bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson–Crick‐like T–HgII–T Base Pairs
Authors: Kondo Jiro , Yamada Tom , Hirose Chika , Okamoto Itaru , Tanaka Yoshiyuki , Ono Akira 
Published: January 2014

AbstractThe metallo DNA duplex containing mercury‐mediated T–T base pairs is an attractive biomacromolecular nanomaterial which can be applied to nanodevices such as ion sensors. Reported herein is the first crystal structure of a B‐form DNA duplex containing two consecutive T–HgII–T base pairs. The HgII ion occupies the center between two T residues. The N3‐HgII bond distance is 2.0 Å. The relatively short HgII‐HgII distance (3.3 Å) observed in consecutive T–HgII–T base pairs suggests that the metallophilic attraction could exist between them and may stabilize the B‐form double helix. To support this, the DNA duplex is largely distorted and adopts an unusual nonhelical conformation in the absence of HgII. The structure of the metallo DNA duplex itself and the HgII‐induced structural switching from the nonhelical form to the B‐form provide the basis for structure‐based design of metal‐conjugated nucleic acid nanomaterials.
Blending of TiO2 nanoparticles with cellulose acetate polymer: to study the effect on morphology and gas permeation of blended membranes
Authors: Farrukh Sarah , Javed Sofia , Hussain Arshad , Mujahid Muhammad 
Published: January 2014

ABSTRACTCellulose acetate–titania (CA–TiO2) nanoparticles blended membranes were fabricated using diffusion‐induced phase separation process to observe the effect of inorganic nanofillers on the surface topography and gas permeation properties of CA membrane. Self‐synthesized TiO2 nanoparticles using sol gel reflux condensation were employed as nanofillers, which is the anatase phase of TiO2 with crystallite size of 5–10 nm. The synthesized membranes were characterized using scanning electron microscopy and atomic force microscopy techniques to study the nanoscale distribution of TiO2 nanoparticles, surface roughness, and pores generation in blended membranes, with increasing nanoparticles' concentration in polymer matrix. The permeability of CO2 was found to be increased for CA–TiO2 blended membranes. The CO2/CH4 selectivity up to 23.3 was documented. © 2014 Curtin University of Technology and John Wiley & Sons, Ltd.
Preparation and characterization of bis‐[1,3,5]triazinyl diazenes and their utilization as flame retardants in polypropylene films
Authors: Tirri Teija , Aubert Melanie , Pawelec Weronika , Wilén Carl‐Eric , Pfaendner Rudolf , Hoppe Holger , Roth Michael , Sinkkonen Jari 
Published: January 2014

ABSTRACTA series of bis‐[1,3,5]triazinyl diazenes and two metal complexes thereof were synthesized and tested as new flame retardants in polypropylene films. It was observed that electron withdrawing triazinyl ring substituent (i.e., Cl and phenyl moieties) improved the thermal stability of diazene compounds, whereas electron donating groups (i.e., methoxy, dimethylamino, and ethylthio moieties) had a destabilizing effect. TGA, DTA/DSC, NMR, and ATR‐FTIR were used for the characterization. Quantum mechanical modeling (Gaussian 09) was also utilized to facilitate the interpretation of the NMR data. Bis‐(4,6‐dichloro‐[1,3,5]triazin‐2‐yl)‐diazene 1 and bis‐(4,6‐dimethoxy‐[1,3,5]triazin‐2‐yl)‐diazene 2 were found to be effective flame retardants in polypropylene films and DIN4102‐1 B2 classification was reached already at a loading of 0.5 wt %. Interestingly, the copper complex of 2 showed even higher fire retardant activity than its precursor 2, whereas the corresponding zinc complex exhibited lower flame retardant efficacy than its precursor. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 40413.
Production and isolation of chitosan from Aspergillus terreus and application in tin(II) adsorption
Authors: Cheng Li‐Chun , Wu Tzung‐Shian , Wang Jian‐Wen , Wu Szu‐Han , Chung Mei‐Hui , Kuo Yi‐Ming , Tsai Cheng‐Hsien 
Published: January 2014

ABSTRACTFed‐batch fermentation was used for biomass and fungal chitosan production by Aspergillus terreus (BCRC 32068) grown in a potato dextrose agar medium. The polysaccharides were extracted by an alkali–acid treatment, and structural investigations by X‐ray diffraction, Fourier transform infrared analysis, and viscosity and thermal analysis were done. A high level of chitosan was extracted from A. terreus; this implied that it was feasible to produce chitosan from industrial waste mycelia. Fungal chitosan derived from A. terreus showed the highest adsorption capacity for Sn(II). The order of Sn(II) adsorption capacity for these chitosanaceous materials was Fungal chitosan > Chitin > Biomass. Fungal chitosan derived from A. terreus was well correlated with Langmuir's isotherm model. The maximum capacity for Sn(II) sorption deduced from the use of the Langmuir isotherm equation was 303 mg/g; this was significantly higher than that of A. terreus. Fungal chitosan is an easy and cost‐effective material for the abatement of pollution. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 40436.
Gas permeation properties of poly(2,5‐benzimidazole) derivative membranes
Authors: Jiang Can , Jie Xingming , Kang Guodong , Liu Dandan , Cao Yiming , Yuan Quan 
Published: January 2014

ABSTRACTIn this article, three novel polymers based on poly(2,5‐benzimidazole) (ABPBI) were synthesized by introducing propyl, isobutyl or n‐butyl groups to its side chain through an alkyl substitution reaction. FTIR and 13C NMR were applied to confirm the formation of corresponding chemical groups. Their physical properties including crystallinity, thermal stability, mechanical strength, and micro‐morphology were also characterized. Their solubility in common solvents were also tested to see if the modification will bring any improvement. Gas permeation properties of three derivative membranes prepared by a casting and solvent‐evaporation method were tested with pure gases including H2, N2, O2, CH4, and CO2. It has been revealed that gas with a smaller molecular size owned a larger permeability. This means gas permeation in all prepared membranes should be diffusivity selective. Among all three modified ABPBI membranes, isobutyl substitution modified ABPBI (IBABPBI) showed the best selectivity of H2 over other gases such as N2 (∼185) and CO2 (∼6.3) with a comparable permeability (∼9.33 barrer) when tested at 35°C and 3.0 atm. Testing temperature increase facilitated gas permeation for all three membranes obviously; while in term of gas selectivity temperature increase showed diverse alteration because it brought variable impact on gas solubility of different gases. Even so, IBABPBI membrane still owned acceptable selectivity of H2 over N2 (∼118) and CO2 (∼6.3) with an almost doubled permeability (∼17.5 barrer) when tested at 75°C and 3.0 atm. Additional tests showed that running at high pressure did not bring any obvious deterioration to gas separation performance of IBABPBI membrane. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 40440.
Metagenomic insights into the human gut resistome and the forces that shape it
Authors: Forslund Kristoffer , Sunagawa Shinichi , Coelho Luis P. , Bork Peer 
Published: January 2014

We show how metagenomic analysis of the human gut antibiotic resistome, compared across large populations and against environmental or agricultural resistomes, suggests a strong anthropogenic cause behind increasing antibiotic resistance in bacteria. This area has been the subject of intense and polarized debate driven by economic and political concerns; therefore such recently available insights address an important need. We derive and compare antibiotic resistomes of human gut microbes from 832 individuals from ten different countries. We observe and describe significant differences between samples from these countries in the gut resistance potential, in line with expectations from antibiotic usage and exposure in medical and food production contexts. Our results imply roles for both of these sources in increased resistance among pathogens in recent history. In contrast, other available metadata such as age, body mass index, sex, or health status have little effect on the antibiotic resistance potential of human gut microbes.Also watch the Video Abstract.
Decoding spatial and temporal features of neuronal cAMP/PKA signaling with FRET biosensors
Authors: Castro Liliana R. V. , Guiot Elvire , Polito Marina , Paupardin‐Tritsch Daniéle , Vincent Pierre 
Published: January 2014

AbstractCyclic adenosine monophosphate (cAMP) and the cyclic‐AMP‐dependent protein kinase (PKA) regulate a plethora of cellular functions in virtually all eukaryotic cells. In neurons, the cAMP/PKA signaling cascade controls a number of biological properties such as axonal growth, pathfinding, efficacy of synaptic transmission, regulation of excitability, or long term changes. Genetically encoded optical biosensors for cAMP or PKA are considerably improving our understanding of these processes by providing a real‐time measurement in living neurons. In this review, we describe the recent progress made in the creation of biosensors for cAMP or PKA activity. These biosensors revealed profound differences in the amplitude of the cAMP signal evoked by neuromodulators between various neuronal preparations. These responses can be resolved at the level of individual neurons, also revealing differences related to the neuronal type. At the sub‐cellular level, biosensors reported different signal dynamics in domains like dendrites, cell body, nucleus, and axon. Combining this imaging approach with pharmacology or genetic models points at phosphodiesterases and phosphatases as critical regulatory proteins. Biosensor imaging will certainly emerge as a forefront tool to decipher the subtle mechanics of intracellular signaling. This will certainly help us to understand the mechanism of action of current drugs and foster the development of novel molecules for neuropsychiatric diseases.
Factors impeding enzymatic wheat gluten hydrolysis at high solid concentrations
Authors: Hardt N.A. , Janssen A.E.M. , Boom R.M. , van der Goot A.J. 
Published: January 2014

ABSTRACTEnzymatic wheat gluten hydrolysis at high solid concentrations is advantageous from an environmental and economic point of view. However, increased wheat gluten concentrations result in a concentration effect with a decreased hydrolysis rate at constant enzyme‐to‐substrate ratios and a decreased maximum attainable degree of hydrolysis (DH%). We here identified the underlying factors causing the concentration effect. Wheat gluten was hydrolyzed at solid concentrations from 4.4% to 70%. The decreased hydrolysis rate was present at all solid concentrations and at any time of the reaction. Mass transfer limitations, enzyme inhibition and water activity were shown to not cause this hydrolysis rate limitation up to 50% solids. However, the hydrolysis rate limitation can be, at least partly, explained by a second‐order enzyme inactivation process. Furthermore, mass transfer impeded the hydrolysis above 60% solids. Addition of enzyme after 24 h at high solid concentrations scarcely increased the DH%, suggesting that the maximum attainable DH% decreases at high solid concentrations. Reduced enzyme activities caused by low water activities can explain this DH% limitation. Finally, a possible influence of the plastein reaction on the DH% limitation is discussed. Biotechnol. Bioeng. 2014;111: 1304–1312. © 2014 Wiley Periodicals, Inc.
In vitro reconstitution of mevalonate pathway and targeted engineering of farnesene overproduction in Escherichia coli
Authors: Zhu Fayin , Zhong Xiaofang , Hu Mengzhu , Lu Lei , Deng Zixin , Liu Tiangang 
Published: January 2014

ABSTRACTApproaches using metabolic engineering and synthetic biology to overproduce terpenoids, such as the precursors of taxol and artemisinin, in microbial systems have achieved initial success. However, due to the lack of steady‐state kinetic information and incomplete understanding of the terpenoid biosynthetic pathway, it has been difficult to build a highly efficient, universal system. Here, we reconstituted the mevalonate pathway to produce farnesene (a precursor of new jet fuel) in vitro using purified protein components. The information from this in vitro reconstituted system guided us to rationally optimize farnesene production in E. coli by quantitatively overexpressing each component. Targeted proteomic assays and intermediate assays were used to determine the metabolic status of each mutant. Through targeted engineering, farnesene production could be increased predictably step by step, up to 1.1 g/L (∼2,000 fold) 96 h after induction at the shake‐flask scale. The strategy developed to release the potential of the mevalonate pathway for terpenoid overproduction should also work in other multistep synthetic pathways. Biotechnol. Bioeng. 2014;111: 1396–1405. © 2014 Wiley Periodicals, Inc.
Quantitative assessment of in vivo HIV protease activity using genetically engineered QD‐based FRET probes
Authors: Cella Lakshmi N. , Biswas Payal , Yates Marylynn V. , Mulchandani Ashok , Chen Wilfred 
Published: January 2014

ABSTRACTHIV protease plays a central role in its life cycle leading to release of functional viral particles. It has been successfully used as a therapeutic target to block HIV infection. Several protease inhibitors (PIs) are currently being employed as a part of anti‐HIV therapy. However, the constant genetic drift in the virus leads to accumulation of mutations in both cleavage site and the protease, resulting in resistance and failure of therapy. We reported the use of a quantum dot (QD)‐based protein probe for the in vivo monitoring of HIV‐1 protease activity based on fluorescence resonance energy transfer. In the current study, we demonstrate the utility of this approach by quantifying the in vivo cleavage rates of three known protease and cleavage site mutations in the presence or absence of different PIs. The changes in IC50 values for the different PIs were similar to that observed in patients, validating our assay as a rapid platform for PI screening. Biotechnol. Bioeng. 2014;111: 1082–1087. © 2014 Wiley Periodicals, Inc.
Effects of scaffold architecture on mechanical characteristics and osteoblast response to static and perfusion bioreactor cultures
Authors: Bartnikowski Michal , Klein Travis J. , Melchels Ferry P.W. , Woodruff Maria A. 
Published: January 2014

ABSTRACTTissue engineering focuses on the repair and regeneration of tissues through the use of biodegradable scaffold systems that structurally support regions of injury while recruiting and/or stimulating cell populations to rebuild the target tissue. Within bone tissue engineering, the effects of scaffold architecture on cellular response have not been conclusively characterized in a controlled‐density environment. We present a theoretical and practical assessment of the effects of polycaprolactone (PCL) scaffold architectural modifications on mechanical and flow characteristics as well as MC3T3‐E1 preosteoblast cellular response in an in vitro static plate and custom‐designed perfusion bioreactor model. Four scaffold architectures were contrasted, which varied in inter‐layer lay‐down angle and offset between layers, while maintaining a structural porosity of 60 ± 5%. We established that as layer angle was decreased (90° vs. 60°) and offset was introduced (0 vs. 0.5 between layers), structural stiffness, yield stress, strength, pore size, and permeability decreased, while computational fluid dynamics‐modeled wall shear stress was increased. Most significant effects were noted with layer offset. Seeding efficiencies in static culture were also dramatically increased due to offset (∼45% to ∼86%), with static culture exhibiting a much higher seeding efficiency than perfusion culture. Scaffold architecture had minimal effect on cell response in static culture. However, architecture influenced osteogenic differentiation in perfusion culture, likely by modifying the microfluidic environment. Biotechnol. Bioeng. 2014;111: 1440–1451. © 2014 Wiley Periodicals, Inc.
Electrical conditioning of adipose‐derived stem cells in a multi‐chamber culture platform
Authors: Pavesi A. , Soncini M. , Zamperone A. , Pietronave S. , Medico E. , Redaelli A. , Prat M. , Fiore G. B. 
Published: January 2014

ABSTRACTIn tissue engineering, several factors play key roles in providing adequate stimuli for cells differentiation, in particular biochemical and physical stimuli, which try to mimic the physiological microenvironments. Since electrical stimuli are important in the developing heart, we have developed an easy‐to‐use, cost‐effective cell culture platform, able to provide controlled electrical stimulation aimed at investigating the influence of the electric field in the stem cell differentiation process. This bioreactor consists of an electrical stimulator and 12 independent, petri‐like culture chambers and a 3‐D computational model was used to characterize the distribution and the intensity of the electric field generated in the cell culture volume. We explored the effects of monophasic and biphasic square wave pulse stimulation on a mouse adipose‐derived stem cell line (m17.ASC) comparing cell viability, proliferation, protein, and gene expression. Both monophasic (8 V, 2 ms, 1 Hz) and biphasic (+4 V, 1 ms and −4 V, 1 ms; 1 Hz) stimulation were compatible with cell survival and proliferation. Biphasic stimulation induced the expression of Connexin 43, which was found to localize also at the cell membrane, which is its recognized functional mediating intercellular electrical coupling. Electrically stimulated cells showed an induced transcriptional profile more closely related to that of neonatal cadiomyocytes, particularly for biphasic stimulation. The developed platform thus allowed to set‐up precise conditions to drive adult stem cells toward a myocardial phenotype solely by physical stimuli, in the absence of exogenously added expensive bioactive molecules, and can thus represent a valuable tool for translational applications for heart tissue engineering and regeneration. Biotechnol. Bioeng. 2014;111: 1452–1463. © 2014 Wiley Periodicals, Inc.
Chimeric cytochromes P450 engineered by domain swapping and random mutagenesis for producing human metabolites of drugs
Authors: Kang Ji‐Yeon , Ryu Sang Hoon , Park Sun‐Ha , Cha Gun Su , Kim Dong‐Hyun , Kim Keon‐Hee , Hong Austin W. , Ahn Taeho , Pan Jae‐Gu , Joung Young Hee , Kang Hyung‐Sik , Yun Chul‐Ho 
Published: January 2014

ABSTRACTHuman drug metabolites produced by cytochrome P450 enzymes are critical for safety testing and may themselves act as drugs or leads in the drug discovery and development process. Here, highly active chimeric fusion proteins (chimeras) were obtained by reductase domain swapping of mutants at key catalytic residues of the heme domain with that of a natural variant (CYP102A1.2) of P450 BM3 (CYP102A1.1) from Bacillus megaterium. Random mutagenesis at the heme domain of the chimera was also used to generate chimeric mutants that were more active and diverse than the chimeras themselves. To determine whether the chimeras and several mutants of the highly active chimera displayed enhanced catalytic activity and, more importantly, whether they acquired activities of biotechnological importance, we measured the oxidation activities of the chimeras and chimeric mutants toward human P450 substrates, mainly drugs. Some of the chimeric mutants showed high activity toward typical human P450 substrates including drugs. Statin leads, especially chiral products, with inhibitory effects toward HMG‐CoA reductase could be obtained from metabolites of statin drugs generated using these chimeric mutants. This study reveals the critical role of the reductase domain for the activity of P450 BM3 and shows that chimeras generated by domain swapping can be used to develop industrial enzymes for the synthesis of human metabolites from drugs and drug leads. Biotechnol. Bioeng. 2014;111: 1313–1322. © 2014 Wiley Periodicals, Inc.
The impact of elevated CO2 concentration on the quality of algal starch as a potential biofuel feedstock
Authors: Tanadul Orn‐u‐ma , VanderGheynst Jean S. , Beckles Diane M. , Powell Ann L.T. , Labavitch John M. 
Published: January 2014

ABSTRACTCultured microalgae are viewed as important producers of lipids and polysaccharides, both of which are precursor molecules for the production of biofuels. This study addressed the impact of elevated carbon dioxide (CO2) on Chlorella sorokiniana production of starch and on several properties of the starch produced. The production of C. sorokiniana biomass, lipid and starch were enhanced when cultures were supplied with 2% CO2. Starch granules from algae grown in ambient air and 2% CO2 were analyzed by transmission electron microscopy (TEM) and scanning electron microscopy (SEM). The granules from algae grown in 2% CO2 were disk‐shaped and contained mainly stromal starch; granules from cultures grown in ambient air were cup‐shaped with primarily pyrenoid starch. The granules from cells grown in 2% CO2 had a higher proportion of the accumulated starch as the highly branched, amylopectin glucan than did granules from cells grown in air. The rate of hydrolysis of starch from 2% CO2‐grown cells was 1.25 times greater than that from air‐grown cells and 2–11 times higher than the rates of hydrolysis of starches from cereal grains. These data indicate that culturing C. sorokiniana in elevated CO2 not only increases biomass yield but also improves the structure and composition of starch granules for use in biofuel generation. These modifications in culture conditions increase the hydrolysis efficiency of the starch hydrolysis, thus providing potentially important gains for biofuel production. Biotechnol. Bioeng. 2014;111: 1323–1331. © 2014 Wiley Periodicals, Inc.
Prognostic subdivision of ypT3 rectal tumours according to extension beyond the muscularis propria
Authors: Merkel S , Weber K , Schellerer V , Göhl J , Fietkau R , Agaimy A , Hohenberger W , Hermanek P 
Published: January 2014

Abstract

Background
The subdivision of T3 in rectal carcinoma according to the depth of invasion into perirectal fat has been recommended in the TNM Supplement since 1993. This study assessed the prognostic impact of this pathological staging in tumours removed after neoadjuvant chemoradiotherapy (ypT3).

Methods
Data from patients with ypT3 rectal carcinoma (less than 12 cm from the anal verge) treated with neoadjuvant chemoradiation and total mesorectal excision were analysed. Tumour category ypT3 was subdivided into ypT3a (5 mm or less) and ypT3b (more than 5 mm), based on histological measurements of maximal tumour invasion beyond the outer border of the muscularis propria.

Results
Important differences between ypT3a (81 patients) and ypT3b (43) were found in 5-year rates of locoregional recurrence (7 versus 18 per cent; P = 0·049), distant metastasis (20 versus 41 per cent; P = 0·002), disease-free survival (73 versus 47 per cent; P = 0·001), overall survival (79 versus 74 per cent; P = 0·036) and cancer-related survival (81 versus 74 per cent; P = 0·007). In Cox regression analyses, the ypT3 subclassification was identified as an independent prognostic factor for disease-free (ypT3b: hazard ratio (HR) 2·13, 95 per cent confidence interval 1·16 to 3·89; P = 0·014), observed (ypT3b: HR 2·02, 1·05 to 3·87; P = 0·035) and cancer-related (ypT3b: HR 2·46, 1·20 to 5·04; P = 0·014) survival. Extramural venous invasion was found to be an additional prognostic factor, but the pathological node category after chemoradiotherapy (ypN) did not influence survival.

Conclusion
In ypT3 rectal carcinomas, the proposed subclassification is superior to ypN in predicting prognosis.