prediction and circular dichroism (CD) spectroscopy of PhaP revealed that the protein consists of two α-helices, both of them associating with PHB granules. Purified PhaP forms oligomeric structures in solution, and both α-helices of PhaP contribute to oligomerization. Together, these results support the idea that Ssl2501 encodes a cyanobacterial phasin, PhaP, which regulates the surface-to-volume ratio of PHB granules.
Aerobic Hydrogen Production via Nitrogenase in Azotobacter vinelandii CA6
Authors: Noar Jesse , Loveless Telisa , Navarro-Herrero José Luis , Olson Jonathan W. , Bruno-Bárcena José M. 
Published: April 2015

ABSTRACT

The diazotroph
Azotobacter vinelandii
possesses three distinct nitrogenase isoenzymes, all of which produce molecular hydrogen as a by-product. In batch cultures,
A. vinelandii
strain CA6, a mutant of strain CA, displays multiple phenotypes distinct from its parent: tolerance to tungstate, impaired growth and molybdate transport, and increased hydrogen evolution. Determining and comparing the genomic sequences of strains CA and CA6 revealed a large deletion in CA6's genome, encompassing genes related to molybdate and iron transport and hydrogen reoxidation. A series of iron uptake analyses and chemostat culture experiments confirmed iron transport impairment and showed that the addition of fixed nitrogen (ammonia) resulted in cessation of hydrogen production. Additional chemostat experiments compared the hydrogen-producing parameters of different strains: in iron-sufficient, tungstate-free conditions, strain CA6's yields were identical to those of a strain lacking only a single hydrogenase gene. However, in the presence of tungstate, CA6 produced several times more hydrogen.
A. vinelandii
may hold promise for developing a novel strategy for production of hydrogen as an energy compound.
Rich Medium Composition Affects Escherichia coli Survival, Glycation, and Mutation Frequency during Long-Term Batch Culture
Authors: Kram Karin E. , Finkel Steven E. 
Published: April 2015

ABSTRACT

Bacteria such as
Escherichia coli
are frequently grown to high density to produce biomolecules for study in the laboratory. To achieve this, cells can be incubated in extremely rich media that increase overall cell yield. In these various media, bacteria may have different metabolic profiles, leading to changes in the amounts of toxic metabolites produced. We have previously shown that stresses experienced during short-term growth can affect the survival of cells during the long-term stationary phase (LTSP). Here, we incubated cells in LB, 2× yeast extract-tryptone (YT), Terrific Broth, or Super Broth medium and monitored survival during the LTSP, as well as other reporters of genetic and physiological change. We observe differential cell yield and survival in all media studied. We propose that differences in long-term survival are the result of changes in the metabolism of components of the media that may lead to increased levels of protein and/or DNA damage. We also show that culture pH and levels of protein glycation, a covalent modification that causes protein damage, affect long-term survival. Further, we measured mutation frequency after overnight incubation and observed a correlation between high mutation frequencies at the end of the log phase and loss of viability after 4 days of LTSP incubation, indicating that mutation frequency is potentially predictive of long-term survival. Since glycation and mutation can be caused by oxidative stress, we measured expression of the
oxyR
oxidative stress regulator during log-phase growth and found that higher levels of
oxyR
expression during the log phase are consistent with high mutation frequency and lower cell density during the LTSP. Since these complex rich media are often used when producing large quantities of biomolecules in the laboratory, the observed increase in damage resulting in glycation or mutation may lead to production of a heterogeneous population of plasmids or proteins, which could affect the quality of the end products yielded in some laboratory experiments.
The Xanthomonas oryzae pv. oryzae PilZ Domain Proteins Function Differentially in Cyclic di-GMP Binding and Regulation of Virulence and Motility
Authors: Yang Fenghuan , Tian Fang , Chen Huamin , Hutchins William , Yang Ching-Hong , He Chenyang 
Published: April 2015

ABSTRACT

The PilZ domain proteins have been demonstrated to be one of the major types of receptors mediating cyclic di-GMP (c-di-GMP) signaling pathways in several pathogenic bacteria. However, little is known about the function of PilZ domain proteins in c-di-GMP regulation of virulence in the bacterial blight pathogen of rice
Xanthomonas oryzae
pv. oryzae. Here, the roles of PilZ domain proteins PXO_00049 and PXO_02374 in c-di-GMP binding, regulation of virulence and motility, and subcellular localization were characterized in comparison with PXO_02715, identified previously as an interactor with the c-di-GMP receptor Filp to regulate virulence. The c-di-GMP binding motifs in the PilZ domains were conserved in PXO_00049 and PXO_02374 but were less well conserved in PXO_02715. PXO_00049 and PXO_02374 but not PXO_02715 proteins bound to c-di-GMP with high affinity
in vitro
, and the R
141
and R
10
residues in the PilZ domains of PXO_00049 and PXO_02374, respectively, were crucial for c-di-GMP binding. Gene deletion of PXO_00049 and PXO_02374 resulted in significant increases in virulence and
hrp
gene transcription, indicating their negative regulation of virulence via type III secretion system expression. All mutants showed significant changes in sliding motility but not exopolysaccharide production and biofilm formation. In
trans
expression of the full-length open reading frame (ORF) of each gene in the relevant mutants led to restoration of the phenotype to wild-type levels. Moreover, PXO_00049 and PXO_02374 displayed mainly multisite subcellular localizations, whereas PXO_02715 showed nonpolar distributions in the
X. oryzae
pv. oryzae cells. Therefore, this study demonstrated the different functions of the PilZ domain proteins in mediation of c-di-GMP regulation of virulence and motility in
X. oryzae
pv. oryzae.
Distribution and Characterization of Salmonella enterica Isolates from Irrigation Ponds in the Southeastern United States
Authors: Luo Zhiyao , Gu Ganyu , Ginn Amber , Giurcanu Mihai C. , Adams Paige , Vellidis George , van Bruggen Ariena H. C. , Danyluk Michelle D. , Wright Anita C. 
Published: April 2015

ABSTRACT

Irrigation water has been implicated as a likely source of produce contamination by
Salmonella enterica
. Therefore, the distribution of
S. enterica
was surveyed monthly in irrigation ponds (
n
= 10) located within a prime agricultural region in southern Georgia and northern Florida. All ponds and 28.2% of all samples (
n
= 635) were positive for
Salmonella
, with an overall geometric mean concentration (0.26 most probable number [MPN]/liter) that was relatively low compared to prior reports for rivers in this region.
Salmonella
peaks were seasonal; the levels correlated with increased temperature and rainfall (
P
< 0.05). The numbers and occurrence were significantly higher in water (0.32 MPN/liter and 37% of samples) than in sediment (0.22 MPN/liter and 17% of samples) but did not vary with depth. Representative isolates (
n
= 185) from different ponds, sample types, and seasons were examined for resistance to 15 different antibiotics; most strains were resistant to streptomycin (98.9%), while 20% were multidrug resistant (MDR) for 2 to 6 antibiotics. DiversiLab repetitive extragenic palindromic-element sequence-based PCR (rep-PCR) revealed genetic diversity and showed 43 genotypes among 191 isolates, as defined by >95% similarity. The genotypes did not partition by pond, season, or sample type. Genetic similarity to known serotypes indicated Hadar, Montevideo, and Newport as the most prevalent. All ponds achieved the current safety standards for generic
Escherichia coli
in agricultural water, and regression modeling showed that the
E. coli
level was a significant predictor for the probability of
Salmonella
occurrence. However, persistent populations of
Salmonella
were widely distributed in irrigation ponds, and the associated risks for produce contamination and subsequent human exposure are unknown, supporting continued surveillance of this pathogen in agricultural settings.
The Aspergillus fumigatus sitA Phosphatase Homologue Is Important for Adhesion, Cell Wall Integrity, Biofilm Formation, and Virulence
Authors: Bom Vinícius Leite Pedro , de Castro Patrícia Alves , Winkelströter Lizziane K. , Marine Marçal , Hori Juliana I. , Ramalho Leandra Naira Zambelli , dos Reis Thaila Fernanda , Goldman Maria Helena S. , Brown Neil Andrew , Rajendran Ranjith , Ramage Gordon , Walker Louise A. , Munro Carol A. , Rocha Marina Campos , Malavazi Iran , Hagiwara Daisuke , Goldman Gustavo H. 
Published: April 2015

ABSTRACTAspergillus fumigatusis an opportunistic pathogenic fungus able to infect immunocompromised patients, eventually causing disseminated infections that are difficult to control and lead to high mortality rates. It is important to understand how the signaling pathways that regulate these factors involved in virulence are orchestrated. Protein phosphatases are central to numerous signal transduction pathways. Here, we characterize theA. fumigatusprotein phosphatase 2A SitA, theSaccharomyces cerevisiaeSit4p homologue. ThesitAgene is not an essential gene, and we were able to construct anA. fumigatusnull mutant. The ΔsitAstrain had decreased MpkA phosphorylation levels, was more sensitive to cell wall-damaging agents, had increased β-(1,3)-glucan and chitin, was impaired in biofilm formation, and had decreased protein kinase C activity. The ΔsitAstrain is more sensitive to several metals and ions, such as MnCl2, CaCl2, and LiCl, but it is more resistant to ZnSO4. The ΔsitAstrain was avirulent in a murine model of invasive pulmonary aspergillosis and induces an augmented tumor necrosis factor alpha (TNF-α) response in mouse macrophages. These results stress the importance ofA. fumigatusSitA as a possible modulator of PkcA/MpkA activity and its involvement in the cell wall integrity pathway.
Single-Blinded, Randomised Preliminary Study Evaluating the Effects of 2 hz Electroacupuncture for Postoperative Pain in Patients with Total Knee Arthroplasty
Authors: Tzeng Chung-Yuh , Chang Shih-Liang , Wu Chih-Cheng , Chang Chu-Ling , Chen Wen-Gii , Tong Kwok-Man , Huang Kui-Chou , Hsieh Ching-Liang 
Published: April 2015

Objective To explore the point-specific clinical effect of 2 Hz electroacupuncture (EA) in treating postoperative pain in patients undergoing total knee arthroplasty (TKA), Methods In a randomised, partially single-blinded preliminary study, 47patients with TKA were randomly divided into three groups: control group (CG, n=17) using only patient-controlled analgesia (PCA); EA group (EAG, n=16) with 2 Hz EA applied at ST36 ( Zusanli) and GB34 ( Yanglingquan) contralateral to the operated leg for 30 min on the first two postoperative days, also receiving PCA; and non-point group (NPG, n=14), with EA identical to the EAG except given 1 cm lateral to both ST36 and GB34. The Mann–Whitney test was used to show the difference between two groups and the Kruskal–Wallis test to show the difference between the three groups. Results The time until patients first required PCA in the CG was 34.1±22.0 min, which was significantly shorter than the 92.0±82.7 min in the EAG (p<0.001) and 90.7±94.8 min in the NPG (p<0.001); there was no difference between the EAG and NPG groups (p>0.05). The total dosage of PCA solution given was 4.6±0.9 mL/kg body weight in the CG, 4.2±1.0 mL/kg in the EAG and 4.5±1.0 mL/kg in the NPG; there were no significant differences (p>0.05) among the three groups. Conclusions In this small preliminary study, EA retarded the first demand for PCA in comparison with no EA. No effect was seen on the total dosage of PCA required and no point-specific effect was seen.
Lower levels of 25-hydroxyvitamin D3are associated with a higher prevalence of microvascular complications in patients with type 2 diabetes
Authors: Zoppini Giacomo , Galletti Anna , Targher Giovanni , Brangani Corinna , Pichiri Isabella , Trombetta Maddalena , Negri Carlo , De Santi Francesca , Stoico Vincenzo , Cacciatori Vittorio , Bonora Enzo 
Published: April 2015

ObjectiveLow levels of serum 25-hydroxyvitamin D [25(OH)D] are commonly found in type 2 diabetes. We examined whether there is an association between circulating 25(OH)D concentrations and the presence of microvascular complications in people with type 2 diabetes.Research design and methodsWe studied 715 outpatients with type 2 diabetes who regularly attended our clinic. Participants were evaluated for the presence of microvascular complications (namely retinopathy and/or nephropathy) by clinical evaluation, fundus examination, urine examination and biochemical tests. Serum 25(OH)D levels were also measured for each participant.ResultsHypovitaminosis D (ie, a serum 25(OH)D level <30 ng/mL) was found in 75.4%, while deficiency (ie, a 25(OH)D level <20 ng/mL) was found in 36.6% of these patients. Serum 25(OH)D levels decreased significantly in relation to the severity of either retinopathy or nephropathy or both. In multivariate logistic regression analysis, lower 25(OH)D levels were independently associated with the presence of microvascular complications (considered as a composite end point; OR 0.758; 95% CI 0.607 to 0.947, p=0.015). Notably, this association remained significant even after excluding those with an estimated glomerular filtration rate <60 mL/min/1.73 m2.ConclusionsWe found an inverse and independent relationship between circulating 25(OH)D levels and the prevalence of microvascular complications in patients with type 2 diabetes. However, vitamin D may be simply a marker and causality cannot be implied from our cross-sectional study. Whether vitamin D supplementation in patients with type 2 diabetes may have beneficial effects on the risk of microvascular complications remains to be investigated.
Diabetic muscle infarction: a systematic review
Authors: Horton William B , Taylor Jeremy S , Ragland Timothy J , Subauste Angela R 
Published: April 2015

ContextDiabetic muscle infarction (DMI) is a rare complication associated with poorly controlled diabetes mellitus. Less than 200 cases have been reported in the literature since it was first described over 45 years ago. There is no clear ‘standard of care’ for managing these patients.Evidence acquisitionPubMed searches were conducted for ‘diabetic muscle infarction’ and ‘diabetic myonecrosis’ from database inception through July 2014. All articles identified by these searches were reviewed in detail if the article text was available in English.Evidence synthesisThe current literature exists as case reports or small case series, with no prospective or higher-order treatment studies available. Thus, an evidence-based approach to data synthesis was difficult. The available literature is presented objectively with an attempt to describe clinically relevant trends and findings in the diagnosis and management of DMI.ConclusionsEarly recognition of DMI is key, so appropriate treatment can be initiated. MRI is the radiological study of choice. A combination of bed rest, glycemic control, and non-steroidal anti-inflammatory drug therapy appears to yield the shortest time to symptom resolution and the lowest risk of recurrence.
The association of hospital prevention processes and patient risk factors with the risk ofClostridium difficileinfection: a population-based cohort study
Authors: Daneman N , Guttmann A , Wang X , Ma X , Gibson D , Stukel TA 
Published: April 2015

BackgroundClostridium difficileis the most common cause of healthcare-acquired infection; the real-world impacts of some proposedC. difficileprevention processes are unknown.MethodsWe conducted a population-based retrospective cohort study of all patients admitted to acute care hospitals between April 2011 and March 2012 in Ontario, Canada. Hospital prevention practices were determined by survey of infection control programmes; responses were linked to patient-level risk factors andC. difficileoutcomes in Ontario administrative databases. Multivariable generalised estimating equation (GEE) regression models were used to assess the impact of selected understudied hospital prevention processes on the patient-level risk ofC. difficileinfection, accounting for patient risk factors, baselineC. difficilerates and structural hospital characteristics.ResultsC. difficileinfections complicated 2341 of 653 896 admissions (3.6 per 1000 admissions). Implementation of the selectedC. difficileprevention practices was variable across the 159 hospitals with isolation of all patients at onset of diarrhoea reported by 43 (27%), auditing of antibiotic stewardship compliance by 26 (16%), auditing of cleaning practices by 115 (72%), on-site diagnostic testing by 74 (47%), vancomycin as first-line treatment by 24 (15%) and reporting rates to senior leadership by 52 (33%). None of these processes were associated with a significantly reduced risk ofC. difficileafter adjustment for baselineC. difficilerates, structural hospital characteristics and patient-level factors. Patient-level factors were strongly associated withC. difficilerisk, including age, comorbidities, non-elective and medical admissions.ConclusionsIn the largest study to date, selected hospital prevention strategies were not associated with a statistically significant reduction in patients’ risk ofC. difficileinfection. These prevention strategies have either limited effectiveness or were ineffectively implemented during the study period.
Mother's education and the risk of preterm and small for gestational age birth: a DRIVERS meta-analysis of 12 European cohorts
Authors: Ruiz Milagros , Goldblatt Peter , Morrison Joana , Kukla Lubomír , Švancara Jan , Riitta-Järvelin Marjo , Taanila Anja , Saurel-Cubizolles Marie-Josèphe , Lioret Sandrine , Bakoula Chryssa , Veltsista Alexandra , Porta Daniela , Forastiere Francesco , van Eijsden Manon , Vrijkotte Tanja G M , Eggesbø Merete , White Richard A , Barros Henrique , Correia Sofia , Vrijheid Martine , Torrent Maties , Rebagliato Marisa , Larrañaga Isabel , Ludvigsson Johnny , Olsen Faresjö Åshild , Hryhorczuk Daniel , Antipkin Youriy , Marmot Michael , Pikhart Hynek 
Published: April 2015

BackgroundA healthy start to life is a major priority in efforts to reduce health inequalities across Europe, with important implications for the health of future generations. There is limited combined evidence on inequalities in health among newborns across a range of European countries.MethodsProspective cohort data of 75 296 newborns from 12 European countries were used. Maternal education, preterm and small for gestational age births were determined at baseline along with covariate data. Regression models were estimated within each cohort and meta-analyses were conducted to compare and measure heterogeneity between cohorts.ResultsMother's education was linked to an appreciable risk of preterm and small for gestational age (SGA) births across 12 European countries. The excess risk of preterm births associated with low maternal education was 1.48 (1.29 to 1.69) and 1.84 (0.99 to 2.69) in relative and absolute terms (Relative/Slope Index of Inequality, RII/SII) for all cohorts combined. Similar effects were found for SGA births, but absolute inequalities were greater, with an SII score of 3.64 (1.74 to 5.54). Inequalities at birth were strong in the Netherlands, the UK, Sweden and Spain and marginal in other countries studied.ConclusionsThis study highlights the value of comparative cohort analysis to better understand the relationship between maternal education and markers of fetal growth in different settings across Europe.
Preparing to take the USMLE Step 1: a survey on medical students’ self-reported study habits
Authors: Kumar Andre D , Shah Monisha K , Maley Jason H , Evron Joshua , Gyftopoulos Alex , Miller Chad 
Published: April 2015

ABSTRACT

Background
The USA Medical Licensing Examination Step 1 is a computerised multiple-choice examination that tests the basic biomedical sciences. It is administered after the second year in a traditional four-year MD programme. Most Step 1 scores fall between 140 and 260, with a mean (SD) of 227 (22). Step 1 scores are an important selection criterion for residency choice. Little is known about which study habits are associated with a higher score.

Objective
To identify which self-reported study habits correlate with a higher Step 1 score.

Methods
A survey regarding Step 1 study habits was sent to third year medical students at Tulane University School of Medicine every year between 2009 and 2011. The survey was sent approximately 3 months after the examination.

Results
256 out of 475 students (54%) responded. The mean (SD) Step 1 score was 229.5 (22.1). Students who estimated studying more than 8–11 h per day had higher scores (p&lt;0.05), but there was no added benefit with additional study time. Those who reported studying &lt;40 days achieved higher scores (p&lt;0.05). Those who estimated completing &gt;2000 practice questions also obtained higher scores (p&lt;0.01). Students who reported studying in a group, spending the majority of study time on practice questions or taking &gt;40 preparation days did not achieve higher scores.

Conclusions
Certain self-reported study habits may correlate with a higher Step 1 score compared with others. Given the importance of achieving a high Step 1 score on residency choice, it is important to further identify which characteristics may lead to a higher score.