bluuebunny/crossref_metadata_2025 huggingface dataset:
Depletion of eIF4G from yeast cells narrows the range of translational efficiencies genome-wide
Authors: Park Eun-Hee , Zhang Fan , Warringer Jonas , Sunnerhagen Per , Hinnebusch Alan G
Published: January 2011

Background

Eukaryotic translation initiation factor 4G (eIF4G) is thought to influence the translational efficiencies of cellular mRNAs by its roles in forming an eIF4F-mRNA-PABP mRNP that is competent for attachment of the 43S preinitiation complex, and in scanning through structured 5' UTR sequences. We have tested this hypothesis by determining the effects of genetically depleting eIF4G from yeast cells on global translational efficiencies (TEs), using gene expression microarrays to measure the abundance of mRNA in polysomes relative to total mRNA for ~5900 genes.

Results

Although depletion of eIF4G is lethal and reduces protein synthesis by ~75%, it had small effects (less than a factor of 1.5) on the relative TE of most genes. Within these limits, however, depleting eIF4G narrowed the range of translational efficiencies genome-wide, with mRNAs of better than average TE being translated relatively worse, and mRNAs with lower than average TE being translated relatively better. Surprisingly, the fraction of mRNAs most dependent on eIF4G display an average 5' UTR length at or below the mean for all yeast genes.

Conclusions

This finding suggests that eIF4G is more critical for ribosome attachment to mRNAs than for scanning long, structured 5' UTRs. Our results also indicate that eIF4G, and the closed-loop mRNP it assembles with the m7 G cap- and poly(A)-binding factors (eIF4E and PABP), is not essential for translation of most (if not all) mRNAs but enhances the differentiation of translational efficiencies genome-wide.
Insects in confined swine operations carry a large antibiotic resistant and potentially virulent enterococcal community
Authors: Ahmad Aqeel , Ghosh Anuradha , Schal Coby , Zurek Ludek
Published: January 2011

Background

Extensive use of antibiotics as growth promoters in the livestock industry constitutes strong selection pressure for evolution and selection of antibiotic resistant bacterial strains. Unfortunately, the microbial ecology and spread of these bacteria in the agricultural, urban, and suburban environments are poorly understood. Insects such as house flies (Musca domestica) and German cockroaches (Blattella germanica) can move freely between animal waste and food and may play a significant role in the dissemination of antibiotic resistant bacteria within and between animal production farms and from farms to residential settings.

Results

Enterococci from the digestive tract of house flies (n = 162), and feces of German cockroaches (n = 83) and pigs (n = 119), collected from two commercial swine farms were isolated, quantified, identified, and screened for antibiotic resistance and virulence. The majority of samples (93.7%) were positive for enterococci with concentrations 4.2 ± 0.7 × 104 CFU/house fly, 5.5 ± 1.1 × 106 CFU/g of cockroach feces, and 3.2 ± 0.8 × 105 CFU/g of pig feces. Among all the identified isolates (n = 639) Enterococcus faecalis was the most common (55.5%), followed by E. hirae (24.9%), E. faecium (12.8%), and E. casseliflavus (6.7%). E. faecalis was most prevalent in house flies and cockroaches, and E. hirae was most common in pig feces. Our data showed that multi-drug (mainly tetracycline and erythromycin) resistant enterococci were common from all three sources and frequently carried antibiotic resistance genes including tet(M) and erm(B) and Tn916/1545 transposon family. E. faecalis frequently harbored virulence factors gelE, esp, and asa1. PFGE analysis of selected E. faecalis and E. faecium isolates demonstrated that cockroaches and house flies shared some of the same enterococcal clones that were detected in the swine manure indicating that insects acquired enterococci from swine manure.

Conclusions

This study shows that house flies and German cockroaches in the confined swine production environment likely serve as vectors and/or reservoirs of antibiotic resistant and potentially virulent enterococci and consequently may play an important role in animal and public health.
Functional mapping of reaction norms to multiple environmental signals through nonparametric covariance estimation
Authors: Yap John S , Li Yao , Das Kiranmoy , Li Jiahan , Wu Rongling
Published: January 2011

Background

The identification of genes or quantitative trait loci that are expressed in response to different environmental factors such as temperature and light, through functional mapping, critically relies on precise modeling of the covariance structure. Previous work used separable parametric covariance structures, such as a Kronecker product of autoregressive one [AR(1)] matrices, that do not account for interaction effects of different environmental factors.

Results

We implement a more robust nonparametric covariance estimator to model these interactions within the framework of functional mapping of reaction norms to two signals. Our results from Monte Carlo simulations show that this estimator can be useful in modeling interactions that exist between two environmental signals. The interactions are simulated using nonseparable covariance models with spatio-temporal structural forms that mimic interaction effects.

Conclusions

The nonparametric covariance estimator has an advantage over separable parametric covariance estimators in the detection of QTL location, thus extending the breadth of use of functional mapping in practical settings.
Immunologically reactive M. leprae antigens with relevance to diagnosis and vaccine development
Authors: Sampaio Lucas H , Stefani Mariane MA , Oliveira Regiane M , Sousa Ana LM , Ireton Greg C , Reed Steven G , Duthie Malcolm S
Published: January 2011

Background

Leprosy is a chronic infectious disease caused by Mycobacterium leprae that can manifest a wide variety of immunological and clinical outcomes ranging from potent humoral responses among borderline lepromatous (BL) and lepromatous (LL) patients to strong cellular responses among tuberculoid (TT) and borderline tuberculoid (BT) patients. Until recently, relatively little has been known about the immune responses to individual proteins of M. leprae recognized during leprosy.

Methods

The immune reactivity to a panel of 33 M. leprae recombinant proteins was evaluated among leprosy patients and controls from a high endemic area for leprosy (Goiania/GO, Central Brazil). Serum IgG responses were measured by ELISA (45 participants/group) and T cell responses (20 participants/group) were evaluated by IFN-gamma production in 24 hours whole blood cultures with antigen (whole blood assay-WBA). Study groups were newly diagnosed, untreated TT/BT and BL/LL leprosy patients classified by Ridley Jopling criteria and household contacts of BL/LL patients (HHC). Control groups were HIV-1 negative pulmonary tuberculosis patients (TB) and healthy individuals from the same endemic area (EC). In silico predictions indicated the level of identity of M. leprae proteins with homologues in other mycobacteria and the presence of T cell and B cell epitopes.

Results

Despite the prediction that all proteins would be reactive, 16 of 33 (48%) of the single proteins tested were immunogenic (recognized in WBA or ELISA) and seventeen were non-immunogenic (not recognized in either assay). Among the 16 immunogenic proteins, 9 were considered leprosy specific in WBA inducing cell-mediated IFN-gamma secretion from TT/BT patients and HHC. Three of these proteins were also leprosy specific in serology being recognized by serum IgG from LL/BL patients. Seven of the immunogenic proteins were not leprosy specific.

Conclusions

New M. leprae antigens recognized by antibody responses of BL/LL patients and cellular responses of TT/BT leprosy patients were identified. An improved serological diagnostic test for leprosy could be developed by incorporating these IgG-reactive antigens to the current PGL-I based tests. Moreover our data indicate that the WBA is a robust, relatively simple and user friendly format for a T cell based diagnostic test. The field use of these test formats in leprosy endemic countries could contribute to early leprosy diagnosis before the development of deformities and disabilities.
Graphical analysis of pH-dependent properties of proteins predicted using PROPKA
Authors: Rostkowski Michał , Olsson Mats HM , Søndergaard Chresten R , Jensen Jan H
Published: January 2011

Background

Charge states of ionizable residues in proteins determine their pH-dependent properties through their pKa values. Thus, various theoretical methods to determine ionization constants of residues in biological systems have been developed. One of the more widely used approaches for predicting pKa values in proteins is the PROPKA program, which provides convenient structural rationalization of the predicted pKa values without any additional calculations.

Results

The PROPKA Graphical User Interface (GUI) is a new tool for studying the pH-dependent properties of proteins such as charge and stabilization energy. It facilitates a quantitative analysis of pKa values of ionizable residues together with their structural determinants by providing a direct link between the pKa data, predicted by the PROPKA calculations, and the structure via the Visual Molecular Dynamics (VMD) program. The GUI also calculates contributions to the pH-dependent unfolding free energy at a given pH for each ionizable group in the protein. Moreover, the PROPKA-computed pKa values or energy contributions of the ionizable residues in question can be displayed interactively. The PROPKA GUI can also be used for comparing pH-dependent properties of more than one structure at the same time.

Conclusions

The GUI considerably extends the analysis and validation possibilities of the PROPKA approach. The PROPKA GUI can conveniently be used to investigate ionizable groups, and their interactions, of residues with significantly perturbed pKa values or residues that contribute to the stabilization energy the most. Charge-dependent properties can be studied either for a single protein or simultaneously with other homologous structures, which makes it a helpful tool, for instance, in protein design studies or structure-based function predictions. The GUI is implemented as a Tcl/Tk plug-in for VMD, and can be obtained online at http://propka.ki.ku.dk/~luca/wiki/index.php/GUI_Web.
Comparison of Dietary Control and Atorvastatin on High Fat Diet Induced Hepatic Steatosis and Hyperlipidemia in Rats
Authors: Ji Guiyuan , Zhao Xihong , Leng Liang , Liu Peiyi , Jiang Zhuoqin
Published: January 2011

Background

Treatment with atorvastatin (ATO) or dietary control has been demonstrated to benefit patients with non-alcoholic fatty liver disease (NAFLD) and hyperlipidemia. However, little is known on whether combination of dietary control and ATO treatment could enhance the therapeutic effect.

Methods

We employed a rat model of NAFLD to examine the therapeutic efficacy of dietary control and/or ATO treatment. Sprague-Dawley rats were fed with normal chow diet as normal controls or with high fat diet (HFD) for 12 weeks to establish NAFLD. The NAFLD rats were randomized and continually fed with HFD, with normal chow diet, with HFD and treated with 30 mg/kg of ATO or with normal chow diet and treated with the same dose of ATO for 8 weeks. Subsequently, the rats were sacrificed and the serum lipids, aminotranferase, hepatic lipids, and liver pathology were characterized. The relative levels of fatty acid synthesis and β-oxidation gene expression in hepatic tissues were measured by quantitative real-time polymerase chain reaction (qRT-PCR). Hepatic expression of hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase was determined by Western blot assay.

Results

While continual feeding with HFD deteriorated NAFLD and hyperlipidemia, treatment with dietary control, ATO or ATO with dietary control effectively improved serum and liver lipid metabolism and liver function. In comparison with ATO treatment, dietary control or combined with ATO treatment significantly reduced the liver weight and attenuated the HFD-induced hyperlipidemia and liver steatosis in rats. Compared to ATO treatment or dietary control, combination of ATO and dietary control significantly reduced the levels of serum total cholesterol and low density lipoprotein cholesterol (LDL-C). However, the combination therapy did not significantly improve triglyceride and free fatty acid metabolism, hepatic steatosis, and liver function, as compared with dietary control alone.

Conclusions

ATO treatment effectively improved NAFLD-related hyperlipidemia and inhibited liver steatosis, accompanied by modulating the expression of genes for regulating lipid metabolism. ATO enhanced the effect of dietary control on reducing the levels of serum total cholesterol and LDL-C, but not triglyceride, free fatty acid and hepatic steatosis in HFD-induced fatty liver and hyperlipidemia in rats.
Effects of low-temperature capping on the optical properties of GaAs/AlGaAs quantum wells
Authors: Jo Masafumi , Duan Guotao , Mano Takaaki , Sakoda Kazuaki
Published: January 2011

We study the effects of low-temperature capping (200-450°C) on the optical properties of GaAs/AlGaAs quantum wells. Photoluminescence measurements clearly show the formation of abundant nonradiative recombination centers in an AlGaAs capping layer grown at 200°C, while there is a slight degradation of the optical quality in AlGaAs capping layers grown at temperatures above 350°C compared to that of a high-temperature capping layer. In addition, the optical quality can be restored by post-growth annealing without any structural change, except for the 200°C-capped sample.
Characterization of MHz pulse repetition rate femtosecond laser-irradiated gold-coated silicon surfaces
Authors: Sivakumar Manickam , Venkatakrishnan Krishnan , Tan Bo
Published: January 2011

In this study, MHz pulse repetition rate femtosecond laser-irradiated gold-coated silicon surfaces under ambient condition were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction analysis (XRD), and X-ray photoelectron spectroscopy (XPS). The radiation fluence used was 0.5 J/cm2 at a pulse repetition rate of 25 MHz with 1 ms interaction time. SEM analysis of the irradiated surfaces showed self-assembled intermingled weblike nanofibrous structure in and around the laser-irradiated spots. Further TEM investigation on this nanostructure revealed that the nanofibrous structure is formed due to aggregation of Au-Si/Si nanoparticles. The XRD peaks at 32.2°, 39.7°, and 62.5° were identified as (200), (211), and (321) reflections, respectively, corresponding to gold silicide. In addition, the observed chemical shift of Au 4f and Si 2p lines in XPS spectrum of the irradiated surface illustrated the presence of gold silicide at the irradiated surface. The generation of Si/Au-Si alloy fibrous nanoparticles aggregate is explained by the nucleation and subsequent condensation of vapor in the plasma plume during irradiation and expulsion of molten material due to high plasma pressure.
Formation and reinforcement of clusters composed of C60 molecules
Authors: Kurosu Shunji , Fukuda Takahiro , Shibuya Yuichi , Maekawa Toru
Published: January 2011

We carry out two experiments: (1) the formation of clusters composed of C60 molecules via self-assembly and (2) the reinforcement of the clusters. Firstly, clusters such as fibres and helices composed of C60 molecules are produced via self-assembly in supercritical carbon dioxide. However, C60 molecules are so weakly bonded to each other in the clusters that the clusters are broken by the irradiation of electron beams during scanning electron microscope observation. Secondly, UV photons are irradiated inside a chamber in which air is filled at 1 atm and the above clusters are placed, and it was found that the clusters are reinforced; that is, they are not broken by electron beams any more. C60 molecules located at the surface of the clusters are oxidised, i.e. C60O
n
molecules, where n = 1, 2, 3 and 4, are produced according to time-of-flight mass spectroscopy. It is supposed that oxidised C60 molecules at the surface of the clusters may have an important role for the reinforcement, but the actual mechanism of the reinforcement of the clusters has not yet been clearly understood and therefore is an open question.
Improvement of performance of InAs quantum dot solar cell by inserting thin AlAs layers
Authors: Hu Dongzhi , McPheeters Claiborne CO , Yu Edward T , Schaadt Daniel M
Published: January 2011

A new measure to enhance the performance of InAs quantum dot solar cell is proposed and measured. One monolayer AlAs is deposited on top of InAs quantum dots (QDs) in multistack solar cells. The devices were fabricated by molecular beam epitaxy. In situ annealing was intended to tune the QD density. A set of four samples were compared: InAs QDs without in situ annealing with and without AlAs cap layer and InAs QDs in situ annealed with and without AlAs cap layer. Atomic force microscopy measurements show that when in situ annealing of QDs without AlAs capping layers is investigated, holes and dashes are present on the device surface, while capping with one monolayer AlAs improves the device surface. On unannealed samples, capping the QDs with one monolayer of AlAs improves the spectral response, the open-circuit voltage and the fill factor. On annealed samples, capping has little effect on the spectral response but reduces the short-circuit current, while increasing the open-circuit voltage, the fill factor and power conversion efficiency.
Formation of Ge-Sn nanodots on Si(100) surfaces by molecular beam epitaxy
Authors: Mashanov Vladimir , Ulyanov Vladimir , Timofeev Vyacheslav , Nikiforov Aleksandr , Pchelyakov Oleg , Yu Ing-Song , Cheng Henry
Published: January 2011

The surface morphology of Ge0.96Sn0.04/Si(100) heterostructures grown at temperatures from 250 to 450°C by atomic force microscopy (AFM) and scanning tunnel microscopy (STM) ex situ has been studied. The statistical data for the density of Ge0.96Sn0.04 nanodots (ND) depending on their lateral size have been obtained. Maximum density of ND (6 × 1011 cm-2) with the average lateral size of 7 nm can be obtained at 250°C. Relying on the reflection of high energy electron diffraction, AFM, and STM, it is concluded that molecular beam growth of Ge1-x
Sn
x
heterostructures with the small concentrations of Sn in the range of substrate temperatures from 250 to 450°C follows the Stranski-Krastanow mechanism. Based on the technique of recording diffractometry of high energy electrons during the process of epitaxy, the wetting layer thickness of Ge0.96Sn0.04 films is found to depend on the temperature of the substrate.
Electrical behavior of multi-walled carbon nanotube network embedded in amorphous silicon nitride
Authors: Stavarache Ionel , Lepadatu Ana-Maria , Teodorescu Valentin Serban , Ciurea Magdalena Lidia , Iancu Vladimir , Dragoman Mircea , Konstantinidis George , Buiculescu Raluca
Published: January 2011

The electrical behavior of multi-walled carbon nanotube network embedded in amorphous silicon nitride is studied by measuring the voltage and temperature dependences of the current. The microstructure of the network is investigated by cross-sectional transmission electron microscopy. The multi-walled carbon nanotube network has an uniform spatial extension in the silicon nitride matrix. The current-voltage and resistance-temperature characteristics are both linear, proving the metallic behavior of the network. The I-V curves present oscillations that are further analyzed by computing the conductance-voltage characteristics. The conductance presents minima and maxima that appear at the same voltage for both bias polarities, at both 20 and 298 K, and that are not periodic. These oscillations are interpreted as due to percolation processes. The voltage percolation thresholds are identified with the conductance minima.
Preparation and characterization of spindle-like Fe3O4 mesoporous nanoparticles
Authors: Zhang Shaofeng , Wu Wei , Xiao Xiangheng , Zhou Juan , Ren Feng , Jiang Changzhong
Published: January 2011

Magnetic spindle-like Fe3O4 mesoporous nanoparticles with a length of 200 nm and diameter of 60 nm were successfully synthesized by reducing the spindle-like α-Fe2O3 NPs which were prepared by forced hydrolysis method. The obtained samples were characterized by transmission electron microscopy, powder X-ray diffraction, attenuated total reflection fourier transform infrared spectroscopy, field emission scanning electron microscopy, vibrating sample magnetometer, and nitrogen adsorption-desorption analysis techniques. The results show that α-Fe2O3 phase transformed into Fe3O4 phase after annealing in hydrogen atmosphere at 350°C. The as-prepared spindle-like Fe3O4 mesoporous NPs possess high Brunauer-Emmett-Teller (BET) surface area up to ca. 7.9 m2 g-1. In addition, the Fe3O4 NPs present higher saturation magnetization (85.2 emu g-1) and excellent magnetic response behaviors, which have great potential applications in magnetic separation technology.
Resonant frequency of gold/polycarbonate hybrid nano resonators fabricated on plastics via nano-transfer printing
Authors: Dechaumphai Edward , Zhang Zhao , Siwak Nathan P , Ghodssi Reza , Li Teng
Published: January 2011

We report the fabrication of gold/polycarbonate (Au/PC) hybrid nano resonators on plastic substrates through a nano-transfer printing (nTP) technique, and the parametric studies of the resonant frequency of the resulting hybrid nano resonators. nTP is a nanofabrication technique that involves an assembly process by which a printable layer can be transferred from a transfer substrate to a device substrate. In this article, we applied nTP to fabricate Au/PC hybrid nano resonators on a PC substrate. When an AC voltage is applied, the nano resonator can be mechanically excited when the AC frequency reaches the resonant frequency of the nano resonator. We then performed systematic parametric studies to identify the parameters that govern the resonant frequency of the nano resonators, using finite element method. The quantitative results for a wide range of materials and geometries offer vital guidance to design hybrid nano resonators with a tunable resonant frequency in a range of more than three orders of magnitude (e.g., 10 KHz-100 MHz). Such nano resonators could find their potential applications in nano electromechanical devices. Fabricating hybrid nano resonators via nTP further demonstrates nTP as a potential fabrication technique to enable a low-cost and scalable roll-to-roll printing process of nanodevices.
Two novel hierarchical homogeneous nanoarchitectures of TiO2 nanorods branched and P25-coated TiO2 nanotube arrays and their photocurrent performances
Authors: Hu Anzheng , Cheng Cuixia , Li Xin , Jiang Jian , Ding Ruimin , Zhu Jianhui , Wu Fei , Liu Jinping , Huang Xintang
Published: January 2011

We report here for the first time the synthesis of two novel hierarchical homogeneous nanoarchitectures of TiO2nanorods branched TiO2nanotube arrays (BTs) and P25-coated TiO2nanotube arrays (PCTs) using two-step method including electrochemical anodization and hydrothermal modification process. Then the photocurrent densities versus applied potentials of BTs, PCTs, and pure TiO2nanotube arrays (TNTAs) were investigated as well. Interestingly, at -0.11 V and under the same illumination condition, the photocurrent densities of BTs and PCTs show more than 1.5 and 1 times higher than that of pure TNTAs, respectively, which can be mainly attributed to significant improvement of the light-absorbing and charge-harvesting efficiency resulting from both larger and rougher surface areas of BTs and PCTs. Furthermore, these dramatic improvements suggest that BTs and PCTs will achieve better photoelectric conversion efficiency and become the promising candidates for applications in DSSCs, sensors, and photocatalysis.
Scalable synthesis of aligned carbon nanotubes bundles using green natural precursor: neem oil
Authors: Kumar Rajesh , Tiwari Radhey Shyam , Srivastava Onkar Nath
Published: January 2011

Practical application of aligned carbon nanotubes (ACNTs) would have to be determined by a matter of its economical and large-scale preparation. In this study, neem oil (also named Margoaa oil, extracted from the seeds of the neem--Azadirachta indica) was used as carbon source to fabricate the bundles of ACNTs. ACNTs have been synthesized by spray pyrolysis of neem oil and ferrocene mixture at 825°C. The major components of neem oil are hydrocarbon with less amount of oxygen, which provided the precursor species in spray pyrolysis growth of CNTs. The bundles of ACNTs have been grown directly inside the quartz tube. The as-grown ACNTs have been characterized through Raman spectroscopy, scanning and transmission electron microscopic (SEM/TEM) techniques. SEM images reveal that the bundles of ACNTs are densely packed and are of several microns in length. High-resolution TEM analysis reveals these nanotubes to be multi-walled CNTs. These multi-walled CNTs were found to have inner diameter between 15 and 30 nm. It was found that present technique gives high yield with high density of bundles of ACNTs.
Recombinant luciferase-expressing human cytomegalovirus (CMV) for evaluation of CMV inhibitors
Authors: He Ran , Sandford Gordon , Hayward Gary S , Burns William H , Posner Gary H , Forman Michael , Arav-Boger Ravit
Published: January 2011

Recombinant Towne CMV expressing luciferase under the control of CMV-DNA polymerase (POL) or the late pp28 (UL99) promoters were evaluated for potential application in high-throughput screening of anti-viral compounds. POL-and pp28-luciferase displayed maximal expression 48 and 72 hours post infection, respectively. The pp28-luciferase virus achieved a wider dynamic range of luciferase expression (6-7 logs) and was selected for testing of inhibition by five anti-viral compounds. Luciferase expression highly correlated with plaque reduction and real-time PCR. The pp28-luciferase reporter system is rapid, reproducible, and highly sensitive. It may be applied to screening of novel anti-CMV compounds.
High serum cortisol level is associated with increased risk of delirium after coronary artery bypass graft surgery: a prospective cohort study
Authors: Mu Dong-Liang , Wang Dong-Xin , Li Li-Huan , Shan Guo-Jin , Li Jun , Yu Qin-Jun , Shi Chun-Xia
Published: January 2011

Introduction

The pathophysiology of postoperative delirium remains poorly understood. The purpose of this study was to examine the relationship between serum cortisol level and occurrence of early postoperative delirium in patients undergoing coronary artery bypass graft (CABG) surgery.

Methods

A total of 243 patients undergoing elective CABG surgery were enrolled. Patients were examined twice daily during the first five postoperative days and postoperative delirium was diagnosed by using the Confusion Assessment Method for the Intensive Care Unit (CAM-ICU). Blood samples were obtained between 7 a.m. and 8 a.m. on the first postoperative day and serum cortisol concentrations were then measured. Multivariate logistic regression analyses were performed to identify risk factors of postoperative delirium.

Results

Postoperative delirium occurred in 50.6% (123 of 243) of patients. High serum cortisol level was significantly associated with increased risk of postoperative delirium (OR 3.091, 95% CI 1.763-5.418, P < 0.001). Other independent risk factors of postoperative delirium included increasing age (OR 1.111, 95% CI 1.065-1.159, P < 0.001), history of diabetes mellitus (OR 1.905, 95% CI 1.001-3.622, P = 0.049), prolonged duration of surgery (OR 1.360, 95% CI 1.010-1.831, P = 0.043), and occurrence of complications within the first day after surgery (OR 2.485, 95% CI 1.184-5.214, P = 0.016). Patients who developed postoperative delirium had a higher incidence of postoperative complications and a prolonged duration of postoperative ICU and hospital stay.

Conclusions

Delirium was a common complication after CABG surgery. High serum cortisol level was associated with increased risk of postoperative delirium. Patients who developed delirium had outcomes worse than those who did not.
Inflammation-induced hepcidin-25 is associated with the development of anemia in septic patients: an observational study
Authors: van Eijk Lucas T , Kroot Joyce JC , Tromp Mirjam , van der Hoeven Johannes G , Swinkels Dorine W , Pickkers Peter
Published: January 2011

Introduction

Anemia is a frequently encountered problem during inflammation. Hepcidin is an interleukin-6 (IL-6)-induced key modulator of inflammation-associated anemia. Human sepsis is a prototypical inflammatory syndrome, often complicated by the development of anemia. However, the association between inflammation, hepcidin release and anemia has not been demonstrated in this group of patients. Therefore, we explored the association between hepcidin and sepsis-associated anemia.

Methods

92 consecutive patients were enrolled after presentation on the emergency ward of a university hospital with sepsis, indicated by the presence of a proven or suspected infection and ≥ 2 extended systemic inflammatory response syndrome (SIRS) criteria. Blood was drawn at day 1, 2 and 3 after admission for the measurement of IL-6 and hepcidin-25. IL-6 levels were correlated with hepcidin concentrations. Hemoglobin levels and data of blood transfusions during 14 days after hospitalisation were retrieved and the rate of hemoglobin decrease was correlated to hepcidin levels.

Results

53 men and 39 women with a mean age of 53.3 ± 1.8 yrs were included. Hepcidin levels were highest at admission (median[IQR]): 17.9[10.1 to 28.4]nmol/l and decreased to normal levels in most patients within 3 days (9.5[3.4 to 17.9]nmol/l). Hepcidin levels increased with the number of extended SIRS criteria (P = 0.0005). Highest IL-6 levels were measured at admission (125.0[46.3 to 330.0]pg/ml) and log-transformed IL-6 levels significantly correlated with hepcidin levels at admission (r = 0.28, P = 0.015), day 2 (r = 0.51, P < 0.0001) and day 3 (r = 0.46, P < 0.0001). Twelve patients received one or more blood transfusions during the first 2 weeks of admission, not related to active bleeding. These patients had borderline significant higher hepcidin level at admission compared to non-transfused patients (26.9[17.2 to 53.9] vs 17.9[9.9 to 28.8]nmol/l, P = 0.052). IL-6 concentrations did not differ between both groups. Correlation analyses showed significant associations between hepcidin levels on day 2 and 3 and the rate of decrease in hemoglobin (Spearman's r ranging from -0.32, P = 0.03 to -0.37, P = 0.016, respectively).

Conclusions

These data suggest that hepcidin-25 may be an important modulator of anemia in septic patients with systemic inflammation.
Pivotal Advance: CD45RB glycosylation is specifically regulated during human peripheral B cell differentiation
Authors: Koethe Susanne , Zander Linda , Köster Sofia , Annan Adelaide , Ebenfelt Anders , Spencer Jo , Bemark Mats
Published: January 2011

A screen of cell surface markers differentially expressed during peripheral B cell differentiation identified that the CD45RB epitope detected by the mAb MEM-55 was highly expressed on CD27+ memory B cells and absent on CD27– naïve B cells. IgG+CD27– memory and a previously unacknowledged CD27– population in blood also expressed high levels of CD45RBMEM55. Naïve and memory B cells from tonsils followed the pattern observed in blood, and CD38high B cells had a bimodal expression pattern when analyzed using flow cytometry. No CD38high GC B cells, however, expressed the CD45RBMEM55 epitope when assayed using immunohistochemistry. Rather, CD38highCD45RBMEM55high B cells had a distinct cellular phenotype and were localized outside of GCs. CD45RB epitopes, detected by other antibody clones, were expressed at high levels through B cell differentiation, and no changes in splicing of the CD45RB exon were observed during B cell differentiation. Instead, B cells regulated their expression of the CD45RBMEM55 epitope through site-specific modifications of an O-linked glycochain. CD4+ T cells differentially spliced CD45 but did not vary the glycosylation of the CD45RBMEM55 epitope, and CD8+ cells modified CD45RBMEM55 expression in a similar manner as B cells. Monocytes expressed the CD45RB exon but not the CD45RBMEM55 epitope. As CD45 is a highly expressed tyrosine phosphatase that regulates antigen receptor signaling strength in lymphocytes, we conclude that regulated O-linked glycosylation of CD45RB can be used to follow B cell differentiation and that this regulation may be involved in fine-tuning antigen signaling in the cell.
Role of EphA4 Receptor Signaling in Thyroid Development: Regulation of Folliculogenesis and Propagation of the C-Cell Lineage
Authors: Andersson Louise , Westerlund Jessica , Liang Shawn , Carlsson Therese , Amendola Elena , Fagman Henrik , Nilsson Mikael
Published: January 2011

Transcriptome analysis revealed that the tyrosine kinase receptor EphA4 is enriched in the thyroid bud in mouse embryos. We used heterozygous EphA4-EGFP knock-in mice in which enhanced green fluorescent protein (EGFP) replaced the intracellular receptor domain (EphA4+/EGFP) to localize EphA4 protein in thyroid primordial tissues. This showed that thyroid progenitors originating in the pharyngeal floor express EphA4 at all embryonic stages and when follicles are formed in late development. Also, the ultimobranchial bodies developed from the pharyngeal pouch endoderm express EphA4, but the ultimobranchial epithelium loses the EGFP signal before it merges with the median thyroid primordium. Embryonic C cells invading the thyroid are exclusively EphA4-negative. EphA4 expression continues in the adult thyroid. EphA4 knock-out mice and EphA4-EGFP homozygous mutants are euthyroid and have a normal thyroid anatomy but display subtle histological alterations regarding number, size, and shape of follicles. Of particular interest, the pattern of follicular abnormality differs between EphA4−/− and EphA4EGFP/EGFP thyroids. In addition, the number of C cells is reduced by >50% exclusively in animals lacking EphA4 forward signaling (EphA4EGFP/EGFP). Heterozygous EphA4 mutants have no apparent thyroid phenotype. We conclude that EphA4 is a novel regulator of thyroid morphogenesis that impacts on postnatal development of the two endocrine cell lineages of the differentiating gland. In this process both EphA4 forward signaling (in the follicular epithelium) and reverse signaling mediated by its cognate ligand(s) (A- and/or B-ephrins expressed in follicular cells and C cells, respectively) are probably functionally important.
Low-Grade Hypothalamic Inflammation Leads to Defective Thermogenesis, Insulin Resistance, and Impaired Insulin Secretion
Authors: Arruda Ana Paula , Milanski Marciane , Coope Andressa , Torsoni Adriana S. , Ropelle Eduardo , Carvalho Denise P. , Carvalheira Jose B. , Velloso Licio A.
Published: January 2011

Hypothalamic inflammation is present in animal models of obesity, and the intracerebroventricular injection of TNFα can reproduce a number of features of the hypothalamus of obese animals. Because obesity is a risk factor for type 2 diabetes (DM2) we hypothesized that, by inducing hypothalamic inflammation, we could reproduce some clinical features of DM2. Lean Wistar rats and TNF receptor 1-knockout mice were employed to determine the effects of hypothalamic actions of TNFα on thermogenesis and metabolic parameters. Signal transduction and protein expression were evaluated by immunoblot and real-time PCR. Thermogenesis was evaluated in living rats, and respirometry was determined in isolated muscle fiber. In Wistar rats, hypothalamic TNFα blunts the anorexigenic effect of leptin, which is accompanied by reduced leptin signaling and increased expression of suppressor of cytokine signaling 3. In addition, hypothalamic TNFα reduces O2 consumption and the expression of thermogenic proteins in brown adipose tissue and skeletal muscle. Furthermore, hypothalamic inflammation increases base-line plasma insulin and insulin secretion by isolated pancreatic islets, which is accompanied by an impaired insulin signal transduction in liver and skeletal muscle. Hypothalamic inflammation induced by stearic acid also reduces O2 consumption and blunts peripheral insulin signal transduction. The use of intracerebroventricular infliximab restores O2 consumption in obese rats, whereas TNF receptor 1-knockout mice are protected from diet-induced reduced thermogenesis and defective insulin signal transduction. Thus, low-grade inflammation of the hypothalamus is sufficient to induce changes in a number of parameters commonly impaired in obesity and DM2, and TNFα is an important mediator of this process.
Fetal Programming of Gene Expression in Growth-Restricted Rats Depends on the Cause of Low Birth Weight
Authors: Nüsken Kai-Dietrich , Schneider Holm , Plank Christian , Trollmann Regina , Nüsken Eva , Rascher Wolfgang , Dötsch Jörg
Published: January 2011

Low birth weight and intrauterine growth restriction (IUGR) can be caused by numerous different conditions. In many experimental settings, however, these different causes are not accounted for. This study aimed at comparing the impact of two frequent causes of IUGR (low utero-placental blood flow vs. malnutrition) on fetal programming of gene expression. We studied offspring of dams treated by uterine artery ligation or sham operation compared with untreated controls and offspring of dams that were fed either a low protein or normal protein diet. After Cesarean section at term, placental and fetal hepatic expression of key “metabolic” and “vasoregulative” genes was investigated by quantitative RT-PCR. Ligation neonates showed IUGR, reduced expression of placental leptin, placental and hepatic IGF-I, hepatic inducible nitric oxide synthase, and increased expression of placental IGF binding protein 1, hepatic IGF-II receptor and erythropoietin (EPO). Low protein offspring also showed IUGR but increased expression of placental leptin; IGF-I; placental and hepatic inducible nitric oxide synthase; hepatic insulin, IGF-I, and IGF-II receptors; and reduced expression of placental IGF binding protein 1, IGF-II, leptin-receptor type A, placental and hepatic leptin receptor type B, and EPO. Expression was independent of sex, birth weight, fetal intrauterine position, and EPO expression. In conclusion, the impact of IUGR on fetal and placental gene expression depends on the cause of low birth weight. Therefore, morbidity after IUGR should be analyzed referring to its pathophysiological cause rather than referring to low birth weight itself. Fetal hypoxia as estimated by hepatic EPO expression does not seem to be a key regulator of transcriptional activity in our models.
An RNA-zipcode-independent mechanism that localizesDia1mRNA to the perinuclear ER through interactions between Dia1 nascent peptide and Rho–GTP
Authors: Liao Guoning , Ma Xinghong , Liu Gang
Published: January 2011

Signal-peptide-mediated ER localization of mRNAs encoding for membrane and secreted proteins, and RNA-zipcode-mediated intracellular targeting of mRNAs encoding for cytosolic proteins are two well-known mechanisms for mRNA localization. Here, we report a previously unidentified mechanism by which mRNA encoding for Dia1, a cytosolic protein without the signal peptide, is localized to the perinuclear ER in an RNA-zipcode-independent manner in fibroblasts. Dia1 mRNA localization is also independent of the actin and microtubule cytoskeleton but requires translation and the association of Dia1 nascent peptide with the ribosome–mRNA complex. Sequence mapping suggests that interactions of the GTPase binding domain of Dia1 peptide with active Rho are important for Dia1 mRNA localization. This mechanism can override the β-actin RNA zipcode and redirect β-actin mRNA to the perinuclear region, providing a new way to manipulate intracellular mRNA localization.
TNFα-induced noncanonical NF-κB activation is attenuated by RIP1 through stabilization of TRAF2
Authors: Kim Joo-Young , Morgan Michael , Kim Dong-Gun , Lee Ju-Yeon , Bai Lang , Lin Yong , Liu Zheng-gang , Kim You-Sun
Published: January 2011

The current paradigm of noncanonical NF-κB signaling suggests that the loss of TRAF2, TRAF3 or cIAP1 and cIAP2 leads to stabilization of NF-κB-inducing kinase (NIK) to activate the noncanonical pathway. Although a crucial role of RIP1 in the TNFα-induced canonical NF-κB pathway has been well established, its involvement in noncanonical activation of NF-κB through the TNFR1 receptor, is unknown. Here we show that TNFα is capable of activating the noncanonical NF-κB pathway, but that activation of this pathway is negatively regulated by RIP1. In the absence of RIP1, TNFR1 stimulation leads to activation of the noncanonical NF-κB pathway through TRAF2 degradation, leading to NIK stabilization, IKKα phosphorylation and the processing of p100 to generate p52. Thus although RIP1−/− mouse embryonic fibroblasts are sensitive at early time points to cell death induced by TNFα, probably as a result of lack of canonical NF-κB activation, the late activation of the noncanonical NF-κB pathway protects the remaining cells from further cell death. The TNFR1-dependent noncanonical NF-κB activation in RIP1−/− cells suggests that there is functional interplay between the two NF-κB pathways during TNFR1 signaling, which might regulate the number and kinds of NF-κB transcription factors and thus finely control NF-κB-dependent gene transcription.
Multivesicular bodies in the enigmatic amoeboflagellateBreviata anathemaand the evolution of ESCRT 0
Authors: Herman Emily K. , Walker Giselle , van der Giezen Mark , Dacks Joel B.
Published: January 2011

Endosomal sorting complexes required for transport (ESCRTs) are heteromeric protein complexes required for multivesicular body (MVB) morphogenesis. ESCRTs I, II, III and III-associated are ubiquitous in eukaryotes and presumably ancient in origin. ESCRT 0 recruits cargo to the MVB and appears to be opisthokont-specific, bringing into question aspects of the current model of ESCRT mechanism. One caveat to the restricted distribution of ESCRT 0 was the previous limited availability of amoebozoan genomes, the supergroup closest to opisthokonts. Here, we significantly expand the sampling of ESCRTs in Amoebozoa. Our electron micrographic and bioinformatics evidence confirm the presence of MVBs in the amoeboflagellate Breviata anathema. Searches of genomic databases of amoebozoans confirm the ubiquitous nature of ESCRTs I–III-associated and the restriction of ESCRT 0 to opisthokonts. Recently, an alternate ESCRT 0 complex, centering on Tom1 proteins, has been proposed. We determine the distribution of Tom1 family proteins across eukaryotes and show that the Tom1, Tom1L1 and Tom1L2 proteins are a vertebrate-specific expansion of the single Tom1 family ancestor, which has indeed been identified in at least one member of each of the major eukaryotic supergroups. This implies a more widely conserved and ancient role for the Tom1 family in endocytosis than previously suspected.
Locomotory transition from water to sand and its effects on undulatory kinematics in sand lances (Ammodytidae)
Authors: Gidmark Nicholas J. , Strother James A. , Horton Jaquan M. , Summers Adam P. , Brainerd Elizabeth L.
Published: January 2011

Sand lances, fishes in the genus Ammodytes, exhibit a peculiar burrowing behavior in which they appear to swim rapidly into the substrate. They use posteriorly propagated undulations of the body to move in both water, a Newtonian fluid, and in sand, a non-Newtonian, granular substrate. In typical aquatic limbless locomotion, undulations of the body push against water, which flows because it is incapable of supporting the static stresses exerted by the animal, thus the undulations move in world space (slipping wave locomotion). In typical terrestrial limbless locomotion, these undulations push against substrate irregularities and move relatively little in world space (non-slipping wave locomotion). We used standard and X-ray video to determine the roles of slipping wave and non-slipping wave locomotion during burrowing in sand lances. We find that sand lances in water use slipping wave locomotion, similar to most aquatic undulators, but switch to non-slipping waves once they burrow. We identify a progression of three stages in the burrowing process: first, aquatic undulations similar to typical anguilliform locomotion (but without head yaw) push the head into the sand; second, more pronounced undulations of the aquatic portion of the body push most of the animal below ground; third, the remaining above-ground portion of the body ceases undulation and the subterranean portion takes over, transitioning to non-slipping wave locomotion. We find no evidence that sand lances use their body motions to fluidize the sand. Instead, as soon as enough of the body is underground, they undergo a kinematic shift and locomote like terrestrial limbless vertebrates.
Food preferences of Knysna and purple-crested turacos fed varying concentrations of equicaloric and equimolar artificial fruit
Authors: Wilson Amy-Leigh , Downs Colleen T.
Published: January 2011

The effects that different fruit sugar types and concentrations have on food preferences of avian frugivores have been relatively poorly studied. Although it has been recently advocated that preference is based on equicaloric energy it is also important to note whether preferences change as energy content changes. Therefore, sugar preferences of equicaloric and equimolar artificial fruit of different sugar types at varying concentrations and molarities were investigated in two relatively large South African frugivores, Knysna (Tauraco corythaix) and purple-crested (Gallirex porphyreolophus) turacos. Artificial fruits containing 6.6, 12.4 or 22% sucrose or glucose, and artificial fruits containing 0.42, 0.83 or 1.66 mol l–1 sucrose or glucose, were used to determine sugar preferences. Knysna turacos preferred the sucrose to the glucose equicaloric artificial fruit diet at low concentrations whereas purple-crested turacos showed no preference for either diet. Both turacos species preferred the sucrose equimolar artificial fruit diet to the glucose at low concentrations. At high concentrations neither species showed a preference for either equicaloric or equimolar artificial fruit diets. This suggests that energy requirements influence food preferences more than sugar type and that birds will select fruit that is higher in energy irrespective of sugar type. This complements an earlier study on digestion of differing equicaloric and equimolar artificial fruit sugar types. It again emphasizes the need for future studies looking at the composition of indigenous forest fruit sugars in order to obtain insight into the role of these avian frugivores as potential seed dispersers of fruiting tree species.