bluuebunny/crossref_metadata_2025_split huggingface dataset:
An improved method of xylose utilization by recombinant Saccharomyces cerevisiae
Authors: Ma Tien-Yang , Lin Ting-Hsiang , Hsu Teng-Chieh , Huang Chiung-Fang , Guo Gia-Luen , Hwang Wen-Song 
Published: July 2012

Abstract
The aim of this study was to develop a method to optimize expression levels of xylose-metabolizing enzymes to improve xylose utilization capacity of Saccharomyces cerevisiae. A xylose-utilizing recombinant S. cerevisiae strain YY2KL, able to express nicotinamide adenine dinucleotide phosphate, reduced (NADPH)-dependent xylose reductase (XR), nicotinamide adenine dinucleotide (NAD+)-dependent xylitol dehydrogenase (XDH), and xylulokinase (XK), showed a low ethanol yield and sugar consumption rate. To optimize xylose utilization by YY2KL, a recombinant expression plasmid containing the XR gene was transformed and integrated into the aur1 site of YY2KL. Two recombinant expression plasmids containing an nicotinamide adenine dinucleotide phosphate (NADP+)-dependent XDH mutant and XK genes were dually transformed and integrated into the 5S ribosomal DNA (rDNA) sites of YY2KL. This procedure allowed systematic construction of an S. cerevisiae library with different ratios of genes for xylose-metabolizing enzymes, and well-grown colonies with different xylose fermentation capacities could be further selected in yeast protein extract (YPX) medium (1 % yeast extract, 2 % peptone, and 2 % xylose). We successfully isolated a recombinant strain with a superior xylose fermentation capacity and designated it as strain YY5A. The xylose consumption rate for strain YY5A was estimated to be 2.32 g/gDCW/h (g xylose/g dry cell weight/h), which was 2.34 times higher than that for the parent strain YY2KL (0.99 g/gDCW/h). The ethanol yield was also enhanced 1.83 times by this novel method. Optimal ratio and expression levels of xylose-metabolizing enzymes are important for efficient conversion of xylose to ethanol. This study provides a novel method that allows rapid and effective selection of ratio-optimized xylose-utilizing yeast strains. This method may be applicable to other multienzyme systems in yeast.
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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 &gt;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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.
Giving in early modern history: philanthropy in Amsterdam in the Golden Age
Authors: VAN LEEUWEN MARCO H. D. 
Published: July 2012

ABSTRACTPhilanthropy 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

ABSTRACTThis 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.
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.
MEDIATOR25 Acts as an Integrative Hub for the Regulation of Jasmonate-Responsive Gene Expression in Arabidopsis
Authors: Çevik Volkan , Kidd Brendan N. , Zhang Peijun , Hill Claire , Kiddle Steve , Denby Katherine J. , Holub Eric B. , Cahill David M. , Manners John M. , Schenk Peer M. , Beynon Jim , Kazan Kemal 
Published: July 2012

Abstract
The PHYTOCHROME AND FLOWERING TIME1 gene encoding the MEDIATOR25 (MED25) subunit of the eukaryotic Mediator complex is a positive regulator of jasmonate (JA)-responsive gene expression in Arabidopsis (Arabidopsis thaliana). Based on the function of the Mediator complex as a bridge between DNA-bound transcriptional activators and the RNA polymerase II complex, MED25 has been hypothesized to function in association with transcriptional regulators of the JA pathway. However, it is currently not known mechanistically how MED25 functions to regulate JA-responsive gene expression. In this study, we show that MED25 physically interacts with several key transcriptional regulators of the JA signaling pathway, including the APETALA2 (AP2)/ETHYLENE RESPONSE FACTOR (ERF) transcription factors OCTADECANOID-RESPONSIVE ARABIDOPSIS AP2/ERF59 and ERF1 as well as the master regulator MYC2. Physical interaction detected between MED25 and four group IX AP2/ERF transcription factors was shown to require the activator interaction domain of MED25 as well as the recently discovered Conserved Motif IX-1/EDLL transcription activation motif of MED25-interacting AP2/ERFs. Using transcriptional activation experiments, we also show that OCTADECANOID-RESPONSIVE ARABIDOPSIS AP2/ERF59- and ERF1-dependent activation of PLANT DEFENSIN1.2 as well as MYC2-dependent activation of VEGETATIVE STORAGE PROTEIN1 requires a functional MED25. In addition, MED25 is required for MYC2-dependent repression of pathogen defense genes. These results suggest an important role for MED25 as an integrative hub within the Mediator complex during the regulation of JA-associated gene expression.
Angiotensin‐II receptor 1 antagonist fetopathy – risk assessment, critical time period and vena cava thrombosis as a possible new feature
Authors: Oppermann Marc , Padberg Stephanie , Kayser Angela , Weber‐Schoendorfer Corinna , Schaefer Christof 
Published: July 2012

AimsAngiotensin‐II receptor 1 antagonists (AT1‐antagonists) may cause severe and even lethal fetopathy in late pregnancy. However, exposure still occurs in spite of warnings in package leaflets. This study aimed to assess the risk of fetopathy, the sensitive time window, and possible new symptoms in prospective as well as retrospective cases with AT1‐antagonist treatment during the second or third trimester of pregnancy.MethodsPatients were enrolled by the Berlin Institute for Clinical Teratology and Drug Risk Assessment in Pregnancy between 1999 and 2011 through risk consultation. Symptoms defined as indicative of AT1‐antagonist fetopathy were: oligo‐/anhydramnios, renal insufficiency, lung hypoplasia, joint contractures, skull hypoplasia and fetal/neonatal death.ResultsIn 5/29 (17%) prospectively enrolled cases with AT1‐antagonist exposure beyond the first trimester oligo‐/anhydramnios was diagnosed. Two infants showed additional symptoms of fetopathy. The risk is more than 30% if treatment continues beyond the 20th week of pregnancy. Oligo‐/anhydramnios was reversible after AT1‐antagonist withdrawal. Among 16 retrospective case reports, three infants presented with a thrombosis of the inferior vena cava in the vicinity of the renal veins. Four out of 13 live births did not survive.ConclusionsOur survey suggests that the risk increases with duration of AT1‐antagonist treatment into late pregnancy and oligo‐/anhydramnios may be reversible after AT1‐antagonist discontinuation. Thrombosis of inferior vena cava may be a new feature of AT1‐antagonist fetopathy. AT1‐antagonist medication during pregnancy constitutes a considerable risk and must be discontinued immediately. In case of indicative diagnostic findings in either the fetus or newborn, previous maternal AT1‐antagonist exposure should be considered.