bluuebunny/crossref_metadata_2025 huggingface dataset:
Engineering the elongation factor Tu for efficient selenoprotein synthesis
Authors: Haruna Ken-ichi , Alkazemi Muhammad H. , Liu Yuchen , Söll Dieter , Englert Markus
Published: July 2014

Selenocysteine (Sec) is naturally co-translationally incorporated into proteins by recoding the UGA opal codon with a specialized elongation factor (SelB in bacteria) and an RNA structural signal (SECIS element). We have recently developed a SECIS-free selenoprotein synthesis system that site-specifically—using the UAG amber codon—inserts Sec depending on the elongation factor Tu (EF-Tu). Here, we describe the engineering of EF-Tu for improved selenoprotein synthesis. A Sec-specific selection system was established by expression of human protein O6-alkylguanine-DNA alkyltransferase (hAGT), in which the active site cysteine codon has been replaced by the UAG amber codon. The formed hAGT selenoprotein repairs the DNA damage caused by the methylating agent N-methyl-N′-nitro-N-nitrosoguanidine, and thereby enables Escherichia coli to grow in the presence of this mutagen. An EF-Tu library was created in which codons specifying the amino acid binding pocket were randomized. Selection was carried out for enhanced Sec incorporation into hAGT; the resulting EF-Tu variants contained highly conserved amino acid changes within members of the library. The improved UTu-system with EF-Sel1 raises the efficiency of UAG-specific Sec incorporation to >90%, and also doubles the yield of selenoprotein production.
Homodimerization of RBPMS2 through a new RRM-interaction motif is necessary to control smooth muscle plasticity
Authors: Sagnol Sébastien , Yang Yinshan , Bessin Yannick , Allemand Fréderic , Hapkova Ilona , Notarnicola Cécile , Guichou Jean-François , Faure Sandrine , Labesse Gilles , Santa Barbara Pascal de
Published: July 2014

In vertebrates, smooth muscle cells (SMCs) can reversibly switch between contractile and proliferative phenotypes. This involves various molecular mechanisms to reactivate developmental signaling pathways and induce cell dedifferentiation. The protein RBPMS2 regulates early development and plasticity of digestive SMCs by inhibiting the bone morphogenetic protein pathway through its interaction with NOGGIN mRNA. RBPMS2 contains only one RNA recognition motif (RRM) while this motif is often repeated in tandem or associated with other functional domains in RRM-containing proteins. Herein, we show using an extensive combination of structure/function analyses that RBPMS2 homodimerizes through a particular sequence motif (D-x-K-x-R-E-L-Y-L-L-F: residues 39–51) located in its RRM domain. We also show that this specific motif is conserved among its homologs and paralogs in vertebrates and in its insect and worm orthologs (CPO and MEC-8, respectively) suggesting a conserved molecular mechanism of action. Inhibition of the dimerization process through targeting a conserved leucine inside of this motif abolishes the capacity of RBPMS2 to interact with the translational elongation eEF2 protein, to upregulate NOGGIN mRNA in vivo and to drive SMC dedifferentiation. Our study demonstrates that RBPMS2 possesses an RRM domain harboring both RNA-binding and protein-binding properties and that the newly identified RRM-homodimerization motif is crucial for the function of RBPMS2 at the cell and tissue levels.
Plasmodium falciparum Infection Does Not Affect Human Immunodeficiency Virus Viral Load in Coinfected Rwandan Adults
Authors: Subramaniam Krishanthi , Plank Rebeca M. , Lin Nina , Goldman-Yassen Adam , Ivan Emil , Becerril Carlos , Kemal Kimdar , Heo Moonseong , Keller Marla J. , Mutimura Eugene , Anastos Kathryn , Daily Johanna P.
Published: July 2014

Background.  Plasmodium falciparum infection has been reported to increase human immunodeficiency virus (HIV) viral load (VL), which can facilitate HIV transmission. We prospectively studied the impact of mild P falciparum coinfection on HIV VL in Rwanda.

Methods.  We measured plasma HIV VL at presentation with malaria infection and weekly for 4 weeks after artemether-lumefantrine treatment in Rwandan adults infected with HIV with P falciparum malaria. Regression analyses were used to examine associations between malaria infection and HIV VL changes. Samples with detectable virus underwent genotypic drug-resistance testing.

Results.  We enrolled 28 HIV-malaria coinfected patients and observed 27 of them for 5 weeks. Three patients (11%) were newly diagnosed with HIV. Acute P falciparum infection had no significant effect on HIV VL slope over 28 days of follow-up. Ten patients with VL <40 copies/mL at enrollment maintained viral suppression throughout. Seventeen patients had a detectable VL at enrollment including 9 (53%) who reported 100% adherence to ARVs; 3 of these had detectable genotypic drug resistance.

Conclusions.  Unlike studies from highly malaria-endemic areas, we did not identify an effect of P falciparum infection on HIV VL; therefore, malaria is not likely to increase HIV-transmission risk in our setting. However, routine HIV testing should be offered to adults presenting with acute malaria in Rwanda. Most importantly, we identified a large percentage of patients with detectable HIV VL despite antiretroviral (ARV) therapy. Some of these patients had HIV genotypic drug resistance. Larger studies are needed to define the prevalence and factors associated with detectable HIV VL in patients prescribed ARVs in Rwanda.
Pupillary Effects of High-dose Opioid Quantified with Infrared Pupillometry
Authors: Rollins Mark D. , Feiner John R. , Lee Jessica M. , Shah Sameer , Larson Merlin
Published: July 2014

Background:

The pupillary light reflex is a critical component of the neurologic examination, yet whether it is present, depressed, or absent is unknown in patients with significant opioid toxicity. Although opioids produce miosis by activating the pupillary sphincter muscle, these agents may induce significant hypercarbia and hypoxia, causing pupillary constriction to be overcome via sympathetic activation. The presence of either “pinpoint pupils” or sympathetically mediated pupillary dilation might prevent light reflex assessment. This study was designed to determine whether the light reflex remains quantifiable during opioid-induced hypercarbia and hypoxia.

Methods:

Ten volunteers were administered remifentanil with a gradually increasing infusion rate and intermittent boluses, until the increasing respiratory depression produced an oxyhemoglobin saturation of 85% or less with associated hypercarbia. Subjects’ heart rate, blood pressure, respiration, and transcutaneous carbon dioxide level were continuously recorded. Arterial blood gases and pupillary measures were taken before opioid administration, at maximal desaturation, and 15 min after recovery.

Results:

The opioid-induced oxygen desaturation (≤85%) was associated with significant hypercarbia and evidence of sympathetic activation. During maximal hypoxia and hypercarbia, the pupil displayed parasympathetic dominance (2.5 ± 0.2 mm diameter) with a robust quantifiable light reflex. The reflex amplitude was linearly related to pupil diameter.

Conclusions:

Opioid administration with significant accompanying hypercarbia and hypoxia results in pupil diameters of 2 to 3 mm and a reduced but quantifiable pupillary light reflex. The authors conclude that the pupillary examination and evaluation of the light reflex remain useful for neurologic assessment during opioid toxicity.
Transperineal Template-guided Mapping Biopsy Identifies Pathologic Differences Between Very–Low-risk and Low-risk Prostate Cancer
Authors: Merrick Gregory S. , Delatore Alexandra , Butler Wayne M. , Bennett Abbey , Fiano Ryan , Anderson Richard , Adamovich Edward
Published: July 2014

Objectives:

Active surveillance (AS) is increasingly utilized for low-grade prostate cancer with the greatest risk being the possibility of missing a high-grade cancer. We evaluate the role of transperineal template-guided mapping biopsy (TTMB) to select patients for AS.

Methods:

A total of 131 consecutive, prospectively evaluated men with transrectal ultrasound-guided needle biopsy (TRUS)-diagnosed very low risk (Gleason score ≤6, ≤2 positive biopsies, prostate-specific antigen [PSA] density <0.15, and ≤50% involvement on any core) and low risk (Gleason score ≤6, clinical stage T1c, and PSA ≤10 ng/mL) underwent TTMB as a staging procedure. Biopsies were obtained corresponding to 24 regional biopsy locations. For each patient, the location of each positive biopsy core, the number of positive cores, and the percentage involvement of each core were reported.

Results:

After TTMB, TRUS-detected very–low-risk prostate cancer patients were less likely to be diagnosed with higher Gleason score, were less likely to have bilateral involvement, and had statistically fewer number of positive biopsy cores on TTMB. After TTMB, no cancer, very–low-risk, or low-risk prostate cancer was detected in 60 of 72 (83.3%) and 19 of 59 (32.2%) of patients with very low and low risk, respectively. In multivariate analysis, older age and low risk predicted for higher Gleason score at the time of TTMB.

Conclusions:

Very–low-risk prostate cancer patients have a significantly lower incidence of Gleason score upgrading than those with low-risk disease. After TTMB, 83.3% of patients with very–low-risk and 32.2% of patients with low-risk disease appear to be outstanding candidates for AS.
Treatment-related Hypertension as a Pharmacodynamic Biomarker for the Efficacy of Bevacizumab in Advanced Pancreas Cancer
Authors: Pant Shubham , Martin Ludmila K. , Geyer Susan , Wei Lai , Van Loon Katherine , Sommovilla Nili , Zalupski Mark , Iyer Renuka , Fogelman David , Ko Andrew H. , Bekaii-Saab Tanios
Published: July 2014

Purpose:

Phase III studies of bevacizumab in advanced pancreas cancer (APCA) demonstrated no improvement in outcome. No validated biomarkers for bevacizumab efficacy exist. We evaluated bevacizumab-related hypertension (B-HTN) as a biomarker in APCA patients in a pooled analysis from 4 prospective clinical trials of gemcitabine-based therapy combined with bevacizumab.

Materials and Methods:

Data were collected from individual databases from 4 prospective, single-arm phase II trials. Patients were grouped according to B-HTN or no hypertension (HTN), and patients with HTN were further grouped according to highest Common Terminology Criteria for Adverse Events grade of HTN: grade 1-2 or grade 3-4. Clinical outcomes of overall survival, time to progression, overall response rate (ORR), and disease control rate (ORR+SD>16 wk) were compared.

Results:

A total of 163 patients with stage IV APCA and Eastern Cooperative Oncology Group 0-1 were included. Median age was 59 years (range, 33 to 85 y). Thirty-four patients had B-HTN, and 129 patients had no HTN. Prognostic factors were balanced between groups. Patients with any grade B-HTN had a significantly improved median overall survival (13.1 vs. 8.1 mo, P=0.0006), median time to tumor progression (7.6 vs. 5.5 mo, P=0.0074), ORR (47% vs. 16%, P=0.0001), and disease control rate (85% vs. 59%, P=0.004). There were no differences in outcomes according to HTN grade (1-2 [N=16] vs. 3-4 [N=18]).

Conclusions:

APCA patients who develop any grade of B-HTN appear to derive benefit from bevacizumab. Additional investigation is needed to identify subgroups of patients who develop B-HTN and are more likely to benefit from bevacizumab.
Comparison of Initial Experiences of Robot-Assisted Radical Cystectomy with those of Laparoscopic for Bladder Cancer
Authors: Teishima Jun , Hieda Keisuke , Inoue Shogo , Goto Keisuke , Ikeda Kenichiro , Ohara Shinya , Kobayashi Kanao , Kajiwara Mitsuru , Matsubara Akio
Published: July 2014

Objective

The aim of the present study was to evaluate perioperative outcomes in initial experiences of robot-assisted laparoscopic radical cystectomy (RARC) in comparison with those of laparoscopic radical cystectomy (LRC) for muscle-invasive or high-risk non-muscle-invasive bladder cancer.

Methods

We performed RARC on six patients with muscle-invasive or high-risk non-muscle-invasive bladder cancer starting in October 2011. During the same period, another five patients underwent LRC. Perioperative outcomes in initial experiences of RARC were elucidated by comparing them with those of LRC.

Results

Robot-assisted procedures were completed in all cases without conversion to open surgery. The median time of pneumoperitoneum was 252 minutes, and the median blood loss was 340 mL. No severe complications were observed. Perioperative outcomes did not significantly differ between RARC and LRC. Although two cases of troubles in uretero-conduit anastomosis sites were observed after LRC, no patients experienced postoperative complication related to urinary diversion after RARC.

Conclusions

Our data indicate that RARC is an acceptable option even in the initial period, and it may become one of the most favorable procedures for treatment of muscle-invasive bladder cancer in the near future, although more tests and longer follow-ups are required to confirm its effectiveness and safety.
One-and-a-Half Ventricular Repair for Isolated Right Ventricle Metastatic Tumor Resection after Lobectomy for Lung Cancer
Authors: Shiose Akira , Desai Parag , Criner Gerard J. , Pai Sheela , Steiner Robert M. , Kaiser Larry R. , Guy T. Sloane , Toyoda Yoshiya
Published: July 2014

A 77-year-old woman presented with shortness of breath 1 year after a right upper lobectomy for lung cancer. She showed a possible intracardiac metastasis on positron emission tomography scan. There was no other evidence of recurrence. The large right ventricular mass was associated with the right ventricle free wall, the apex, the papillary muscle, and the chordae to the tricuspid valve. After mass resection of the right ventricle, a one-and-a-half ventricular repair was performed with tricuspid valve replacement and defect closure. The patient was discharged on postoperative day 14 without complications and has been well for the first 3 months after the surgery.
Aortic Valve Replacement and Concomitant Right Coronary Artery Bypass Grafting Performed via a Right Minithoracotomy Approach
Authors: Mihos Christos G. , Santana Orlando , Pineda Andres M. , La Pietra Angelo , Lamelas Joseph
Published: July 2014

Objective

We present our experience of concomitant right coronary artery bypass grafting (CABG) and aortic valve replacement performed via a right minithoracotomy in patients with coronary lesions not amenable to percutaneous intervention.

Methods

A total of 17 patients underwent concomitant aortic valve replacement and right CABG between April 2008 and July 2013.A5-to 6-cm minithoracotomy incision was made over the right second or third intercostal space, and the costochondral cartilage was transected. A saphenous vein bypass to the right coronary artery was then performed, initiating the anastomosis from the toe of the graft. Subsequently, the aortic valve was replaced using standard techniques.

Results

There were 6 men and 11 women. The median European System for Cardiac Operative Risk Evaluation II score mortality risk was 5% [interquartile range (IQR), 2%-8%]. The mean (SD) age was 77 (10) years, the left ventricular ejection fraction was 59% (8%), and the New York Heart Association functional class was 2.4 (0.8). One patient had a history of CABG. The mean (SD) cardiopulmonary bypass time was 168 (57) minutes, and the aortic cross-clamp time was 133 (36) minutes. Three patients underwent concomitant mitral valve surgery (replacement, 2; repair, 1). The median intensive care unit and hospital lengths of stay were 47 hours (IQR, 24–90) and 9 days (IQR, 5–13), respectively. There was one reoperation for bleeding, and there was one postoperative stroke. All patients were alive at a mean (SD) follow-up of 2 (1.1) years.

Conclusions

Aortic valve replacement with concomitant CABG performed via a right minithoracotomy approach is feasible.
Prolonged Colonic Manometry in Children With Defecatory Disorders
Authors: Liem O. , Burgers R.E. , Connor F.L. , Benninga M.A. , Mousa H.M. , Di Lorenzo C.
Published: July 2014

Objectives:

Colonic manometry is a test used in the evaluation of children with defecation disorders unresponsive to conventional treatment. The most commonly reported protocol in pediatrics consists of a study that lasts approximately 4 hours. Given the wide physiological variations in colonic motility throughout the day, longer observation may detect clinically relevant information. The aim of the present study was to compare prolonged colonic manometry studies in children referred for colonic manometry with the more traditional short water‐perfused technology.

Methods:

Colonic manometry studies of 19 children (8 boys, mean age 9.4 ± 0.9, range 3.9–16.3) with severe defecation disorders were analyzed. First, a “standard test” was performed with at least 1‐hour fasting, 1‐hour postprandial, and 1‐hour postbisacodyl provocation recording. Afterwards, recordings continued until the next day.

Results:

In 2 of the 19 children, prolonged recording gave us extra information. In 1 patient with functional nonretentive fecal incontinence who demonstrated no abnormalities in the short recording, 2 long clusters of high‐amplitude contractions were noted in the prolonged study, possibly contributing to the fecal incontinence. In another patient evaluated after failing use of antegrade enemas through a cecostomy, short recordings showed colonic activity only in the most proximal part of the colon, whereas the prolonged study showed normal motility over a larger portion of the colon.

Conclusions:

Prolonged colonic measurement provides more information regarding colonic motor function and allows detection of motor events missed by the standard shorter manometry study.
Analysis of Viral Testing in Nonacetaminophen Pediatric Acute Liver Failure
Authors: Schwarz Kathleen B. , Olio Dominic Dell , Lobritto Steven J. , Lopez M. James , Rodriguez‐Baez Norberto , Yazigi Nada A. , Belle Steven H. , Zhang Song , Squires Robert H. ,   Pediatric Acute Liver Failure Study Group
Published: July 2014

Objective:

Viral infections are often suspected to cause pediatric acute liver failure (PALF), but large‐scale studies have not been performed. We analyzed the results of viral testing among nonacetaminophen PALF study participants.

Methods:

Participants were enrolled in the PALF registry. Diagnostic evaluation and final diagnosis were determined by the site investigator and methods for viral testing by local standard of care. Viruses were classified as either causative viruses (CVs) or associated viruses (AVs). Supplemental testing for CV was performed if not done clinically and serum was available. Final diagnoses included “viral,” “indeterminate,” and “other.”

Results:

Of 860 participants, 820 had at least 1 test result for a CV or AV. A positive viral test was found in 166/820 (20.2%) participants and distributed among “viral” (66/80 [82.5%]), “indeterminate” (52/420 [12.4%]), and “other” (48/320 [15.0%]) diagnoses. CVs accounted for 81/166 (48.8%) positive tests. Herpes simplex virus (HSV) was positive in 39/335 (11.6%) who were tested 26/103 (25.2%) and 13/232 (5.6%) among infants 0 to 6 and >6 months, respectively. HSV was not tested in 61.0% and 53% of the overall cohort and those 0 to 6 months, respectively. Supplemental testing yielded 17 positive, including 5 HSV.

Conclusions:

Viral testing in PALF occurs frequently but is often incomplete. The evidence for acute viral infection was found in 20.2% of those tested for viruses. HSV is an important viral cause for PALF in all age groups. The etiopathogenic role of CV and AV in PALF requires further investigation.
Transient Neonatal Liver Disease After Maternal Antenatal Intravenous Ig Infusions in Gestational Alloimmune Liver Disease Associated With Neonatal Haemochromatosis
Authors: Baruteau Julien , Heissat Sophie , Broué Pierre , Collardeau‐Frachon Sophie , Bouvier Raymonde , Fabre Monique , Debiec Hannah , Ronco Pierre , Uzan Martine , Narcy Philippe , Cordier Marie‐Pierre , Lachaux Alain , Lamireau Thierry , Elleau Christophe , Filet Jean Philippe , Mitanchez Delphine , Dupuy Marie‐Pierre , Salaün Jean François , Odent Sylvie , Davison James , Debray Dominique , Guigonis Vincent
Published: July 2014

Objectives:

Neonatal haemochromatosis is a rare gestational disease that results in severe foetal liver disease with extrahepatic iron overload, sparing the reticuloendothelial system. Recurrence can be prevented with intravenous immunoglobulin (IVIG) infusions during pregnancy, supporting an alloimmune aetiology. The aim of the study was to assess the effect of antenatal treatment with IVIG infusion on the outcome of pregnancies in women with a history of documented neonatal haemochromatosis likely owing to gestational alloimmune disease and to analyse IVIG tolerance.

Methods:

From 2004 to 2012, 8 pregnant women were treated with IVIG at 1 g/kg body weight weekly from 18 weeks' gestation until birth in a prospective multicentre study.

Results:

All 8 neonates born to the treated women survived. Five developed mild neonatal liver disease with hepatomegaly (n = 1), hyperechogenic liver (n = 2), abnormal liver function tests (n = 1), raised serum ferritin (n = 3) and α‐fetoprotein (n = 5) levels, or mild iron overload on liver magnetic resonance imaging (n = 1). Ferritin and α‐fetoprotein levels normalised before 14 days and 2 months, respectively. A per‐mother‐basis analysis comparing outcomes of treated (n = 8) and untreated (n = 9) gestations showed a significant improvement in the survival of neonates with gestational IVIG therapy (survival 8/8 vs 0/9, P < 0.001). Adverse effects of IVIG infusion occurred in 5 mothers leading to discontinuation of treatment in 1 case. Preterm neonates born before 37 weeks' gestation had a decreased risk of neonatal liver disease (P = 0.04).

Conclusions:

Antenatal treatment with IVIG infusion in women at risk for gestational alloimmune disease recurrence improves the outcome of pregnancies despite mild signs of transient neonatal liver disease.
Pseudomonas salegens sp. nov., a halophilic member of the genus Pseudomonas
isolated from a wetland
Authors: Amoozegar Mohammad Ali , Shahinpei Azadeh , Sepahy Abbas Akhavan , Makhdoumi-Kakhki Ali , Seyedmahdi Shima Sadat , Schumann Peter , Ventosa Antonio
Published: July 2014

A novel Gram-stain-negative, aerobic, non-endospore-forming, non-pigmented, rod-shaped, slightly halophilic bacterium, designated GBPy5T, was isolated from aquatic plants of the Gomishan wetland, Iran. Cells of strain GBPy5T were motile. Growth occurred with between 1 and 10 % (w/v) NaCl and the isolate grew optimally with 3 % (w/v) NaCl. The optimum pH and temperature for growth of the strain were pH 8.0 and 30 °C, respectively, while it was able to grow over a pH range of 6.5–9.0 and a temperature range of 4–35 °C. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain GBPy5T is a member of the genus

Pseudomonas

forming a monophyletic branch. The novel strain exhibited 16S rRNA gene sequence similarity of 95.4 % with type strains of

Pseudomonas guariconensis

PCAVU11T and

Pseudomonas sabulinigri

J64T, respectively. The major cellular fatty acids of the isolate were C18 : 1ω7c (37.8 %), C16 : 0 (14.9 %), C16 : 1ω7c (12.9 %), C12 : 0 3-OH (7.1 %) and C12 : 0 (7.0 %). The polar lipid pattern of strain GBPy5T comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and one phospholipid. Ubiquinone 9 (Q-9) was the predominant lipoquinone. The G+C content of the genomic DNA of strain GBPy5T was 59.2 mol%. On the basis of the phenotypic and phylogenetic data, strain GBPY5T represents a novel species of the genus

Pseudomonas

, for which the name Pseudomonas salegens sp. nov. is proposed. The type strain is GBPy5T ( = IBRC-M 10762T = CECT 8338T).
Salinispirillum marinum gen. nov., sp. nov., a haloalkaliphilic bacterium in the family ‘Saccharospirillaceae’
Authors: Shahinpei Azadeh , Amoozegar Mohammad Ali , Fazeli Seyed Abolhassan Shahzadeh , Schumann Peter , Ventosa Antonio
Published: July 2014

A novel Gram-staining-negative, motile, non-pigmented, facultatively anaerobic, spirillum-shaped, halophilic and alkaliphilic bacterium, designated strain GCWy1T, was isolated from water of the coastal–marine wetland Gomishan in Iran. The strain was able to grow at NaCl concentrations of 1–10 % (w/v) and optimal growth was achieved at 3 % (w/v). The optimum pH and temperature for growth were pH 8.5 and 30 °C, while the strain was able to grow at pH 7.5–10 and 4–40 °C. Phylogenetic analysis based on the comparison of the 16S rRNA gene sequence placed the isolate within the class

Gammaproteobacteria

as a separate deep branch, with 92.1 % or lower sequence similarity to representatives of the genera

Saccharospirillum

and

Reinekea

and less than 91.0 % sequence similarity with other remotely related genera. The major cellular fatty acids of the isolate were C18 : 1ω7c, C16 : 0 and C17 : 0, and the major components of its polar lipid profile were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The cells of strain GCWy1T contained the isoprenoid quinones Q-9 and Q-8 (81 % and 2 %, respectively). The G+C content of the genomic DNA of this strain was 52.3 mol%. On the basis of 16S rRNA gene sequence analysis in combination with chemotaxonomic and phenotypic data, strain GCWy1T represents a novel species in a new genus in the family ‘

Saccharospirillaceae

’, order

Oceanospirillales

, for which the name Salinispirillum marinum gen. nov., sp. nov. is proposed. The type strain of the type species is GCWy1T ( = IBRC-M 10765T = CECT 8342T).
Aquibacillus halophilus gen. nov., sp. nov., a moderately halophilic bacterium from a hypersaline lake, and reclassification of Virgibacillus koreensis as Aquibacillus koreensis comb. nov. and Virgibacillus albus as Aquibacillus albus comb. nov.
Authors: Amoozegar Mohammad Ali , Bagheri Maryam , Didari Maryam , Mehrshad Maliheh , Schumann Peter , Spröer Cathrin , Sánchez-Porro Cristina , Ventosa Antonio
Published: July 2014

A novel Gram-stain-positive, moderately halophilic bacterium, designated strain B6BT, was isolated from the water of an Iranian hypersaline lake, Aran-Bidgol, and characterized taxonomically using a polyphasic approach. Cells of strain B6BT were rod-shaped, motile and produced ellipsoidal endospores in terminal positions in non-swollen sporangia. Strain B6BT was a strictly aerobic bacterium and catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 0.5–20.0 % (w/v), with optimum growth occurring at 10.0 % (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.0. On the basis of 16S rRNA gene sequence analysis, strain B6BT was shown to belong to the phylum

Firmicutes

and its closest phylogenetic similarities were with the species

Virgibacillus koreensis

BH30097T (97.5 %),

Virgibacillus albus

YIM 93624T (97.4 %),

Sediminibacillus halophilus

EN8dT (96.8 %),

Sediminibacillus albus

NHBX5T (96.6 %),

Virgibacillus carmonensis

LMG 20964T (96.3 %) and

Paraliobacillus quinghaiensis

YIM-C158T (96.0 %), respectively. Phylogenetic analysis revealed that strain B6BT, along with

V. koreensis

BH30097T and

V. albus

YIM 93624T, clustered in a separate clade in the family

Bacillaceae

. The DNA G+C content of the novel isolate was 35.8 mol%. DNA–DNA hybridization experiments revealed low levels of relatedness between strain B6BTand

V. koreensis

BH30097T (13 %) and

V. albus

YIM 93624T (33 %). The major cellular fatty acid of strain B6BT was anteiso-C15 : 0 (75.1 %) and its polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, an unknown phospholipid and an unknown glycolipid. The isoprenoid quinones were MK-7 (90 %) and MK-6 (3 %). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All of these features support the placement of isolate B6BT within the phylum

Firmicutes

. It is closely related to

V. koreensis

and

V. albus

, but with features that clearly distinguish it from species of the genus

Virgibacillus

or of other related genera. On the basis of the polyphasic evidence derived in this study, we propose that strain B6BT be placed within a new genus, as Aquibacillus halophilus gen. nov., sp. nov., with B6BT as the type strain ( = IBRC-M 10775T = KCTC 13828T). We also propose that

V. koreensis

and

V. albus

should be transferred to this new genus and be named Aquibacillus koreensis comb. nov. and Aquibacillus albus comb. nov., respectively. The type strain of Aquibacillus koreensis comb. nov. is BH30097T ( = KCTC 3823T = IBRC-M 10657T = JCM 12387T) and the type strain of Aquibacillus albus comb. nov. is YIM 93624T ( = DSM 23711T = IBRC-M 10798T = JCM 17364T).
Comparison of two approaches for the classification of 16S rRNA gene sequences
Authors: Chatellier Sonia , Mugnier Nathalie , Allard Françoise , Bonnaud Bertrand , Collin Valérie , van Belkum Alex , Veyrieras Jean-Baptiste , Emler Stefan
Published: July 2014

The use of 16S rRNA gene sequences for microbial identification in clinical microbiology is accepted widely, and requires databases and algorithms. We compared a new research database containing curated 16S rRNA gene sequences in combination with the lca (lowest common ancestor) algorithm (RDB-LCA) to a commercially available 16S rDNA Centroid approach. We used 1025 bacterial isolates characterized by biochemistry, matrix-assisted laser desorption/ionization time-of-flight MS and 16S rDNA sequencing. Nearly 80 % of isolates were identified unambiguously at the species level by both classification platforms used. The remaining isolates were mostly identified correctly at the genus level due to the limited resolution of 16S rDNA sequencing. Discrepancies between both 16S rDNA platforms were due to differences in database content and the algorithm used, and could amount to up to 10.5 %. Up to 1.4 % of the analyses were found to be inconclusive. It is important to realize that despite the overall good performance of the pipelines for analysis, some inconclusive results remain that require additional in-depth analysis performed using supplementary methods.
Acinetobacter sp. isolates from emergency departments in two hospitals of South Korea
Authors: Choi Ji-Young , Ko Eun Ah , Kwon Ki Tae , Lee Shinwon , Kang Choel In , Chung Doo-Ryeon , Peck Kyong Ran , Song Jae-Hoon , Ko Kwan Soo
Published: July 2014

A total of 114 Acinetobacter sp. isolates were collected from patients in the emergency departments (EDs) of two Korean hospitals. Most isolates belonged to the Acinetobacter baumannii complex (105 isolates, 92.1 %). Imipenem resistance was found in 39 isolates (34.2 %) of the Acinetobacter sp. isolates, and 6 colistin-resistant isolates were also identified. Species distribution and antimicrobial-resistance rates were different between the two hospitals. In addition, two main clones were identified in the imipenem-resistant A. baumannii isolates from hospital B, but very diverse and novel genotypes were found in those from hospital A. Many Acinetobacter sp. isolates, including the imipenem-resistant A. baumannii, are considered to be associated with the community. The evidence of high antimicrobial resistance and different features in these Acinetobacter sp. isolates between the two EDs suggests the need for continuous testing to monitor changes in epidemiology.
Genetic structure and biological properties of the first ancient multiresistance plasmid pKLH80 isolated from a permafrost bacterium
Authors: Petrova Mayya , Kurakov Anton , Shcherbatova Natalya , Mindlin Sofia
Published: July 2014

A novel multidrug-resistance plasmid, pKLH80, previously isolated from Psychrobacter maritimus MR29-12 found in ancient permafrost, was completely sequenced and analysed. In our previous studies, we focused on the pKLH80 plasmid region containing streptomycin and tetracycline resistance genes, and their mobilization with an upstream-located ISPpy1 insertion sequence (IS) element. Here, we present the complete sequence of pKLH80 and analysis of its backbone genetic structure, including previously unknown features of the plasmid’s accessory region, notably a novel variant of the β-lactamase gene bla
RTG-6. Plasmid pKLH80 was found to be a circular 14 835 bp molecule that has an overall G+C content of 40.3 mol% and encodes 20 putative ORFs. There are two distinctive functional modules within the plasmid backbone sequence: (i) the replication module consisting of repB and the oriV region; and (ii) the mobilization module consisting of mobA, mobC and oriT. All of the aforementioned genes share sequence identities with corresponding genes of different species of Psychrobacter. The plasmid accessory region contains antibiotic resistance genes and IS elements (ISPsma1 of the IS982 family, and ISPpy1 and ISAba14 of the IS3 family) found in environmental and clinical bacterial strains of different taxa. We revealed that the sequences flanking bla
RTG-6 and closely related genes from clinical bacteria are nearly identical. This fact suggests that bla
RTG-6 from the environmental strain of Psychrobacter is a progenitor of bla
RTG genes of clinical bacteria. We also showed that pKLH80 can replicate in different strains of Acinetobacter and Psychrobacter genera. The roles of IS elements in the horizontal transfer of antibiotic resistance genes are examined and discussed.
Novel divergent nidovirus in a python with pneumonia
Authors: Bodewes Rogier , Lempp Charlotte , Schürch Anita C. , Habierski Andre , Hahn Kerstin , Lamers Mart , von Dörnberg Katja , Wohlsein Peter , Drexler Jan Felix , Haagmans Bart L. , Smits Saskia L. , Baumgärtner Wolfgang , Osterhaus Albert D. M. E.
Published: July 2014

The order Nidovirales contains large, enveloped viruses with a non-segmented positive-stranded RNA genome. Nidoviruses have been detected in man and various animal species, but, to date, there have been no reports of nidovirus in reptiles. In the present study, we describe the detection, characterization, phylogenetic analyses and disease association of a novel divergent nidovirus in the lung of an Indian python (Python molurus) with necrotizing pneumonia. Characterization of the partial genome (>33 000 nt) of this virus revealed several genetic features that are distinct from other nidoviruses, including a very large polyprotein 1a, a putative ribosomal frameshift signal that was identical to the frameshift signal of astroviruses and retroviruses and an accessory ORF that showed some similarity with the haemagglutinin–neuraminidase of paramyxoviruses. Analysis of genome organization and phylogenetic analysis of polyprotein 1ab suggests that this virus belongs to the subfamily Torovirinae. Results of this study provide novel insights into the genetic diversity within the order Nidovirales.
Bayesian mixture analysis for metagenomic community profiling
Authors: Morfopoulou Sofia , Plagnol Vincent
Published: July 2014

Deep sequencing of clinical samples is now an established tool for the detection of infectious pathogens, with direct medical applications. The large amount of data generated provides an opportunity to detect species even at very low levels, provided that computational tools can effectively interpret potentially complex metagenomic mixtures. Data interpretation is complicated by the fact that short sequencing reads can match multiple organisms and by the lack of completeness of existing databases, in particular for viral pathogens. This interpretation problem can be formulated statistically as a mixture model, where the species of origin of each read is missing, but the complete knowledge of all species present in the mixture helps with the individual reads assignment. Several analytical tools have been proposed to approximately solve this computational problem. Here, we show that the use of parallel Monte Carlo Markov chains (MCMC) for the exploration of the species space enables the identification of the set of species most likely to contribute to the mixture. The added accuracy comes at a cost of increased computation time. Our approach is useful for solving complex mixtures involving several related species. We designed our method specifically for the analysis of deep transcriptome sequencing datasets and with a particular focus on viral pathogen detection, but the principles are applicable more generally to all types of metagenomics mixtures. The work is implemented as a user friendly R package, available from CRAN:http://cran.r-project.org/web/packages/metaMix.
“Long non-coding RNA discovery inAnopheles gambiaeusing deep RNA sequencing”
Authors: Jenkins Adam M. , Waterhouse Robert M. , Kopin Alan S. , Muskavitch Marc A.T.
Published: July 2014

Long non-coding RNAs (lncRNAs) are mRNA-like transcripts longer than 200 bp that have no protein-coding potential. lncRNAs have recently been implicated in epigenetic regulation, transcriptional and post-transcriptional gene regulation, and regulation of genomic stability in mammals,Caenorhabditis elegans, andDrosophila melanogaster. Using deep RNA sequencing of multipleAnopheles gambiaelife stages, we have identified over 600 novel lncRNAs and more than 200 previously unannotated putative protein-coding genes. The lncRNAs exhibit differential expression profiles across life stages and adult genders. Those lncRNAs that are antisense to known protein-coding genes or are contained within intronic regions of protein-coding genes may mediate transcriptional repression or stabilization of associated mRNAs. lncRNAs exhibit faster rates of sequence evolution across anophelines compared to previously known and newly identified protein-coding genes. This initial description of lncRNAs inAn. gambiaeoffers the first genome-wide insights into long non-coding RNAs in this vector mosquito and defines a novel set of potential targets for the development of vector-based interventions that may curb the human malaria burden in disease-endemic countries.
Comparing Local, National and EU Knowledge: The Ignorant Public Reassessed
Authors: Rapeli Lauri
Published: July 2014

Empirical research has repeatedly confirmed the political ignorance of ordinary citizens, but democracy prevails. This article offers a new perspective into this paradox by arguing that typical political knowledge indicators are inadequate because they only measure national‐level knowledge. The study makes two contributions. First, it compares national, local and European Union political knowledge. Second, it does so with a nationally representative dataset, which comes from a survey from Finland (n = 1,020) devoted solely to political knowledge. Two questions are posed: Are the sociodemographic determinants of knowledge the same on all levels of politics? And is public ignorance equally widespread on all levels? Challenging some established findings, the study shows that people in rural communities know more about local politics than urban counterparts, that women know more about local politics than men and that young people are equally knowledgeable about the EU as older people. The results thus indicate that people are to varying extents knowledgeable about varying aspects of politics.
Gender Differences in Assessments of Party Leaders
Authors: Kosiara‐Pedersen Karina , Hansen Kasper M.
Published: July 2014

Is there a relationship between party leader gender and voters' assessments? The answer is ‘yes’ according to theses on gender identity and stereotyping. A voter survey during the 2011Danish general election allows for a comprehensive analysis of a less likely case with four male and four female party leaders. Female party leaders are assessed more positively by female voters than male voters both in regard to general party leader sympathy and assessment of specific characteristics, whereas it is not the case that male party leaders are assessed more positively by male voters than female voters. The impact of gender does not increase with age; in fact, the opposite is the case among men since younger male voters have less sympathy for female party leaders. Furthermore, there is no support for the expectation that voters with more education or with higher levels of political interest and knowledge are more positive towards party leaders of their own gender than voters with less education. Also, the relationship between gender and voter assessment is not stronger prior to an election campaign than immediately after an election. Hence, in sum, gender identity does not seem to require a higher level of political sophistication, nor does it decrease with higher levels of information.
Rituximab with chemotherapy in children and adolescents with central nervous system and/or bone marrow‐positive Burkitt lymphoma/leukaemia: a Children's Oncology Group Report
Authors: Goldman Stanton , Smith Lynette , Galardy Paul , Perkins Sherrie L. , Frazer John Kimble , Sanger Warren , Anderson James R. , Gross Thomas G. , Weinstein Howard , Harrison Lauren , Shiramizu Bruce , Barth Matthew , Cairo Mitchell S.
Published: July 2014

Children and adolescents with Burkitt Lymphoma (BL) and combined central nervous system (CNS) and bone marrow involvement still have a poor prognosis with chemotherapy alone. We therefore investigated in children and adolescents with bone marrow (≥25% blasts) and/or CNS‐positive Burkitt lymphoma the chemoimmunotherapy combination of rituximab (375 mg/m2) and the standard chemotherapy arm of our previously reported French‐American‐British (FAB) Lymphome Malins de Burkitt (LMB) 96 trial. Central pathological and cytogenetic characterization was also performed. There were 40 evaluable patients with Burkitt histology (25 with leukaemia and 15 with CNS disease ± leukaemia). The chemoimmunotherapy regimen was well tolerated. The incidence of grade III/IV mucositis during induction cycles with combined chemotherapy and rituximab was 31% and 26%, respectively. The 3‐year event‐free survival (EFS)/overall survival (OS) was 90% (95% confidence interval [CI], 76–96%) in the entire cohort and 93% (95% CI, 61–99%) in patients with CNS disease. Based on the results of this trial, an international randomized study of FAB/LMB 96 chemotherapy ± rituximab for high‐risk patients is currently under investigation.
The Intersectionality of Postsecondary Pathways: The Case of High School Students with Special Education Needs
Authors: Robson Karen L. , Anisef Paul , Brown Robert S. , Parekh Gillian
Published: July 2014

Utilisant des données du Toronto District School Board, cette étude examine les parcours postsecondaires des étudiants qui ont besoin de services d’éducation de l'enfance en difficulté. Nous observons les parcours qui mènent au collège ainsi que ceux menant à l'université et nous nous servons de régression logistique multinomiale à plusieurs niveaux afin de situer nos résultats dans le contexte du cycle de vie. Nos résultants démontrent que les étudiants qui ont besoin de services d'éducation de l'enfance en difficulté ont moins de chances d'accepter une offre d'une université mais plus de chances d'accepter une offre d'un collège. Nous analysons un groupe de facteurs connus et bien documentés qui influencent le parcours postsecondaire afin de connaître leur rôle quant au parcours des étudiants qui ont besoin de services d'éducation de l'enfance en difficulté. Nos résultats démontrent que le niveau d'éducation des parents, le revenu du quartier, la race et la filière scolaire ont tous un impact sur le parcours postsecondaire de cette population étudiante.

Using data from the Toronto District School Board, we examine the postsecondary pathways of students with special education needs (SEN). We consider both university and college pathways, employing multilevel multinomial logistic regressions, conceptualizing our findings within a life course and intersectionality framework. Our findings reveal that having SEN reduces the likelihood of confirming university, but increases the likelihood of college confirmation. We examine a set of known determinants of postsecondary education (PSE) pathways that were derived from the literature and employ exploratory statistical interactions to examine if the intersection of various traits differentially impacts upon the PSE trajectories of students with SEN. Our findings reveal that parental education, neighborhood wealth, race, and streaming impact on the postsecondary pathways of students with SEN in Toronto.
Social and Political Convergence on Environmental Events: The Roles of Simplicity and Visuality in the BP Oil Spill
Authors: Hoffbauer Andreas , Ramos Howard
Published: July 2014

Cet article étudie de quelle façon et à quel moment les journaux, les ONG environnementales, les entreprises privées et le gouvernement convergent autour des événements environnementaux. En utilisant les données sur le déversement de pétrole BP en 2010 tirées des journaux aux États‐Unis, au Canada et en Grande‐Bretagne et des communiqués de presses de Greenpeace, du Club Sierra, de Halliburton, de Transocean, d’Exxon/Mobil et les annonce de presse de la secrétaire de presse pour le Maison Blanche, nous étudions la capacité d'un événement à faire converger des actions sociales et politiques. En concevant les événements comme des actants, nous vérifions les arguments tirés des publications sur les mouvements sociaux et sur la définition de l'agenda politique à propos du timing, de la simplicité et de la visualité afin de comprendre comment les acteurs politiques convergent. Nous observons que l'effet de convergence est lié au timing, mais pas à la simplicité ou à la visualité.

This paper examines how and when newspapers, environmental nongovernmental organizations, businesses, and the government converge on environmental events. Using data on the 2010 BP Oil Spill from newspaper articles in the United States, Canada, and the United Kingdom, press releases by Greenpeace and Sierra Club, press releases by BP, Halliburton, Transocean, ExxonMobil, and Shell, and press statements by the White House Press Secretary, we examine an event's potential to trigger convergence of social and political action. By treating events as political actants, we examine arguments from the agenda‐setting and social movement literatures on timing, simplicity, and visuality to understand when political actors converge. We find that convergence is related to temporal cycles but not simplicity or visuality.