bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel endophytic yeast Rhodotorula mucilaginosa strain PTD3 II: production of xylitol and ethanol in the presence of inhibitors
Authors: Vajzovic Azra , Bura Renata , Kohlmeier Kevin , Doty Sharon L
Published: July 2012

A systematic study was conducted characterizing the effect of furfural, 5-hydroxymethylfurfural (5-HMF), and acetic acid concentration on the production of xylitol and ethanol by a novel endophytic yeast, Rhodotorula mucilaginosa strain PTD3. The influence of different inhibitor concentrations on the growth and fermentation abilities of PTD3 cultivated in synthetic nutrient media containing 30 g/l xylose or glucose were measured during liquid batch cultures. Concentrations of up to 5 g/l of furfural stimulated production of xylitol to 77 % of theoretical yield (10 % higher compared to the control) by PTD3. Xylitol yields produced by this yeast were not affected in the presence of 5-HMF at concentrations of up to 3 g/l. At higher concentrations of furfural and 5-HMF, xylitol and ethanol yields were negatively affected. The higher the concentration of acetic acid present in a media, the higher the ethanol yield approaching 99 % of theoretical yield (15 % higher compared to the control) was produced by the yeast. At all concentrations of acetic acid tested, xylitol yield was lowered. PTD3 was capable of metabolizing concentrations of 5, 15, and 5 g/l of furfural, 5-HMF, and acetic acid, respectively. This yeast would be a potent candidate for the bioconversion of lignocellulosic sugars to biochemicals given that in the presence of low concentrations of inhibitors, its xylitol and ethanol yields are stimulated, and it is capable of metabolizing pretreatment degradation products.
Biological activities of an engineered tautomycetin analogue via disruption of tmcR-encoding hydroxylase in Streptomyces sp. CK4412
Authors: Kim Dongju , Nah Ji-Hye , Choi Si-Sun , Shin Hwa Sung , Sherman David H , Kim Eung-Soo
Published: July 2012

Tautomycetin (TMC), originally isolated from Streptomyces griseochromogenes, has been reported to possess biological functions including T cell-specific immunosuppressive and anticancer activities through a mechanism of differential inhibition of protein phosphatases such as PP1, PP2A, and SHP2. Independently isolated Streptomyces sp. CK4412 was also reported to produce a structurally identical TMC compound. Previously, we isolated and characterized the entire TMC biosynthetic gene cluster from Streptomyces sp. CK4412. In silico database comparison revealed a 1,359-bp tmcR as a putative bacterial Cytochrome P450 hydroxylase gene in the TMC biosynthetic gene cluster. Through targeted gene disruption and complementation, the tmcR mutant was confirmed to produce a C5-deoxy-TMC, the same analogue produced by the S. griseochromogenes ttnI mutant, implying that TmcR behaves as a regiospecific C5-oxygenase in the TMC biosynthetic pathway in Streptomyces sp. CK4412. In particular, the C5-deoxy-TMC from the tmcR mutant exhibited 3.2-fold higher inhibition activity toward SHP2 with significantly reduced inhibition activities toward PP1, and human Vero and lung cancer cells. These results suggested that C5 regiospecific modification of the TMC polyketide moiety may result in a drug development target for use in preferentially enhancing immunosuppressive activity while minimizing its undesirable biological activities.
Enzymatic transformation of the major ginsenoside Rb2 to minor compound Y and compound K by a ginsenoside-hydrolyzing β-glycosidase from Microbacterium esteraromaticum
Authors: Quan Lin-Hu , Jin Yan , Wang Chao , Min Jin-Woo , Kim Yeon-Ju , Yang Deok-Chun
Published: July 2012

The ginsenoside-hydrolyzing β-glycosidase (Bgp3) derived from Microbacterium esteraromaticum transformed the major ginsenoside Rb2 to more pharmacologically active minor ginsenosides including compounds Y and K. The bgp3 gene consists of 2,271 bp encoding 756 amino acids which have homology to the glycosyl hydrolase family 3 protein domain. Bgp3 is capable of hydrolyzing beta-glucose links and arabinose links. HPLC analysis of the time course of ginsenoside Rb2 hydrolysis by Bgp3 (0.1 mg enzyme ml−1 in 20 mM sodium phosphate buffer at 40 °C and pH 7.0) showed that the glycosidase first hydrolyzed the inner glucose moiety attached to the C-3 position and then the arabinopyranose moiety attached to the C-20 position. Thus, Bgp3 hydrolyzed the ginsenoside Rb2 via the following pathway: Rb2 → compound Y → compound K.
Towards the discovery of alcohol dehydrogenases: NAD(P)H fluorescence-based screening and characterization of the newly isolated Rhodococcus erythropolis WZ010 in the preparation of chiral aryl secondary alcohols
Authors: Yang Chi , Ying Xiangxian , Yu Meilan , Zhang Yinjun , Xiong Bin , Song Qingqing , Wang Zhao
Published: July 2012

A simple and reliable procedure was developed to screen biocatalysts with high alcohol dehydrogenase activity, efficient internal coenzyme regeneration, and high stereoselectivity. The strategy of activity screening in a microtitre plate format was based on the detection of fluorescence of NAD(P)H originating from the oxidation of alcohols. The primary and secondary screenings from soil samples yielded a versatile bacterial biocatalyst Rhodococcus erythropolis WZ010 demonstrating potential for the preparation of chiral aryl secondary alcohols. In terms of activity and stereoselectivity, the optimized reaction conditions in the stereoselective oxidation were 30 °C, pH 10.5, and 250 rpm, whereas bioreduction using glucose as co-substrate was the most favorable at 35 °C and pH 7.5 in the static reaction mixture. Under the optimized conditions, fresh cells of the strain stereoselectively oxidized the (S)-enantiomer of racemic 1-phenylethanol (120 mM) to acetophenone and afforded the unoxidized (R)-1-phenylethanol in 49.4 % yield and >99.9 % enantiomeric excess (e.e.). In the reduction of 10 mM acetophenone, the addition of 100 mM glucose significantly increased the conversion rate from 3.1 to 97.4 %. In the presence of 800 mM glucose, acetophenone and other aromatic ketones (80 mM) were enantioselectively reduced to corresponding (S)-alcohols with excellent e.e. values. Both stereoselective oxidation and asymmetric reduction required no external cofactor regeneration system.
A novel thin-layer chromatography method to screen 1,3-propanediol producers
Authors: Anand Pinki , Saxena Rajendra Kumar
Published: July 2012

To date, there is no established protocol for the screening of 1,3-propanediol producers. The proposed method has a wide applicability to harness the commercial potential of microorganisms which produce 1,3-propanediol as the end product. Glycerol fermentation broth of 50 bacteria spotted on thin-layer chromatography plates and run by appropriate solvent systems followed by colour development using vanillin reagent gave different coloured spots with most of the compounds present in the fermentation broth. The appearance of a purple-coloured spot of 1,3-propanediol with a retention factor (R  f) of 0.62 forms the basis for the selection of 1,3-propanediol producers. Apart from being a rapid detection system the proposed method is pH independent and its authenticity was reconfirmed by HPLC.
Identification of a newly isolated erythritol-producing yeast and cloning of its erythritol reductase genes
Authors: Deng Huihui , Han Ye , Liu Yuanyuan , Jia Wei , Zhou Zhijiang
Published: July 2012

A new erythritol-producing yeast (strain BH010) was isolated in this study. Analysis of the D1/D2 domain of the 26S rDNA sequence, the ITS/5.8S rDNA sequence, and the 18S rDNA sequence allowed the taxonomic position of strain BH010 to be discussed and it was identified and named Moniliella sp. BH010. Physiological characteristics were described. Scanning electron micrography clearly indicated that the cells were cylindrical to elliptical with an average size of 5 × 10 μm when growing in liquid medium, and that pseudohyphae and blastoconidia were observed when cultivated in agar plates. The erythritol reductase genes were cloned, sequenced, and analyzed. BLAST analysis and multiple sequence alignment demonstrated that erythritol reductase genes of Moniliella sp. BH010 shared very high homology with that of Trichosporonoides megachiliensis SNG-42 except for the presence of introns. The deduced amino acid sequences showed high homology to the aldo–keto reductase superfamily.
Encapsulation of Pseudomonas sp. ADP cells in electrospun microtubes for atrazine bioremediation
Authors: Klein Shiri , Avrahami Ron , Zussman Eyal , Beliavski Michael , Tarre Sheldon , Green Michal
Published: July 2012

Electrospun hollow polymeric microfibers (microtubes) were evaluated as an encapsulation method for the atrazine degrading bacterium Pseudomonas sp. ADP. Pseudomonas sp. ADP cells were successfully incorporated in a formulation containing a core solution of polyethylene oxide dissolved in water and spun with an outer shell solution made of polycaprolactone and polyethylene glycol dissolved in a chloroform and dimethylformamide. The resulting microtubes, collected as mats, were partially collapsed with a ribbon-like structure. Following encapsulation, the atrazine degradation rate was low (0.03 ± 0.01 mg atrazine/h/g fiber) indicating that the electrospinning process negatively affected cell activity. Atrazine degradation was restored to 0.5 ± 0.1 mg atrazine/h/g fiber by subjecting the microtubes to a period of growth. After 3 and 7 days growth periods, encapsulated cells were able to remove 20.6 ± 3 and 47.6 ± 5.9 mg atrazine/g mat, respectively, in successive batches under non-growth conditions (with no additional electron donor) until atrazine was detected in the medium. The loss of atrazine degrading capacity was regained following an additional cell-growth period.
Redefining XynA from Penicillium funiculosum IMI 378536 as a GH7 cellobiohydrolase
Authors: Texier Hélène , Dumon Claire , Neugnot-Roux Virginie , Maestracci Marc , O’Donohue Michael J
Published: July 2012

The secretome of Penicillium funiculosum contains two family GH7 enzymes, one of which (designated XynA) has been described as a xylanase. This is unusual because it is the only xylanase in family GH7, which is mainly composed of cellobiohydrolases and endoglucanases, and also because XynA is highly similar to the cellobiohydrolase I from Talaromyces emersonii and Trichoderma reesei (72 and 65 % identity, respectively). To probe this enigma, we investigated the biochemical properties of XynA, notably its activity on xylans and β-d-glucans. A highly pure sample of XynA was obtained and used to perform hydrolysis tests on polysaccharides. These revealed that XynA is 100-fold more active on β-1,4-glucan than on xylan. Likewise, XynA was active on both 4-nitrophenyl-β-d-lactopyranoside (pNP-β-d-Lac) and 4-nitrophenyl-β-d-cellobioside (pNP-cellobiose), which shows that XynA is principally an exo-acting type 1 cellobiohydrolase enzyme that displays 5.2-fold higher performance on pNP-cellobiose than on pNP-β-d-Lac. Finally, analyses performed using cellodextrins as substrate revealed that XynA mainly produced cellobiose (C2) from substrates containing three or more glucosyl subunits, and that C2 inhibits XynA at high concentrations (IC50  C2 = 17.7 μM). Overall, this study revealed that XynA displays typical cellobiohydrolase 1 activity and confirms that the description of this enzyme in public databases should be definitively amended. Moreover, the data provided here complete the information provided by a previous proteomics investigation and reveal that P. funiculosum secretes a complete set of cellulose-degrading enzymes.
An approximate approach for the joint problem of level of repair analysis and spare parts stocking
Authors: Basten R. J. I. , van der Heijden M. C. , Schutten J. M. J. , Kutanoglu E.
Published: July 2012

For the spare parts stocking problem, generally METRIC type methods are used in the context of capital goods. A decision is assumed on which components to discard and which to repair upon failure, and where to perform repairs. In the military world, this decision is taken explicitly using the level of repair analysis (LORA). Since the LORA does not consider the availability of the capital goods, solving the LORA and spare parts stocking problems sequentially may lead to suboptimal solutions. Therefore, we propose an iterative algorithm. We compare its performance with that of the sequential approach and a recently proposed, so-called integrated algorithm that finds optimal solutions for two-echelon, single-indenture problems. On a set of such problems, the iterative algorithm turns out to be close to optimal. On a set of multi-echelon, multi-indenture problems, the iterative approach achieves a cost reduction of 3 % on average (35 % at maximum) as compared to the sequential approach. Its costs are only 0.6 % more than those of the integrated algorithm on average (5 % at maximum). Considering that the integrated algorithm may take a long time without guaranteeing optimality, we believe that the iterative algorithm is a good approach. This result is further strengthened in a case study, which has convinced Thales Nederland to start using the principles behind our algorithm.
Looking for the impact of peer review: does count of funding acknowledgements really predict research impact?
Authors: Rigby John
Published: July 2012

A small number of studies have sought to establish that research papers with more funding acknowledgements achieve higher impact and have claimed that such a link exists because research supported by more funding bodies undergoes more peer review. In this paper, a test of this link is made using recently available data from the Web of Science, a source of bibliographic data that now includes funding acknowledgements. The analysis uses 3,596 papers from a single year, 2009, and a single journal, the Journal of Biological Chemistry. Analysis of this data using OLS regression and two ranks tests reveals the link between count of funding acknowledgements and high impact papers to be statistically significant, but weak. It is concluded that count of funding acknowledgements should not be considered a reliable indicator of research impact at this level. Relatedly, indicators based on assumptions that may hold true at one level of analysis may not be appropriate at other levels.
The link between restriction endonuclease fidelity and oligomeric state: A study with Bse634I
Authors: Zaremba Mindaugas , Sasnauskas Giedrius , Siksnys Virginijus
Published: July 2012

Type II restriction endonucleases (REases) exist in multiple oligomeric forms. The tetrameric REases have two DNA binding interfaces and must synapse two recognition sites to achieve cleavage. It was hypothesised that binding of two recognition sites by tetrameric enzymes contributes to their fidelity. Here, we experimentally determined the fidelity for Bse634I REase in different oligomeric states. Surprisingly, we find that tetramerisation does not increase REase fidelity in comparison to the dimeric variant. Instead, an inherent ability to act concertedly at two sites provides tetrameric REase with a safety‐catch to prevent host DNA cleavage if a single unmodified site becomes available.
Molecular basis for population variation: From SNPs to SAPs
Authors: Wu Jia-Rui , Zeng Rong
Published: July 2012

Single nucleotide polymorphisms (SNPs) are one type of genomic DNA variations in a population. Correspondingly, single amino‐acid polymorphisms (SAPs) derived from non‐synonymous SNPs represent protein variations in a population. Recently, using proteomic approaches, SAPs in the plasma proteomes of an Asian population were systematically identified for the first time. That study showed that heterozygous and homozygous proteins with various SAPs have different associations with particular traits in the population. Recent discoveries of widespread differences between RNA and DNA sequences indicate that RNA editing is also a source of SAPs – one that is independent of genomic SNPs. Furthermore, we argue that there are de novo SAPs that are not encoded by either DNA or RNA sequences.
Inositol polyphosphate 5‐phosphatases; new players in the regulation of cilia and ciliopathies
Authors: Conduit Sarah E. , Dyson Jennifer M. , Mitchell Christina A.
Published: July 2012

Phosphoinositides regulate numerous cellular events via the recruitment and activation of multiple lipid‐binding effector proteins. The precise temporal and spatial regulation of phosphoinositide signals by the co‐ordinated activities of phosphoinositide kinases and phosphatases is essential for homeostasis and development. Mutations in two inositol polyphosphate 5‐phosphatases, INPP5E and OCRL, cause the cerebrorenal syndromes of Joubert and Lowe's, respectively. INPP5E and OCRL exhibit overlapping phosphoinositide substrate specificity and subcellular localisation, including an association with the primary cilia. Here, we review recent studies that identify a new role for these enzymes in the regulation of primary cilia function. Joubert syndrome has been extensively linked to primary cilia defects, and Lowe's may represent a new class of ‘ciliopathy associated’ syndromes.
Giving in early modern history: philanthropy in Amsterdam in the Golden Age
Authors: VAN LEEUWEN MARCO H. D.
Published: July 2012

Philanthropy was enduring in early modern Europe. For centuries local charities gave small sums that helped many people to survive. Such charity can be studied from below, from the persepective of survival strategies, and from above, from the perspective of social control, but it can also be studied as scholars of philanthropic studies do for contemporary societies. This article does the latter. It pays attention to benefactors and benefactions; how many people gave and who were they?; when, where and what did benefactors give, and what were their motives? The article places an in-depth study of Amsterdam from the late sixteenth to the end of the eighteenth century in the context of the literature on early modern European philanthropy.
Funding and founding private charities: Leiden almshouses and their founders, 1450–1800
Authors: LOOIJESTEIJN HENK
Published: July 2012

This article presents a case study of the founders of almshouses for the elderly in the Dutch city of Leiden during the late middle ages and the early modern age. First, an overview of Leiden's almshouses is given and an assessment made of their importance for the elderly. Next, a prosopography of Leiden's almshouse founders is presented, and reasons for founding almshouses discussed, focusing on religion, status, and the support of one's nearest and dearest. This is followed by an analysis of the social class of almshouse inhabitants. This article contends that via almshouse foundations the wealthy and privileged upper classes of Dutch society looked after (distant) family members, employees and other dependants in their patronage orbit, and that almshouses thus in practice served mostly as a respectable way out of open and disgraceful poverty for members of the lower middle class and the class of wage-dependants.
Practical X-ray Spectrometry with Second-Generation Microcalorimeter Detectors
Authors: Cantor Robin , Naito Hideo
Published: July 2012

X-ray spectroscopy is a widely used and extremely sensitive analytical technique for qualitative as well as quantitative elemental analysis. Typically, high-energy-resolution X-ray spectrometers are integrated with a high-spatial-resolution scanning electron microscope (SEM) or transmission electron microscope (TEM) for X-ray microanalysis applications. The focused electron beam of the SEM or TEM excites characteristic X rays that are emitted by the sample. The integrated X-ray spectrometer can then be used to identify and quantify the elemental composition of the sample on a sub-micron length scale. This combination of energy resolution and spatial resolution makes X-ray microanalysis of great importance to the semiconductor industry.
Oestrogen-dependent regulation of miRNA biogenesis: many ways to skin the cat
Authors: Gupta Ananya , Caffrey Emer , Callagy Grace , Gupta Sanjeev
Published: July 2012

The steroid hormone oestrogen is central to normal female physiology, reproduction and behaviour, through its effects on cellular processes including cell proliferation and cell survival. The effects of oestrogen are mediated by nuclear ERs (oestrogen receptors). ER status is important for the development, progression and treatment of breast cancer. miRNAs (microRNAs) are small non-coding RNAs that bind the 3′-UTR (untranslated region) of target mRNAs to reduce their stability and/or translation. miRNAs participate in oestrogen signalling by regulating oestrogen-responsive genes and pathways. Interestingly expression and maturation of miRNAs can also be regulated by ER signalling at multiple levels. In addition to regulating the expression of miRNAs at the transcriptional level, ER appears to be able to regulate the biogenesis of miRNAs. In the present review, we summarize recent findings on miRNA biogenesis and describe various mechanisms by which oestrogen signalling can modulate the production of miRNAs.
Luminescent conjugated poly- and oligo-thiophenes: optical ligands for spectral assignment of a plethora of protein aggregates
Authors: Klingstedt Therése , Nilsson K. Peter R.
Published: July 2012

The deposition of protein aggregates in various parts of our body gives rise to several devastating diseases, and the development of probes for the selective detection of aggregated proteins is crucial to advance our understanding of the pathogenesis underlying these diseases. LCPs (luminescent conjugated polythiophenes) are fluorescent probes that bind selectively to protein aggregates. The conjugated thiophene backbone is flexible and offers a connection between the conformation and the emission properties, hence binding of LCPs gives the molecule a spectral fingerprint. The present review covers the utilization of LCPs to study the heterogeneity of protein aggregates. It emphasizes specifically the introduction of well-defined probes called LCOs (luminescent conjugated oligothiophenes) and reports how these molecules can be used for real-time in vivo imaging of cerebral plaques as well as for spectral discrimination of protein aggregates and detection of early species in the fibrillation pathway of amyloid β-peptide.
Advances in TERS (tip-enhanced Raman scattering) for biochemical applications
Authors: Treffer Regina , Böhme René , Deckert-Gaudig Tanja , Lau Katherine , Tiede Stephan , Lin Xiumei , Deckert Volker
Published: July 2012

TERS (tip-enhanced Raman scattering) provides exceptional spatial resolution without any need for labelling and has become a versatile tool for biochemical analysis. Two examples will be highlighted here. On the one hand, TERS measurements on a single mitochondrion are discussed, monitoring the oxidation state of the central iron ion of cytochrome c, leading towards a single protein characterization scheme in a natural environment. On the other hand, a novel approach of single molecule analysis is discussed, again based on TERS experiments on DNA and RNA, further highlighting the resolution capabilities of this method.
The relationship between subcortical tau pathology and Alzheimer's disease
Authors: Attems Johannes , Thal Dietmar R. , Jellinger Kurt A.
Published: July 2012

The stepwise progression of tau pathology [NFTs (neurofibrillary tangles) and NTs (neuropil threads)] in AD (Alzheimer's disease) is generally assumed to begin in the transentorhinal region (entorhinal stage) from which it progresses to the hippocampus (limbic stage) and to neocortical regions (neocortical stage). This stepwise progression is reflected in the NFT Braak stages. However, it has been shown recently that tau pathology is frequently seen in subcortical nuclei, in particular the LC (locus coeruleus) in over 90% of individuals under 30 years of age, suggesting that AD-associated tau pathology begins in the LC and not in the transentorhinal region. On the other hand, only minimal amounts of tau pathology are seen in the LC in cases with considerable entorhinal tau pathology, while the severity of tau pathology in the LC significantly increases with increasing NFT Braak stages. These findings suggest that the LC becomes increasingly involved during AD progression rather than representing the site initially affected. Further studies are warranted to answer the question of whether tau pathology in the LC of young individuals is associated with AD or whether it rather reflects non-specific neuronal damage.
Towards understanding the phosphorylation code of tau
Authors: Lippens Guy , Amniai Laziza , Wieruszeski Jean-Michel , Sillen Alain , Leroy Arnaud , Landrieu Isabelle
Published: July 2012

We describe our efforts to combine in vitro enzymatic reactions with recombinant kinases to phosphorylate the neuronal tau protein, and NMR spectroscopy to unravel the resulting phosphorylation pattern in both qualitative and quantitative manners. This approach, followed by functional assays with the same samples, gives access to the complex phosphorylation code of tau. As a result, we propose a novel hypothesis for the link between tau (hyper)phosphorylation and aggregation.
SRPK1 inhibition in vivo: modulation of VEGF splicing and potential treatment for multiple diseases
Authors: Oltean Sebastian , Gammons Melissa , Hulse Richard , Hamdollah-Zadeh Maryam , Mavrou Athina , Donaldson Lucy , Salmon Andrew H. , Harper Steve J. , Ladomery Michael R. , Bates David O.
Published: July 2012

SRPK1 (serine–arginine protein kinase 1) is a protein kinase that specifically phosphorylates proteins containing serine–arginine-rich domains. Its substrates include a family of SR proteins that are key regulators of mRNA AS (alternative splicing). VEGF (vascular endothelial growth factor), a principal angiogenesis factor contains an alternative 3′ splice site in the terminal exon that defines a family of isoforms with a different amino acid sequence at the C-terminal end, resulting in anti-angiogenic activity in the context of VEGF165-driven neovascularization. It has been shown recently in our laboratories that SRPK1 regulates the choice of this splice site through phosphorylation of the splicing factor SRSF1 (serine/arginine-rich splicing factor 1). The present review summarizes progress that has been made to understand how SRPK1 inhibition may be used to manipulate the balance of pro- and anti-angiogenic VEGF isoforms in animal models in vivo and therefore control abnormal angiogenesis and other pathophysiological processes in multiple disease states.
Mechanisms of Drosophila Dscam mutually exclusive splicing regulation
Authors: Hemani Yash , Soller Matthias
Published: July 2012

Alternative splicing of pre-mRNA is a major mechanism to increase protein diversity in higher eukaryotes. Dscam, the Drosophila homologue of human DSCAM (Down's syndrome cell adhesion molecule), generates up to 38016 isoforms through mutually exclusive splicing in four variable exon clusters. This enormous molecular diversity is functionally important for wiring of the nervous system and phagocytosis of invading pathogens. Current models explaining this complex splicing regulation include a default repressed state of the variable exon clusters to prevent the splicing together of adjacent exons, the presence of RNA secondary structures important for the release of one specific variable exon from the repressed state and combinatorial interaction of RNA-binding proteins for choosing a specific exon.
Comparison of the yeast and human nuclear exosome complexes
Authors: Sloan Katherine E. , Schneider Claudia , Watkins Nicholas J.
Published: July 2012

Most RNAs in eukaryotic cells are produced as precursors that undergo processing at the 3′ and/or 5′ end to generate the mature transcript. In addition, many transcripts are degraded not only as part of normal recycling, but also when recognized as aberrant by the RNA surveillance machinery. The exosome, a conserved multiprotein complex containing two nucleases, is involved in both the 3′ processing and the turnover of many RNAs in the cell. A series of factors, including the TRAMP (Trf4–Air2–Mtr4 polyadenylation) complex, Mpp6 and Rrp47, help to define the targets to be processed and/or degraded and assist in exosome function. The majority of the data on the exosome and RNA maturation/decay have been derived from work performed in the yeast Saccharomyces cerevisiae. In the present paper, we provide an overview of the exosome and its role in RNA processing/degradation and discuss important new insights into exosome composition and function in human cells.
BRCA1 exon 11 alternative splicing, multiple functions and the association with cancer
Authors: Tammaro Claudia , Raponi Michela , Wilson David I. , Baralle Diana
Published: July 2012

BRCA1 (breast cancer early-onset 1) alternative splicing levels are regulated in a cell-cycle- and cell-type-specific manner, with splice variants being present in different proportions in tumour cell lines as well as in normal mammary epithelial cells. The importance of this difference in the pathogenesis of breast cancer has yet to be determined. Developing an understanding of the impact of BRCA1 isoform ratio changes on cell phenotype will be of value in breast cancer and may offer therapeutic options. In the present paper, we describe the splicing isoforms of BRCA1 exon 11, their possible role in cancer biology and the importance of maintaining a balanced ratio.
High-resolution time-resolved extreme ultraviolet spectroscopy on NSTX
Authors: Lepson J. K. , Beiersdorfer P. , Clementson J. , Bitter M. , Hill K. W. , Kaita R. , Skinner C. H. , Roquemore A. L. , Zimmer G.
Published: July 2012

We report on upgrades to the flat-field grazing-incidence grating spectrometers X-ray and Extreme Ultraviolet Spectrometer (XEUS) and Long-Wavelength Extreme Ultraviolet Spectrometer (LoWEUS), at the National Spherical Torus Experiment (NSTX) at the Princeton Plasma Physics Laboratory. XEUS employs a variable space grating with an average spacing of 2400 lines/mm and covers the 9–64 Å wavelength band, while LoWEUS has an average spacing of 1200 lines/mm and is positioned to monitor the 90–270 Å wavelength band. Both spectrometers have been upgraded with new cameras that achieve 12.5 ms time resolution. We demonstrate the new time resolution capability by showing the time evolution of iron in the NSTX plasma.
Divertor electron temperature and impurity diffusion measurements with a spectrally resolved imaging radiometer
Authors: Clayton D. J. , Jaworski M. A. , Kumar D. , Stutman D. , Finkenthal M. , Tritz K.
Published: July 2012

A divertor imaging radiometer (DIR) diagnostic is being studied to measure spatially and spectrally resolved radiated power Prad(λ) in the tokamak divertor. A dual transmission grating design, with extreme ultraviolet (∼20–200 Å) and vacuum ultraviolet (∼200–2000 Å) gratings placed side-by-side, can produce coarse spectral resolution over a broad wavelength range covering emission from impurities over a wide temperature range. The DIR can thus be used to evaluate the separate Prad contributions from different ion species and charge states. Additionally, synthetic spectra from divertor simulations can be fit to Prad(λ) measurements, providing a powerful code validation tool that can also be used to estimate electron divertor temperature and impurity transport.
Effect of a polynomial arbitrary dust size distribution on dust acoustic solitons
Authors: Ishak-Boushaki M. , Djellout D. , Annou R.
Published: July 2012

The investigation of dust-acoustic solitons when dust grains are size-distributed and ions adiabatically heated is conducted. The influence of an arbitrary dust size-distribution described by a polynomial function on the properties of dust acoustic waves is investigated. An energy-like integral equation involving Sagdeev potential is derived. The solitary solutions are shown to undergo a transformation into cnoidal ones under some physical conditions. The dust size-distribution can significantly affect both lower and upper critical Mach numbers for both solitons and cnoidal solutions.
Analytical examples of reversal current, zero core current, and surface current, toroidal magnetostatic equilibria with nested flux surfaces
Authors: Aly J.-J.
Published: July 2012

We present exact analytical examples of three types of axisymmetric toroidal magnetostatic equilibria with nested flux surfaces: (1) current reversal equilibria, for which the net toroidal current switches from a negative to a positive value when moving away from the magnetic axis; these equilibria have a non-monotonic pressure profile, in accordance with Hammett et al.’s theorem stating that the pressure on the current reversal surface has to exceed the volume-averaged pressure within that surface; (2) zero core current equilibria, in which the toroidal current density vanishes inside some flux surface; and (3) surface current equilibria, constituted of an arbitrary number of nested layers inside which the plasma pressure is constant and the magnetic field force-free, with two adjacent layers being separated by a current sheet. All these configurations are obtained by shaping in an adequate way the arbitrary function which intervenes in the class of generalized isodynamic equilibria first constructed by Palumbo and recovered later on by Bishop and Taylor. A derivation of these equilibria by a method slightly different from Palumbo’s is given in an Appendix.
Magnetic particle imaging with a cantilever detector
Authors: Alldredge Jacob W. , Moreland John
Published: July 2012

We present a novel imaging method for measuring the position and magnetic moment of single micrometer scale particles. Our technique is based on magnetic force microscopy (MFM) with a magnetically hard magnetic tip in a uniform opposing field. By translating the MFM probe tip laterally and vertically, the local magnetic field at a particle can be precisely controlled. Our technique is similar to magnetic particle imaging, where the harmonic response of a particle to an AC field is measured; the difference is that here, the response is measured with a cantilever instead of a detector coil. We are able to precisely determine individual particle positions to within +/−0.022 μm in a composite sample. In addition, by fitting the force derivative images taken at different distances above the sample and at different applied magnetic fields, we can determine the m-H characteristics of individual particles.
The role of boundaries in the magnetorotational instability
Authors: Gissinger Christophe , Goodman Jeremy , Ji Hantao
Published: July 2012

In this paper, we investigate numerically the flow of an electrically conducting fluid in a cylindrical Taylor-Couette flow when an axial magnetic field is applied. To minimize Ekman recirculation due to vertical no-slip boundaries, two independently rotating rings are used at the vertical endcaps. This configuration reproduces setup used in laboratory experiments aiming to observe the magnetorotational instability (MRI). Our 3D global simulations show that the nature of the bifurcation, the non-linear saturation, and the structure of axisymmetric MRI modes are significantly affected by the presence of boundaries. In addition, large scale non-axisymmetric modes are obtained when the applied field is sufficiently strong. We show that these modes are related to Kelvin-Helmholtz destabilization of a free Shercliff shear layer created by the combined action of the applied field and the rotating rings at the endcaps. Finally, we compare our numerical simulations to recent experimental results obtained in the Princeton MRI experiment.
Correlation of quantum efficiency and photoluminescence lifetime of ZnO tetrapods grown at different temperatures
Authors: Tam M. C. , Ng A. M. C. , Djurišić A. B. , Wong K. S.
Published: July 2012

Absolute external quantum efficiencies (ηs) and photoluminescence (PL) decay lifetimes of ZnO tetrapods grown at different temperatures were measured. All the tetrapods had an UV peak at about 390 nm and a very weak defect emission. Measurements showed that the tetrapods have ηs of 2%-4% at room temperature. The sample, grown at optimal temperature, exhibited the largest absolute η of 4.3% and longest PL decay lifetimes among all the samples. These results showed that precise control of growth temperature plays an important role in making high quality ZnO tetrapods. In time-resolved measurement, the PL decay time constant (τ) versus temperature is well fitted by the theoretical prediction τ=a T32. This increase in PL lifetime with increasing temperature shows that the excited state relaxation is dominated by radiative recombination.
Comparison of arsenide and phosphide based graded buffer layers used in inverted metamorphic solar cells
Authors: Zakaria A. , King Richard R. , Jackson M. , Goorsky M. S.
Published: July 2012

The effect of graded buffer layer (GBL) composition on inverted metamorphic 1.1-eV In0.24Ga0.76As single-junction solar cells, with applications as a subcell in high-efficiency multijunction solar cells, is investigated. In experiment A, AlxInyGa(1−x−y)As was used as a GBL to transition from the GaAs substrate lattice constant to that of the In0.24Ga0.76As cell. In experiment B, In1−xGaxP was employed. Both GBLs were deposited using growth conditions optimized for lattice-matched growth. Reciprocal space maps showed that the InGaAs cell was fully relaxed in both experiments. They also revealed that the AlInGaAs GBL relaxed very quickly after the start of growth (<0.1 μm). The InGaP GBL on the other hand remained partially strained throughout its structure and full relaxation was only achieved after growth of the InGaAs cell. Atomic force microscopy of the surface of the AlInGaAs GBL showed typical cross-hatch morphology with a roughness of 8.9 nm. The surface of the InGaP GBL was much rougher at 18.3 nm with unusual morphology, likely due to 3D island formation due to unrelieved strain. These findings were confirmed by transmission electron microscopy where the InGaAs cell of experiment A was largely free of imperfections with a defect density of 1.1 × 106 cm−2. Experiment B had defects readily seen throughout the GBL and the InGaAs cell above had a defect density of 1.5 × 109 cm−2. The hardness of the AlInGaAs GBL surface was measured to be 7.2 GPa and exhibited an indentation size effect. The hardness of the InGaP GBL surface was 10.2 GPa regardless of the depth of penetration of the indenter. The lack of indentation size effect in InGaP is due to the high density of dislocations already present in the material due to unrelieved strain. Solar cells fabricated from experiment A wafers exhibited excellent band gap-voltage offset Woc = (Eg/q) − Voc of 0.414 V. Cells from experiment B exhibited a poor Woc of 0.686 V, most likely due to the threading dislocations acting as non-radiative recombination centers.
Revealing the sub-structures of the magnetic reconnection separatrix via particle-in-cell simulation
Authors: Zhou M. , Deng X. H. , Pang Y. , Huang S. Y. , Yuan Z. G. , Li H. M. , Xu X. J. , Wang Y. H. , Yao M. , Wang D. D.
Published: July 2012

Magnetic separatrix is an important boundary layer separating the inflow and outflow regions in magnetic reconnection. In this article, we investigate the sub-structures of the separatrix region by using two-and-half dimensional electromagnetic particle-in-cell simulation. The separatrix region can be divided into two sub-regions in terms of the ion and electron frozen-in conditions. Far from the neutral sheet, ions and electrons are magnetized in magnetic fields. Approaching the neutral sheet, ion frozen-in condition is broken in a narrow region (∼c/ωpi) at the edge of a density cavity, while electrons are frozen-in to magnetic fields. In this region, electric field Ez is around zero, and the convective term –(vi × B) is balanced by the Hall term in the generalized Ohm’s law because ions carry the perpendicular current. Inside the density cavity, both ion and electron frozen-in conditions are broken. The region consists of two sub-ion or electron-scale layers, which contain intense electric fields. Formation of the two sub-layers is due to the complex electron flow pattern around the separatrix region. In the layer, Ez is balanced by a combination of Hall term and the divergence of electron pressure tensor, with the Hall term being dominant. Our preliminary simulation result shows that the separatrix region in guide field reconnection also contains two sub-regions: the inner region and the outer region. However, the inner region contains only one current layer in contrast with the case without guide field.
Time-dependent 2-D modeling of edge plasma transport with high intermittency due to blobs
Authors: Pigarov A. Yu. , Krasheninnikov S. I. , Rognlien T. D.
Published: July 2012

The results on time-dependent 2-D fluid modeling of edge plasmas with non-diffusive intermittent transport across the magnetic field (termed cross-field) based on the novel macro-blob approach are presented. The capability of this approach to simulate the long temporal evolution (∼0.1 s) of the background plasma and simultaneously the fast spatiotemporal dynamics of blobs (∼10−4 s) is demonstrated. An analysis of a periodic sequence of many macro-blobs (PSMB) is given showing that the resulting plasma attains a dynamic equilibrium. Plasma properties in the dynamic equilibrium are discussed. In PSMB modeling, the effect of macro-blob generation frequency on edge plasma parameters is studied. Comparison between PSMB modeling and experimental profile data is given. The calculations are performed for the same plasma discharge using two different models for anomalous cross-field transport: time-average convection and PSMB. Parametric analysis of edge plasma variation with transport coefficients in these models is presented. The capability of the models to accurately simulate enhanced transport due to blobs is compared. Impurity dynamics in edge plasma with macro-blobs is also studied showing strong impact of macro-blob on profiles of impurity charge states caused by enhanced outward transport of high-charge states and simultaneous inward transport of low-charge states towards the core. Macro-blobs cause enhancement of sputtering rates, increase radiation and impurity concentration in plasma, and change erosion/deposition patterns.
Raman spectra of bilayer graphene covered with Poly(methyl methacrylate) thin film
Authors: Xia Minggang , Su Zhidan , Zhang Shengli
Published: July 2012

The Raman spectra of bilayer graphene covered with poly(methyl methacrylate) (PMMA) were investigated. Both the G and 2D peaks of PMMA-coated graphene were stiff and broad compared with those of uncovered graphene. This could be attributed to the residual strain induced by high-temperature baking during fabrication of the nanodevice. Furthermore, the two 2D peaks stiffened and broadened with increasing laser power, which is just the reverse to uncovered graphene. The stiffness is likely caused by graphene compression induced by the circular bubble of the thin PMMA film generated by laser irradiation. Our findings may contribute to the application of PMMA in the strain engineering of graphene nanodevices.
Sharp transition from ripple patterns to a flat surface for ion beam erosion of Si with simultaneous co-deposition of iron
Authors: Zhang K. , Brötzmann M. , Hofsäss H.
Published: July 2012

We investigate pattern formation on Si by sputter erosion under simultaneous co-deposition of Fe atoms, both at off-normal incidence, as function of the Fe surface coverage. The patterns obtained for 5 keV Xe ion irradiation at 30° incidence angle are analyzed with atomic force microscopy. Rutherford backscattering spectroscopy of the local steady state Fe content of the Fe-Si surface layer allows a quantitative correlation between pattern type and Fe coverage. With increasing Fe coverage the patterns change, starting from a flat surface at low coverage (< 2×1015 Fe/cm2) over dot patterns (2-8×1015 Fe/cm2), ripples patterns (8-17×1015 Fe/cm2), pill bug structures (1.8×1016 Fe/cm2) and a rather flat surface with randomly distributed weak pits at high Fe coverage (>1.8×1016 Fe/cm2). Our results confirm the observations by Macko et al. for 2 keV Kr ion irradiation of Si with Fe co-deposition. In particular, we also find a sharp transition from pronounced ripple patterns with large amplitude (rms roughness ∼ 18 nm) to a rather flat surface (rms roughness ∼ 0.5 nm). Within this transition regime, we also observe the formation of pill bug structures, i.e. individual small hillocks with a rippled structure on an otherwise rather flat surface. The transition occurs within a very narrow regime of the steady state Fe surface coverage between 1.7 and 1.8×1016 Fe/cm2, where the composition of the mixed Fe-Si surface layer of about 10 nm thickness reaches the stoichiometry of FeSi2. Phase separation towards amorphous iron silicide is assumed as the major contribution for the pattern formation at lower Fe coverage and the sharp transition from ripple patterns to a flat surface.
The effect of context on performance of an acute medical unit: experience from an Australian tertiary hospital
Authors: Suthers Belinda , Pickles Robert , Boyle Michael , Nair Kichu , Cook Justyn , Attia John
Published: July 2012

Objective.
To ascertain the improvements in length of stay and discharge rates following the opening of an acute medical unit (AMU).

Methods.
Retrospective cohort study of all patients admitted under general medicine from June–November 2008. Main outcome measures were length of stay in hospital and in the emergency department (ED).

Results.
The length of time spent in the emergency department for those admitted to the AMU was significantly shorter than those admitted directly to a medical ward (6.83 h v. 9.40 h, P < 0.0001). A trend towards shorter hospital length of stay continued after the AMU opened compared with the same period in the previous year (5.15 days (2.49, 11.57 CI) v. 5.66 days (2.76, 11.52 CI)). However, the number of ward transfers for a patient and the need to wait for a nursing home bed or public rehabilitation affected length of stay much more than the AMU.

Conclusion.
An AMU was successful in decreasing ED length of stay and contributed to decreasing hospital length of stay. However, we suggest that local context is crucially important in tailoring an AMU to obtain maximal benefit, and that AMUs are not a ‘one size fits all’ solution.

What is known about the topic?
Acute Medical Units were pioneered in the UK and have been shown to decrease length of stay with no increase in adverse events. As a result, they have been enthusiastically adopted in Australia. However, most studies have been single point ‘before/after’ designs looking at all medical patients, and there has been little consideration of the context in which AMUs operate and how this might affect their performance.

What does this paper add?
We consider length of stay trends over many years and separate single organ disease from multi-system disease patients, in order to ensure that gains are not simply a result of selective entry of healthier patients into AMUs. We also show that the effect of an AMU is small compared with other systemic issues, such as waiting for nursing home placement and the number of transfers of care.

What are the implications for practitioners?
Although there may be gains in terms of length of stay in the emergency department, those considering the establishment of an AMU need to consider other factors that may mitigate the improvements in hospital length of stay, such as the roadblocks to discharge, the organisation of allied health staff, and the number of transfers of care.
Mechanistic insights into the regulation of metabolic enzymes by acetylation
Authors: Xiong Yue , Guan Kun-Liang
Published: July 2012

The activity of metabolic enzymes is controlled by three principle levels: the amount of enzyme, the catalytic activity, and the accessibility of substrates. Reversible lysine acetylation is emerging as a major regulatory mechanism in metabolism that is involved in all three levels of controlling metabolic enzymes and is altered frequently in human diseases. Acetylation rivals other common posttranslational modifications in cell regulation not only in the number of substrates it modifies, but also the variety of regulatory mechanisms it facilitates.