bluuebunny/crossref_metadata_2025 huggingface dataset:
Imiquimod-Induced TLR7 Signaling Enhances Repair of DNA Damage Induced by Ultraviolet Light in Bone Marrow-Derived Cells
Authors: Fishelevich Rita , Zhao Yuming , Tuchinda Papapit , Liu Hannah , Nakazono Ayako , Tammaro Antonella , Meng Tzu-Ching , Lee Jim , Gaspari Anthony A.
Published: July 2011

Imiquimod is a TLR7/8 agonist that has anticancer therapeutic efficacy in the treatment of precancerous skin lesions and certain nonmelanoma skin cancers. To test our hypothesis that imiquimod enhances DNA repair as a mechanism for its anticancer activity, the nucleotide excision repair genes were studied in bone marrow-derived cells. Imiquimod enhanced the expression of xeroderma pigmentosum (XP) A and other DNA repair genes (quantitative real-time PCR analysis) and resulted in an increased nuclear localization of the DNA repair enzyme XPA. This was dependent on MyD88, as bone marrow-derived cells from MyD88−/− mice did not increase XPA gene expression and did not enhance the survival of MyD88−/−-derived bone marrow-derived cells after UV B exposure as was observed in bone marrow-derived cells from MyD88+/+ mice. Imiquimod also enhanced DNA repair of UV light (UVL)-irradiated gene expression constructs and accelerated the resolution of cyclobutane pyrimidine dimers after UVL exposures in P388 and XS52. Lastly, topical treatment of mouse skin with 5% imiquimod cream prior to UVL irradiation resulted in a decrease in the number of cyclobutane pyridimine dimer-positive APC that were found in local lymph nodes 24 h after UVL irradiation in both wild-type and IL-12 gene-targeted mice. In total, these data support the idea that TLR7 agonists such as imiquimod enhance DNA repair in bone marrow-derived cells. This property is likely to be an important mechanism for its anticancer effects because it protects cutaneous APC from the deleterious effects of UVL.
Blast-induced phenotypic switching in cerebral vasospasm
Authors: Alford Patrick W. , Dabiri Borna E. , Goss Josue A. , Hemphill Matthew A. , Brigham Mark D. , Parker Kevin Kit
Published: July 2011

Vasospasm of the cerebrovasculature is a common manifestation of blast-induced traumatic brain injury (bTBI) reported among combat casualties in the conflicts in Afghanistan and Iraq. Cerebral vasospasm occurs more frequently, and with earlier onset, in bTBI patients than in patients with other TBI injury modes, such as blunt force trauma. Though vasospasm is usually associated with the presence of subarachnoid hemorrhage (SAH), SAH is not required for vasospasm in bTBI, which suggests that the unique mechanics of blast injury could potentiate vasospasm onset, accounting for the increased incidence. Here, using theoretical and in vitro models, we show that a single rapid mechanical insult can induce vascular hypercontractility and remodeling, indicative of vasospasm initiation. We employed high-velocity stretching of engineered arterial lamellae to simulate the mechanical forces of a blast pulse on the vasculature. An hour after a simulated blast, injured tissues displayed altered intracellular calcium dynamics leading to hypersensitivity to contractile stimulus with endothelin-1. One day after simulated blast, tissues exhibited blast force dependent prolonged hypercontraction and vascular smooth muscle phenotype switching, indicative of remodeling. These results suggest that an acute, blast-like injury is sufficient to induce a hypercontraction-induced genetic switch that potentiates vascular remodeling, and cerebral vasospasm, in bTBI patients.
Stage prediction of embryonic stem cell differentiation from genome-wide expression data
Authors: Zagar Lan , Mulas Francesca , Garagna Silvia , Zuccotti Maurizio , Bellazzi Riccardo , Zupan Blaz
Published: July 2011

Motivation: The developmental stage of a cell can be determined by cellular morphology or various other observable indicators. Such classical markers could be complemented with modern surrogates, like whole-genome transcription profiles, that can encode the state of the entire organism and provide increased quantitative resolution. Recent findings suggest that such profiles provide sufficient information to reliably predict the cell's developmental stage.

Results: We use whole-genome transcription data and several data projection methods to infer differentiation stage prediction models for embryonic cells. Given a transcription profile of an uncharacterized cell, these models can then predict its developmental stage. In a series of experiments comprising 14 datasets from the Gene Expression Omnibus, we demonstrate that the approach is robust and has excellent prediction ability both within a specific cell line and across different cell lines.

Availability: Model inference and computational evaluation procedures in the form of Python scripts and accompanying datasets are available at http://www.biolab.si/supp/stagerank.

Contact:  blaz.zupan@fri.uni-lj.si

Supplementary information:  Supplementary data are available at Bioinformatics online.
Three Feruloyl Esterases in Cellulosilyticum ruminicola H1 Act Synergistically To Hydrolyze Esterified Polysaccharides
Authors: Li Jiabao , Cai Shichun , Luo Yuanming , Dong Xiuzhu
Published: July 2011

Feruloyl esterases (Faes) constitute a subclass of carboxyl esterases that specifically hydrolyze the ester linkages between ferulate and polysaccharides in plant cell walls. Until now, the described microbial Faes were mainly from fungi. In this study, we report thatCellulosilyticum ruminicolaH1, a previously described fibrolytic rumen bacterium, possesses three different active feruloyl esterases, FaeI, FaeII, and FaeIII. Phylogenetic analysis classified the described bacterial Faes into two types, FaeI and FaeII in type I and FaeIII in type II. Substrate specificity assays indicated that FaeI is more active against the ester bonds in natural hemicelluloses and FaeIII preferentially attacks the ferulate esters with a small moiety, such as methyl groups, while FaeII is active on both types of substrates. Among the three feruloyl esterase genes,faeIwas the only one induced significantly by xylose and xylan, while pectin appeared to moderately induce the three genes during the late log phase to stationary phase. Western blot analysis determined that FaeI and FaeIII were secreted and cytoplasmic proteins, respectively, whereas FaeII seemed to be cell associated. The addition of FaeI and FaeII but not FaeIII enhanced the activity of a xylanase on maize cob, suggesting a synergy of the former two with xylanase. Hence, we propose that the three feruloyl esterases work in concert to hydrolyze ferulate esters in natural hemicelluloses.
The Impact of Personal Experience on Behavior: Evidence from Video-Rental Fines
Authors: Haselhuhn Michael P. , Pope Devin G. , Schweitzer Maurice E. , Fishman Peter
Published: July 2011

Personal experience matters. In a field setting with longitudinal data, we disentangle the effects of learning new information from the effects of personal experience. We demonstrate that experience with a fine, controlling for the effect of learning new information, significantly boosts future compliance. We also show that experience with a large fine boosts compliance more than experience with a small fine, but that the influence of experience with both large and small fines decays sharply over time.

This paper was accepted by Brad Barber, Teck Ho, and Terrance Odean, special issue editors.
Recurrent Pseudo-TORCH Appearances of the Brain Presenting as “Dandy-Walker” Malformation
Authors: Cohen Marta C. , Karaman Ilgin , Squier Waney , Farrel Tom , Whitby Elspeth H.
Published: July 2011

Dandy-Walker malformation (DWM) is a developmental abnormality characterized by cystic dilatation of the fourth ventricle, complete or partial agenesis of the cerebellar vermis, and enlarged posterior fossa with upward displacement of the lateral sinuses, tentorium, and torcula. Calcification of brain tissue is a feature of congenital infection, particularly those involving the TORCH ( Toxoplasma gondii, rubella virus, Cytomegalovirus, and herpesvirus) group. An autosomal-recessive congenital infection-like syndrome with intracranial and extracranial calcifications has been categorized as pseudo-TORCH syndrome. We describe two male siblings diagnosed as DWM by ultrasound and by in utero and postmortem magnetic resonance imaging (MRI) but in whom the neuropathology revealed features of intracranial necrosis and calcification in the absence of extracranial calcific deposition. The fetal anomaly was identified by routine prenatal ultrasound scan at 16 weeks. In both cases the postmortem MRI showed bilateral ventriculomegaly with distortion of the overlying cortices, enlarged posterior fossa with a cyst related to small cerebellar hemispheres, and an incomplete cerebellar vermis. The diagnosis of DWM was offered. The histology revealed hypoplastic cerebral hemispheres with poorly cellular developing cortex. The white matter and periventricular matrix were disrupted by areas of necrosis and calcification not associated with any inflammatory infiltration, organisms, inclusions, or giant cells. To our knowledge, these two male siblings are the 1st cases that show pseudo-TORCH syndrome with distinctive intracranial calcification presenting as DWM. An autosomal-recessive or X-linked inheritance needs to be considered. Our study confirms the relevance of the multidisciplinary teamwork involved in the diagnosis of these complex cases.
Natural Killer-22 Cells in the Synovial Fluid of Patients with Rheumatoid Arthritis Are an Innate Source of Interleukin 22 and Tumor Necrosis Factor-α
Authors: REN JIE , FENG ZHITAO , LV ZHUO , CHEN XIAOGUANG , LI JUAN
Published: July 2011

Objective.

To determine the role of natural killer (NK)-22 cells in the pathogenesis of rheumatoid arthritis (RA).

Methods.

Using flow cytometry, the proportions of NK-22 cells and intracellular contents of perforin, granzyme B, and interferon-γ (IFN-γ) were determined in the peripheral blood (PB) and synovial fluid (SF) of patients with RA and healthy individuals. The levels of interleukin 22 (IL-22) and tumor necrosis factor-α (TNF-α) in the NK-22 supernatant and gene expressions were measured using ELISA and QuantiGene Plex assay, respectively. The effect of NK-22 supernatant on the proliferation of fibroblast-like synoviocytes (FLS) and recombinant human IL-22 (rhIL-22) on the production of monocyte chemoattractant protein 1 (MCP-1) by RA FLS was detected using the yellow tetrazolium salt method and ELISA, respectively. The relationship between the proportions of NK-22 cells and disease activity was analyzed.

Results.

NKp44 and CCR6 were expressed in a larger population of SF NK cells than in the PB NK cells of patients with RA. NK-22 cells produce low content of perforin, granzyme B, and IFN-γ. NK-22 cellsin vitrocan secrete IL-22 and TNF-α and there was increased messenger RNA coding for IL-22 and TNF-α. NK-22 supernatant can induce the proliferation of RA FLS. Addition of IL-22 antibody plus TNF-α antibody inhibited the proliferation of FLS induced by the NK-22 supernatant. Both rhIL-22 1 ng/ml and rhIL-22 10 ng/ml induced the production of MCP-1 by RA FLS. The NK-22 proportions were positively correlated with disease activity.

Conclusion.

NK-22 cells are increased in patients with RA and might play a role in the pathogenesis of RA through the production of IL-22 and TNF-α. The proportion of NK-22 cells and disease activity were highly correlated.
Some new features of Direct Analysis in Real Time mass spectrometry utilizing the desorption at an angle option
Authors: Chernetsova Elena S. , Revelsky Alexander I. , Morlock Gertrud E.
Published: July 2011

The present study is a first step towards the unexplored capabilities of Direct Analysis in Real Time (DART) mass spectrometry (MS) arising from the possibility of the desorption at an angle: scanning analysis of surfaces, including the coupling of thin‐layer chromatography (TLC) with DART‐MS, and a more sensitive analysis due to the preliminary concentration of analytes dissolved in large volumes of liquids on glass surfaces. In order to select the most favorable conditions for DART‐MS analysis, proper positioning of samples is important. Therefore, a simple and cheap technique for the visualization of the impact region of the DART gas stream onto a substrate was developed. A filter paper or TLC plate, previously loaded with the analyte, was immersed in a derivatization solution. On this substrate, owing to the impact of the hot DART gas, reaction of the analyte to a colored product occurred. An improved capability of detection of DART‐MS for the analysis of liquids was demonstrated by applying large volumes of model solutions of coumaphos into small glass vessels and drying these solutions prior to DART‐MS analysis under ambient conditions. This allowed the introduction of, by up to more than two orders of magnitude, increased quantities of analyte compared with the conventional DART‐MS analysis of liquids. Through this improved detectability, the capabilities of DART‐MS in trace analysis could be strengthened. Copyright © 2011 John Wiley & Sons, Ltd.
Cd-Specific Mutants of Mercury-Sensing Regulatory Protein MerR, Generated by Directed Evolution
Authors: Hakkila Kaisa M. , Nikander Pia A. , Junttila Sini M. , Lamminmäki Urpo J. , Virta Marko P.
Published: July 2011

The mercury-sensing regulatory protein, MerR (Tn
21
), which regulates mercury resistance operons in Gram-negative bacteria, was subjected to directed evolution in an effort to generate a MerR mutant that responds to Cd but not Hg. Oligonucleotide-directed mutagenesis was used to introduce random mutations into the key metal-binding regions of MerR. The effects of these mutations were assessed using a vector in which MerR controlled the expression of green fluorescent protein (GFP) and luciferase via the
mer
operator/promoter. An
Escherichia coli
cell library was screened by fluorescence-activated cell sorting, using a fluorescence-based dual screening strategy that selected for MerR mutants that showed GFP repression when cells were induced with Hg but GFP activation in the presence of Cd. Two Cd-responsive MerR mutants with decreased responses toward Hg were identified through the first mutagenesis/selection round. These mutants were used for a second mutagenesis/selection round, which yielded eight Cd-specific mutants that had no significant response to Hg, Zn, or the other tested metal(loid)s. Seven of the eight Cd-specific MerR mutants showed repressor activities equal to that of wild-type (wt) MerR. These Cd-specific mutants harbored multiple mutations (12 to 22) in MerR, indicating that the alteration of metal specificity with maintenance of repressor function was due to the combined effect of many mutations rather than just a few amino acid changes. The amino acid changes were studied by alignment against the sequences of MerR and other metal-responsive MerR family proteins. The analysis indicated that the generated Cd-specific MerR mutants appear to be unique among the MerR family members characterized to date.
Systematic Analysis of Diguanylate Cyclases That Promote Biofilm Formation by Pseudomonas fluorescens Pf0-1
Authors: Newell Peter D. , Yoshioka Shiro , Hvorecny Kelli L. , Monds Russell D. , O'Toole George A.
Published: July 2011

Cyclic di-GMP (c-di-GMP) is a broadly conserved, intracellular second-messenger molecule that regulates biofilm formation by many bacteria. The synthesis of c-di-GMP is catalyzed by diguanylate cyclases (DGCs) containing the GGDEF domain, while its degradation is achieved through the phosphodiesterase activities of EAL and HD-GYP domains. c-di-GMP controls biofilm formation by
Pseudomonas fluorescens
Pf0-1 by promoting the cell surface localization of a large adhesive protein, LapA. LapA localization is regulated posttranslationally by a c-di-GMP effector system consisting of LapD and LapG, which senses cytoplasmic c-di-GMP and modifies the LapA protein in the outer membrane. Despite the apparent requirement for c-di-GMP for biofilm formation by
P. fluorescens
Pf0-1, no DGCs from this strain have been characterized to date. In this study, we undertook a systematic mutagenesis of 30 predicted DGCs and found that mutations in just 4 cause reductions in biofilm formation by
P. fluorescens
Pf0-1 under the conditions tested. These DGCs were characterized genetically and biochemically to corroborate the hypothesis that they function to produce c-di-GMP
in vivo
. The effects of DGC gene mutations on phenotypes associated with biofilm formation were analyzed. One DGC preferentially affects LapA localization, another DGC mainly controls swimming motility, while a third DGC affects both LapA and motility. Our data support the conclusion that different c-di-GMP-regulated outputs can be specifically controlled by distinct DGCs.
Airway resistance at maximum inhalation as a marker of asthma and airway hyperresponsiveness
Authors: Mendonça Nancy T , Kenyon Jennifer , LaPrad Adam S , Syeda Sohera N , O'Connor George T , Lutchen Kenneth R
Published: July 2011

Background

Asthmatics exhibit reduced airway dilation at maximal inspiration, likely due to structural differences in airway walls and/or functional differences in airway smooth muscle, factors that may also increase airway responsiveness to bronchoconstricting stimuli. The goal of this study was to test the hypothesis that the minimal airway resistance achievable during a maximal inspiration (Rmin) is abnormally elevated in subjects with airway hyperresponsiveness.

Methods

The Rmin was measured in 34 nonasthmatic and 35 asthmatic subjects using forced oscillations at 8 Hz. Rmin and spirometric indices were measured before and after bronchodilation (albuterol) and bronchoconstriction (methacholine). A preliminary study of 84 healthy subjects first established height dependence of baseline Rmin values.

Results

Asthmatics had a higher baseline Rmin % predicted than nonasthmatic subjects (134 ± 33 vs. 109 ± 19 % predicted, p = 0.0004). Sensitivity-specificity analysis using receiver operating characteristic curves indicated that baseline Rmin was able to identify subjects with airway hyperresponsiveness (PC20 < 16 mg/mL) better than most spirometric indices (Area under curve = 0.85, 0.78, and 0.87 for Rmin % predicted, FEV1 % predicted, and FEF25-75 % predicted, respectively). Also, 80% of the subjects with baseline Rmin < 100% predicted did not have airway hyperresponsiveness while 100% of subjects with Rmin > 145% predicted had hyperresponsive airways, regardless of clinical classification as asthmatic or nonasthmatic.

Conclusions

These findings suggest that baseline Rmin, a measurement that is easier to perform than spirometry, performs as well as or better than standard spirometric indices in distinguishing subjects with airway hyperresponsiveness from those without hyperresponsive airways. The relationship of baseline Rmin to asthma and airway hyperresponsiveness likely reflects a causal relation between conditions that stiffen airway walls and hyperresponsiveness. In conjunction with symptom history, Rmin could provide a clinically useful tool for assessing asthma and monitoring response to treatment.
A Survey of Arthrocentesis and Soft-Tissue Injection Procedures Performed in Primary Care Practice: Effect of Resident Training and Using Data to Shape Curriculum
Authors: BAKEWELL CATHERINE J. , GARDNER GREGORY C.
Published: July 2011

Objective.

The purpose of this study is (1) to survey graduates of our internal medicine program for use of musculoskeletal (MSK) procedures in primary care practice and assess the influence of participating in a first-year resident arthrocentesis and soft-tissue injection training course on their MSK procedure comfort/utilization; and (2) to use the results to modify our MSK procedure curriculum.

Methods.

A questionnaire designed to assess numbers of, comfort with, and effect of resident training on MSK procedures in the preceding year was sent to 2002–2006 graduates of the internal medicine training program in outpatient primary care (OPC). Graduates practicing hospital medicine (HM) also received the questionnaire and served as a comparison group.

Results.

There were 52 responses from this group of 84 graduates (64% response rate). OPC graduates (N = 32) were more comfortable doing procedures than those practicing HM exclusively (N = 20), and performed significantly more procedures in the preceding year (32.9 procedures per OPC/year vs 2.2 for HM). The most common procedures performed were knee joint, subacromial bursa, and trochanteric bursa, comprising > 75% of all procedures performed. A structured resident course in MSK procedures had a significant effect on the OPC physicians. Course participants (N = 17) performed almost twice the number of procedures/year as the nonparticipants (N = 15), were more comfortable with the procedures, and were significantly less likely to refer procedures to other clinicians. Written comments by respondents suggest additional MSK procedure training during and after residency is needed.

Conclusion.

Our results suggest a structured resident course in MSK procedures has a longterm influence. A progressively more focused approach to training is needed.
Identification of nitroglycerin‐induced cysteine modifications of pro‐matrix metalloproteinase‐9
Authors: Krishnatry Anu Shilpa , Kamei Tomonori , Wang Hao , Qu Jun , Fung Ho‐Leung
Published: July 2011

Nitroglycerin (NTG), an important cardiovascular agent, has been shown recently to activate matrix metalloproteinase‐9 (MMP‐9) in biological systems, possibly leading to destabilization of atherosclerotic plaques. The chemical mechanism for this activation, particularly on the cysteine switch of the pro‐form of MMP‐9 (proMMP‐9), has not been investigated and was examined here using nano‐flow liquid chromatography coupled to mass spectrometry. In order to obtain high sequence coverage, two orthogonal enzymes (trypsin and GluC) were employed to digest the protein in parallel. Two complementary activation methods, collision‐induced dissociation (CID) and electron‐transfer dissociation (ETD), were employed for the identification of various modifications. A high‐resolution Orbitrap analyzer was used to enable confident identification. Incubation of NTG with proMMP‐9 resulted in the formation of an unstable thionitrate intermediate and oxidation of the cysteine switch to sulfinic and irreversible sulfonic acid derivatives. The unstable thionitrate modification was confirmed by both CID and ETD in the proteolytic peptides produced by both trypsin and GluC. Incubation of proMMP‐9 with diethylenetriamine NONOate (a nitric oxide donor) led to sulfonic acid formation, but no observable sulfinic acid modification. Extensive tyrosine nitration by NTG was observed at Tyr‐262, in close proximity to an oxidized Cys‐256 of proMMP‐9. The intramolecular interaction between these two residues toward NTG‐induced oxidation was examined using a synthesized peptide representing the sequence in this domain, PWCSTTANYDTDDR, and the modification status was compared against an analog in which Cys was substituted by Ala. We observed a thionitrate product, extensive Cys oxidative modifications and enhanced tyrosine nitration with the Cys peptide but not with the Ala analog. Our results indicated that neighboring Cys and Tyr residues can facilitate each other's oxidation in the presence of NTG. Copyright © 2011 John Wiley & Sons, Ltd.
N incorporation and photoluminescence in In-rich InGaAsN grown on InAs by liquid phase epitaxy
Authors: de la Mare M , Das S C , Das T D , Dhar S , Krier A
Published: July 2011

Dilute nitride InGaAsN layers with high In content have been grown on InAs substrates by liquid phase epitaxy using GaN as a precursor for N in the growth solution. Photoluminescence (PL) was obtained in the mid-infrared spectral range at temperatures between 4 and 300 K. Although Ga increases the InAs bandgap, the strong band anti-crossing effect from the N incorporation resulted in an overall bandgap reduction of 11 meV compared with InAs. The temperature-dependent PL exhibited a complicated behaviour and showed an anomalous increase in intensity from 190 K to room temperature. This was due to the formation in a complex defect which behaves as a non-radiative recombination centre and prevents radiative band–band recombination at temperatures <190 K. Above this temperature the PL increases as band–band transitions become allowed. The formation of this defect requires the presence of both Ga and N and becomes de-activated after a high-temperature anneal. Raman spectroscopy confirmed the presence of phonon modes associated with In–N and Ga–N bonds confirming the incorporation of N using liquid phase growth.
Alumina nanoparticles find an application to reduce the ionic effects of ferroelectric liquid crystal
Authors: Joshi T , Prakash J , Kumar A , Gangwar J , Srivastava A K , Singh S , Biradar A M
Published: July 2011

We observed that the doping of alumina nanoparticles (AL-NPs) has suppressed the undesired ionic effect in ferroelectric liquid crystals (FLCs). The pure and AL-NPs doped FLC cells were analysed by means of dielectric spectroscopy and electrical resistivity/conductivity measurements. Dielectric loss spectra confirmed the disappearance of the low-frequency relaxation peak, which appears due to the presence of ionic impurities in the FLC materials. The reduction of ionic effects has been attributed to the strong adsorption of ionic impurities on the surface of AL-NPs. The adsorption capability of AL-NPs has been studied with both the size and their concentration in FLC material. This study would be helpful to minimize the undesired ionic effects of LC-based display devices.
Effects of the action of hydrogen peroxide on the electrical properties of polyaniline-aluminium composites
Authors: Gmati Fethi , Fattoum Arbi , Manaii Aymen , Mohamed Abdellatif Belhadj
Published: July 2011

The effects of the action of hydrogen peroxide (H2O2) as an oxidizing agent on the electrical properties of polyaniline-aluminium (PANI-Al) composites are studied. Direct current (dc) electrical conductivity is investigated in the temperature range 303–453 K. A decrease in the conductivity with attack time is observed. The results are compatible with UV–visible and infrared absorption measurements and scanning electron microscopy analysis. The experimental data show a transition from a negative temperature coefficient of resistivity (TCR) to a positive TCR. This transition becomes more pronounced when the attack time increases. Depending on the H2O2 attack time, we found that the dc conductivity of the composites is described by two distinct models: the first is a series combination between the fluctuation-induced tunnelling (FIT) model with a metallic transport model, the second is a combination between Mott's three-dimensional variable range hopping with an intrinsic metallic model. The different FIT and Mott parameters are evaluated. The change in the conduction mechanism is attributed to the disorder and the localization effect caused by the action of H2O2 on the PANI-Al composite.
Electrode biasing experiment in the Large Helical Device
Authors: Kitajima S. , Takahashi H. , Ishii K. , Sato J. , Ambo T. , Kanno M. , Okamoto A. , Sasao M. , Inagaki S. , Takayama M. , Masuzaki S. , Shoji M. , Ashikawa N. , Tokitani M. , Yokoyama M. , Suzuki Y. , Shimozuma T. , Ido T. , Shimizu A. , Nagayama Y. , Tokuzawa T. , Nishimura K. , Morisaki T. , Kubo S. , Kasahara H. , Mutoh T. , Yamada H. , Tatematsu Y.
Published: July 2011

The transition to the improved confinement mode by electrode biasing was observed for the first time in the Large Helical Device (LHD). A negative resistance was observed in the confinement mode sustained by the cold electrode biasing. The electrode current showed a clear decrease against an increase in the electrode voltage and was characterized by a hysteresis in the transition phenomena. The decrease in the electrode current suggested an improvement in the radial particle transport. An increase in the energy confinement time and remarkable suppression of density fluctuations, which correspond to the transition, were also observed. These results indicated that the electrode biased plasma in LHD showed similar improvements in confinement to those in the H-mode plasmas in tokamaks and stellarators.
Optical detection and femtosecond spectroscopy of a single nanoparticle
Authors: Baida Hatim , Crut Aurélien , Maioli Paolo , Nguyen Thanh Binh , Nguyen Dai Hung , Fatti Natalia Del , Vallée Fabrice
Published: July 2011

An extension to semiconductor quantum dots of the spatial-modulation technique, demonstrated for the optical detection and linear spectroscopy of a single metal nanoparticle, is described. The association of this approach to a high sensitivity femtosecond pump–probe setup is discussed and applied to the investigation of the acoustic vibration of a single silver nanoparticle.
PGAT: a multistrain analysis resource for microbial genomes
Authors: Brittnacher M. J. , Fong C. , Hayden H. S. , Jacobs M. A. , Radey Matthew , Rohmer L.
Published: July 2011

Motivation: The Prokaryotic-genome Analysis Tool (PGAT) is a web-based database application for comparing gene content and sequence across multiple microbial genomes facilitating the discovery of genetic differences that may explain observed phenotypes. PGAT supports database queries to identify genes that are present or absent in user-selected genomes, comparison of sequence polymorphisms in sets of orthologous genes, multigenome display of regions surrounding a query gene, comparison of the distribution of genes in metabolic pathways and manual community annotation.

Availability and Implementation:The PGAT website may be accessed at http://nwrce.org/pgat.

Contact:  mbrittna@uw.edu
IRiS: Construction of ARG networks at genomic scales
Authors: Javed Asif , Pybus Marc , Melé Marta , Utro Filippo , Bertranpetit Jaume , Calafell Francesc , Parida Laxmi
Published: July 2011

Summary: Given a set of extant haplotypes IRiS first detects high confidence recombination events in their shared genealogy. Next using the local sequence topology defined by each detected event, it integrates these recombinations into an ancestral recombination graph. While the current system has been calibrated for human population data, it is easily extendible to other species as well.

Availability: IRiS (Identification of Recombinations in Sequences) binary files are available for non-commercial use in both Linux and Microsoft Windows, 32 and 64 bit environments from https://researcher.ibm.com/researcher/view_project.php?id = 2303

Contact:  parida@us.ibm.com
Development of a Gastroenterology Educational Curriculum for Pediatric Residents Using Fellows as Teachers
Authors: Pentiuk Scott , Baker Raymond
Published: July 2011

Objectives:

At many institutions, the teaching provided on subspecialty gastroenterology rotations is not structured. The purpose of the present study was to describe the development, implementation, and assessment of a structured gastroenterology curriculum for pediatric residents.

Methods:

A needs assessment was performed via a survey of former pediatric resident graduates presently working in general pediatrics. Topics for the curriculum were developed based upon the needs assessment. Second‐year residents on the inpatient gastroenterology rotation attended 4 case‐based, small group sessions per week for 1 month. Sessions were taught primarily by upper‐level gastroenterology fellows. The curriculum was assessed via a pre‐posttest, postrotation survey, and group feedback sessions.

Results:

Resident rating of education received during the rotation was high. Posttest scores increased slightly but significantly compared with pretest values. The curriculum has continued to be used >4 years after its development.

Conclusions:

The creation of a structured subspecialty curriculum with the use of fellows as teachers is both feasible and effective despite limitations in available time for resident teaching.
Mechanism for Aar2p function as a U5 snRNP assembly factor
Authors: Weber Gert , Cristão Vanessa F. , de L. Alves Flavia , Santos Karine F. , Holton Nicole , Rappsilber Juri , Beggs Jean D. , Wahl Markus C.
Published: July 2011

Little is known about how particle-specific proteins are assembled on spliceosomal small nuclear ribonucleoproteins (snRNPs). Brr2p is a U5 snRNP-specific RNA helicase required for spliceosome catalytic activation and disassembly. In yeast, the Aar2 protein is part of a cytoplasmic precursor U5 snRNP that lacks Brr2p and is replaced by Brr2p in the nucleus. Here we show that Aar2p and Brr2p bind to different domains in the C-terminal region of Prp8p; Aar2p interacts with the RNaseH domain, whereas Brr2p interacts with the Jab1/MPN domain. These domains are connected by a long, flexible linker, but the Aar2p–RNaseH complex sequesters the Jab1/MPN domain, thereby preventing binding by Brr2p. Aar2p is phosphorylated in vivo, and a phospho-mimetic S253E mutation in Aar2p leads to disruption of the Aar2p–Prp8p complex in favor of the Brr2p–Prp8p complex. We propose a model in which Aar2p acts as a phosphorylation-controlled U5 snRNP assembly factor that regulates the incorporation of the particle-specific Brr2p. The purpose of this regulation may be to safeguard against nonspecific RNA binding to Prp8p and/or premature activation of Brr2p activity.
Metagenomic Insights into the Evolution, Function, and Complexity of the Planktonic Microbial Community of Lake Lanier, a Temperate Freshwater Ecosystem
Authors: Oh Seungdae , Caro-Quintero Alejandro , Tsementzi Despina , DeLeon-Rodriguez Natasha , Luo Chengwei , Poretsky Rachel , Konstantinidis Konstantinos T.
Published: July 2011

Lake Lanier is an important freshwater lake for the southeast United States, as it represents the main source of drinking water for the Atlanta metropolitan area and is popular for recreational activities. Temperate freshwater lakes such as Lake Lanier are underrepresented among the growing number of environmental metagenomic data sets, and little is known about how functional gene content in freshwater communities relates to that of other ecosystems. To better characterize the gene content and variability of this freshwater planktonic microbial community, we sequenced several samples obtained around a strong summer storm event and during the fall water mixing using a random whole-genome shotgun (WGS) approach. Comparative metagenomics revealed that the gene content was relatively stable over time and more related to that of another freshwater lake and the surface ocean than to soil. However, the phylogenetic diversity of Lake Lanier communities was distinct from that of soil and marine communities. We identified several important genomic adaptations that account for these findings, such as the use of potassium (as opposed to sodium) osmoregulators by freshwater organisms and differences in the community average genome size. We show that the lake community is predominantly composed of sequence-discrete populations and describe a simple method to assess community complexity based on population richness and evenness and to determine the sequencing effort required to cover diversity in a sample. This study provides the first comprehensive analysis of the genetic diversity and metabolic potential of a temperate planktonic freshwater community and advances approaches for comparative metagenomics.
Isolation, Taxonomy, and Antagonistic Properties of Halophilic Actinomycetes in Saharan Soils of Algeria
Authors: Meklat Atika , Sabaou Nasserdine , Zitouni Abdelghani , Mathieu Florence , Lebrihi Ahmed
Published: July 2011

The diversity of a population of 52 halophilic actinomycetes was evaluated by a polyphasic approach, which showed the presence of members of the
Actinopolyspora
,
Nocardiopsis
,
Saccharomonospora
,
Streptomonospora
, and
Saccharopolyspora
genera. One strain was considered to be a new member of the last genus, and several other strains seemed to be new species. Furthermore, 50% of strains were active against a broad range of indicators and contained genes encoding polyketide synthetases and nonribosomal peptide synthetases.
Biodegradation of Polyester Polyurethane by Endophytic Fungi
Authors: Russell Jonathan R. , Huang Jeffrey , Anand Pria , Kucera Kaury , Sandoval Amanda G. , Dantzler Kathleen W. , Hickman DaShawn , Jee Justin , Kimovec Farrah M. , Koppstein David , Marks Daniel H. , Mittermiller Paul A. , Núñez Salvador Joel , Santiago Marina , Townes Maria A. , Vishnevetsky Michael , Williams Neely E. , Vargas Mario Percy Núñez , Boulanger Lori-Ann , Bascom-Slack Carol , Strobel Scott A.
Published: July 2011

Bioremediation is an important approach to waste reduction that relies on biological processes to break down a variety of pollutants. This is made possible by the vast metabolic diversity of the microbial world. To explore this diversity for the breakdown of plastic, we screened several dozen endophytic fungi for their ability to degrade the synthetic polymer polyester polyurethane (PUR). Several organisms demonstrated the ability to efficiently degrade PUR in both solid and liquid suspensions. Particularly robust activity was observed among several isolates in the genus
Pestalotiopsis
, although it was not a universal feature of this genus. Two
Pestalotiopsis microspora
isolates were uniquely able to grow on PUR as the sole carbon source under both aerobic and anaerobic conditions. Molecular characterization of this activity suggests that a serine hydrolase is responsible for degradation of PUR. The broad distribution of activity observed and the unprecedented case of anaerobic growth using PUR as the sole carbon source suggest that endophytes are a promising source of biodiversity from which to screen for metabolic properties useful for bioremediation.
Discovery of an Escherichia coli Esterase with High Activity and Enantioselectivity toward 1,2-
O
-Isopropylideneglycerol Esters
Authors: Godinho Luis F. , Reis Carlos R. , Tepper Pieter G. , Poelarends Gerrit J. , Quax Wim J.
Published: July 2011

Escherichia coli
has been widely used as an expression host for the identification of desired biocatalysts through screening or selection assays. We have previously used
E. coli
in growth selection and screening assays for identification of
Bacillus subtilis
lipase variants (located in the periplasm) with improved activity and enantioselectivity toward 1,2-
O
-isopropylideneglycerol (IPG) esters. In the course of these studies, we discovered that
E. coli
itself exhibits significant cytoplasmic esterase activity toward IPG esters. In order to identify the enzyme (or enzymes) responsible for this esterase activity, we analyzed eight
E. coli
knockout strains, in which single esterase genes were deleted, for their ability to hydrolyze IPG butyrate. This approach led to the identification of esterase YbfF as the major
E. coli
enzyme responsible for the hydrolytic activity toward IPG esters. The gene coding for YbfF was cloned and overexpressed in
E. coli
, and the corresponding protein was purified and characterized for its biocatalytic performance. YbfF displays a high level of activity toward IPG butyrate and IPG caprylate and prefers the
R
-enantiomer of these substrates, producing the
S
-enantiomer of the IPG product with high enantiomeric excess (72 to 94%
ee
). The enantioselectivity of YbfF for IPG caprylate (
E
= 40) could be significantly enhanced when using dimethylformamide (DMF) or dimethyl sulfoxide (DMSO) as cosolvents in kinetic resolution experiments. The enzyme also shows high enantioselectivity toward 1-phenylethyl acetate (
E
≥ 200), giving the chiral product (
R
)-1-phenylethanol with >99%
ee
. The high activity and enantioselectivity of YbfF make it an attractive enzyme for organic synthesis.
pSEUDO, a Genetic Integration Standard for Lactococcus lactis
Authors: Pinto Joao P. C. , Zeyniyev Araz , Karsens Harma , Trip Hein , Lolkema Juke S. , Kuipers Oscar P. , Kok Jan
Published: July 2011

Plasmid pSEUDO and derivatives were used to show that
llmg
_
pseudo
_
10
in
Lactococcus lactis
MG1363 and its homologous locus in
L. lactis
IL1403 are suitable for chromosomal integrations.
L. lactis
MG1363 and IL1403 nisin-induced controlled expression (NICE) system derivatives (JP9000 and IL9000) and two general stress reporter strains (NZ9000::P
hrcA
-GFP and NZ9000::P
groES
-GFP) enabling
in vivo
noninvasive monitoring of cellular fitness were constructed.
Physiological and Transcriptional Characterization of Persistent and Nonpersistent Listeria monocytogenes Isolates
Authors: Fox Edward M. , Leonard Nola , Jordan Kieran
Published: July 2011

This study aimed to characterize physiological differences between persistent and presumed nonpersistent
Listeria monocytogenes
strains isolated at processing facilities and to investigate the molecular basis for this by transcriptomic sequencing. Full metabolic profiles of two strains, one persistent and one nonpersistent, were initially screened using Biolog's Phenotype MicroArray (PM) technology. Based on these results, in which major differences from selected antimicrobial agents were detected, another persistent strain and two nonpersistent strains were characterized using two antimicrobial PMs. Resistance to quaternary ammonium compounds (QACs) was shown to be higher among persistent strains. Growth of persistent and nonpersistent strains in various concentrations of the QACs benzethonium chloride (BZT) and cetylpyridinium chloride (CPC) was determined. Transcriptomic sequencing of a persistent and a presumed nonpersistent strain was performed to compare gene expression among these strains in the presence and absence of BZT. Two strains, designated “frequent persisters” because they were the most frequently isolated at the processing facility, showed overall higher resistance to QACs. Transcriptome analysis showed that BZT induced a complex peptidoglycan (PG) biosynthesis response, which may play a key role in BZT resistance. Comparison of persistent and nonpersistent strains indicated that transcription of many genes was upregulated among persistent strains. This included three gene operons:
pdu
,
cob-cbi
, and
eut
. These genes may play a role in the persistence of
L. monocytogenes
outside the human host.
Coevolution of Morphology and Virulence in Candida Species
Authors: Thompson Delma S. , Carlisle Patricia L. , Kadosh David
Published: July 2011

Many of the major human fungal pathogens are known to undergo morphological changes, which in certain cases are associated with virulence. Although there has been an intense research focus on morphology in fungi, very little is known about how morphology evolved in conjunction with a variety of other virulence properties. However, several recent important discoveries, primarily inCandidaspecies, are beginning to shed light on this important area and answer many longstanding questions. In this minireview, we first provide a description of the major fungal morphologies, as well as the roles of morphology and morphology-associated gene expression in virulence. Next, focusing largely onCandidaspecies, we examine the evolutionary relationships among specific morphological forms. Finally, drawing on recent findings, we begin to address the question of how specific morphological changes came to be associated with virulence ofCandidaspecies during evolution.
RNA Interference in Protozoan Parasites: Achievements and Challenges
Authors: Kolev Nikolay G. , Tschudi Christian , Ullu Elisabetta
Published: July 2011

Protozoan parasites that profoundly affect mankind represent an exceptionally diverse group of organisms, including
Plasmodium
,
Toxoplasma
,
Entamoeba
,
Giardia
, trypanosomes, and
Leishmania
. Despite the overwhelming impact of these parasites, there remain many aspects to be discovered about mechanisms of pathogenesis and how these organisms survive in the host. Combined with the ever-increasing availability of sequenced genomes, RNA interference (RNAi), discovered a mere 13 years ago, has enormously facilitated the analysis of gene function, especially in organisms that are not amenable to classical genetic approaches. Here we review the current status of RNAi in studies of parasitic protozoa, with special emphasis on its use as a postgenomic tool.
Using Superfolder Green Fluorescent Protein for Periplasmic Protein Localization Studies
Authors: Dinh Thuy , Bernhardt Thomas G.
Published: July 2011

Studies investigating the subcellular localization of periplasmic proteins have been hampered by problems with the export of green fluorescent protein (GFP). Here we show that a superfolding variant of GFP (sfGFP) is fluorescent following Sec-mediated transport and works best when the cotranslational branch of the pathway is employed.
Genetic Requirements for High Constitutive SOS Expression inrecA730Mutants of Escherichia coli
Authors: Vlašić Ignacija , Šimatović Ana , Brčić-Kostić Krunoslav
Published: July 2011

The RecA protein in its functional state is in complex with single-stranded DNA, i.e., in the form of a RecA filament. In SOS induction, the RecA filament functions as a coprotease, enabling the autodigestion of the LexA repressor. The RecA filament can be formed by different mechanisms, but all of them require three enzymatic activities essential for the processing of DNA double-stranded ends. These are helicase, 5′–3′ exonuclease, and RecA loading onto single-stranded DNA (ssDNA). In some mutants, the SOS response can be expressed constitutively during the process of normal DNA metabolism. The RecA730 mutant protein is able to form the RecA filament without the help of RecBCD and RecFOR mediators since it better competes with the single-strand binding (SSB) protein for ssDNA. As a consequence, therecA730mutants show high constitutive SOS expression. In the study described in this paper, we studied the genetic requirements for constitutive SOS expression inrecA730mutants. Using a β-galactosidase assay, we showed that the constitutive SOS response inrecA730mutants exhibits different requirements in different backgrounds. In a wild-type background, the constitutive SOS response is partially dependent on RecBCD function. In arecB1080background (therecB1080mutation retains only helicase), constitutive SOS expression is partially dependent on RecBCD helicase function and is strongly dependent on RecJ nuclease. Finally, in arecB-null background, the constitutive SOS expression of therecA730mutant is dependent on the RecJ nuclease. Our results emphasize the importance of the 5′–3′ exonuclease for high constitutive SOS expression inrecA730mutants and show that RecBCD function can further enhance the excellent intrinsic abilities of the RecA730 proteinin vivo.
HlyU Is a Positive Regulator of Hemolysin Expression in Vibrio anguillarum
Authors: Li Ling , Mou Xiangyu , Nelson David R.
Published: July 2011

The two hemolysin gene clusters previously identified in
Vibrio anguillarum
, the
vah1
cluster and the
rtxACHBDE
cluster, are responsible for the hemolytic and cytotoxic activities of
V. anguillarum
in fish. In this study, we used degenerate PCR to identify a positive hemolysin regulatory gene,
hlyU
, from the unsequenced
V. anguillarum
genome. The
hlyU
gene of
V. anguillarum
encodes a 92-amino-acid protein and is highly homologous to other bacterial HlyU proteins. An
hlyU
mutant was constructed, which exhibited an ∼5-fold decrease in hemolytic activity on sheep blood agar with no statistically significant decrease in cytotoxicity of the wild-type strain. Complementation of the
hlyU
mutation restored both hemolytic activity and cytotoxic activity. Both semiquantitative reverse transcription-PCR (RT-PCR) and quantitative real-time RT-PCR (qRT-PCR) were used to examine expression of the hemolysin genes under exponential and stationary-phase conditions in wild-type,
hlyU
mutant, and
hlyU
complemented strains. Compared to the wild-type strain, expression of
rtx
genes decreased in the
hlyU
mutant, while expression of
vah1
and
plp
was not affected in the
hlyU
mutant. Complementation of the
hlyU
mutation restored expression of the
rtx
genes and increased
vah1
and
plp
expression to levels higher than those in the wild type. The transcriptional start sites in both the
vah1-plp
and
rtxH-rtxB
genes' intergenic regions were determined using 5′ random amplification of cDNA ends (5′-RACE), and the binding sites for purified HlyU were discovered using DNA gel mobility shift experiments and DNase protection assays.