bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stepping stones in DNA sequencing
Authors: Stranneheim Henrik , Lundeberg Joakim 
Published: August 2012

AbstractIn recent years there have been tremendous advances in our ability to rapidly and cost‐effectively sequence DNA. This has revolutionized the fields of genetics and biology, leading to a deeper understanding of the molecular events in life processes. The rapid technological advances have enormously expanded sequencing opportunities and applications, but also imposed strains and challenges on steps prior to sequencing and in the downstream process of handling and analysis of these massive amounts of sequence data. Traditionally, sequencing has been limited to small DNA fragments of approximately one thousand bases (derived from the organism's genome) due to issues in maintaining a high sequence quality and accuracy for longer read lengths. Although many technological breakthroughs have been made, currently the commercially available massively parallel sequencing methods have not been able to resolve this issue. However, recent announcements in nanopore sequencing hold the promise of removing this read‐length limitation, enabling sequencing of larger intact DNA fragments. The ability to sequence longer intact DNA with high accuracy is a major stepping stone towards greatly simplifying the downstream analysis and increasing the power of sequencing compared to today. This review covers some of the technical advances in sequencing that have opened up new frontiers in genomics.
HDAC8 substrates: Histones and beyond
Authors: Wolfson Noah A. , Pitcairn Carol Ann , Fierke Carol A. 
Published: August 2012

AbstractThe lysine deacetylase family of enzymes (HDACs) was first demonstrated to catalyze deacetylation of acetyllysine residues on histones. In subsequent years, HDACs have been shown to recognize a large pool of acetylated nonhistone proteins as substrates. Recently, thousands of acetylated proteins have been discovered, yet in most cases, the HDAC that catalyzes deacetylation in vivo has not been identified. This gap has created the need for better in vivo, in vitro, and in silico approaches for determining HDAC substrates. While HDAC8 is the best kinetically and structurally characterized HDAC, few efficient substrates have yet been substantiated in vivo. In this review, we delineate factors that may be important for determining HDAC8 substrate recognition and catalytic activity, including structure, complex formation, and post‐translational modifications. This summary provides insight into the challenges of identifying in vivo substrates for HDAC8, and provides a good vantage point for understanding the variables important for predicting HDAC substrate recognition. © 2012 Wiley Periodicals, Inc. Biopolymers 99: 112–126, 2013.
Effect of detergents on the thermal behavior of elastin‐like polypeptides
Authors: Thapa Arjun , Han Wei , Simons Robin H. , Chilkoti Ashutosh , Chi Eva Y. , López Gabriel P. 
Published: August 2012

AbstractElastin‐like polypeptide (ELP) fusions have been designed to allow large‐scale, nonchromatographic purification of many soluble proteins by using the inverse transition cycling (ITC) method; however, the sensitivity of the aqueous lower critical solubility phase transition temperature (Tt) of ELPs to the addition of cosolutes, including detergents, may be a potential hindrance in purification of proteins with surface hydrophobicity in such a manner. To identify detergents that are known to solubilize such proteins (e.g., membrane proteins) and that have little effect on the Tt of the ELP, we screened a number of detergents with respect to their effects on the Tt and secondary structures of a model ELP (denoted here as ELP180). We found that mild detergents (e.g., n‐dodecyl‐β‐D‐maltoside, Triton‐X100, and 3‐[(3‐cholamidopropyl) dimethylamino]‐1‐propanesulfonate) do not alter the phase transition behavior or structure (as probed by circular dichroism) of ELP180. This result is in contrast to previous studies that showed a strong effect of other detergents (e.g., sodium dodecylsulfate) on the Tt of ELPs. Our results clearly indicate that mild detergents do not preclude ITC‐based separation of ELPs, and thus that ELP fusions may prove to be useful in the purification of detergent‐solubilized recombinant hydrophobic proteins, including membrane proteins, which are otherwise notoriously difficult to extract and purify by conventional separation methods (e.g., chromatography). © 2012 Wiley Periodicals, Inc.
Structural and dynamical properties of KTS‐disintegrins: A comparison between Obtustatin and Lebestatin
Authors: Daidone Isabella , Aschi Massimiliano , Patamia Maria , Bozzi Argante , Petruzzelli Raffaele 
Published: August 2012

AbstractObtustatin and Lebestatin are lysine‐threonine‐serine (KTS)‐disintegrins, which are a family of low molecular weight polypeptides present in many viperidae venoms and are potent and specific inhibitors of collagen‐binding integrins. The integrin binding loop, harboring the 21KTS23 motif, and the C‐terminal tail are known to be responsible for the selective binding to the α1β1 integrin. Despite a very high sequence homology (only two mutations are present in Lebestatin relative to Obtustatin, namely R24L and S38L), Lebestatin exhibits a higher inhibitory effect than Obtustatin on cell adhesion and cell migration to collagens I and IV. Here we show, by means of molecular dynamics simulations of the two polypeptides in aqueous solution, that Lebestatin possesses a higher flexibility of the C‐terminal tail and a greater solvent accessibility of the integrin binding loop than Obtustatin. It may be hypothesized that these properties may contribute to the higher binding‐affinity of Lebestatin to its biological partner. © 2012 Wiley Periodicals, Inc.
Enzymatic Glycosylation of Small Molecules: Challenging Substrates Require Tailored Catalysts
Authors: Desmet Tom , Soetaert Wim , Bojarová Pavla , Křen Vladimir , Dijkhuizen Lubbert , Eastwick‐Field Vanessa , Schiller Alexander 
Published: August 2012

AbstractGlycosylation can significantly improve the physicochemical and biological properties of small molecules like vitamins, antibiotics, flavors, and fragrances. The chemical synthesis of glycosides is, however, far from trivial and involves multistep routes that generate lots of waste. In this review, biocatalytic alternatives are presented that offer both stricter specificities and higher yields. The advantages and disadvantages of different enzyme classes are discussed and illustrated with a number of recent examples. Progress in the field of enzyme engineering and screening are expected to result in new applications of biocatalytic glycosylation reactions in various industrial sectors.
Absolute Configuration and Enantiodifferentiation of a Hemicryptophane Incorporating an Azaphosphatrane Moiety
Authors: Payet Elina , Dimitrov‐Raytchev Pascal , Chatelet Bastien , Guy Laure , Grass Stephane , Lacour Jerome , Dutasta Jean‐Pierre , Martinez Alexandre 
Published: August 2012

ABSTRACTThe hemicryptophane racemate (±)‐M-1, P-1 was optically resolved by semipreparative HPLC on Chiralpak IC column. The absolute configuration of each isolated enantiomer was established from the analysis of their electronic circular dichroism spectra. Enantiodifferentiation of the chiral cationic cage (±)‐M-1, P-1 was evidenced in solution using Δ‐TRISPHAT as chiral solvating agent, and the diastereomeric associations were observed in 1H and 31P NMR spectra. Chirality 24:1077–1081, 2012. © 2012 Wiley Periodicals, Inc.
Mass transfer around prolate spheroidal drops in an extensional flow
Authors: Favelukis Moshe , Lavrenteva Olga M. 
Published: August 2012

AbstractMass transfer in the continuous phase around a small eccentricity prolate spheroidal drop in an axisymmetric extensional creeping flow and at large Peclet numbers was investigated theoretically. The results show that, at very short times, the total quantity of solute transferred to or from the drop represents, at O(Ca1), mass transfer by diffusion only around a sphere. For long times, or at steady‐state, the total quantity of solute transferred is, at O(Ca1), slightly smaller than that of a spherical drop, and it decreases with an increase of the capillary number or the viscosity ratio. © 2012 Canadian Society for Chemical Engineering
Imputation for statistical inference with coarse data
Authors: Kim Jae Kwang , Hong Minki 
Published: August 2012

AbstractCoarse data is a general type of incomplete data that includes grouped data, censored data, and missing data. The likelihood‐based estimation approach with coarse data is challenging because the likelihood function is in integral form. The Monte Carlo EM algorithm of Wei & Tanner [Wei & Tanner (1990).Journal of the American Statistical Association, 85, 699–704] is adapted to compute the maximum likelihood estimator in the presence of coarse data. Stochastic coarse data is also covered and the computation can be implemented using the parametric fractional imputation method proposed by Kim [Kim (2011).Biometrika, 98, 119–132]. Results from a limited simulation study are presented. The proposed method is also applied to the Korean Longitudinal Study of Aging (KLoSA).The Canadian Journal of Statistics40: 604–618; 2012 © 2012 Statistical Society of Canada
Potential Retention and Release Capacity of Phosphorus in the Newly Formed Wetland Soils from the Yellow River Delta, China
Authors: Sun Junna , Xu Gang , Shao Hongbo , Xu Shaohui 
Published: August 2012

AbstractThere are few researches on the characteristics of phosphorus (P) in the newly born wetland soils from Yellow River Delta of China. Meanwhile, whether the wetland soils can protect the aquatic ecosystem from excessive P input or not and the risk of P release from the soils to the water quality have generated considerable interests. Through isothermal batch static equilibrium sorption experiments followed by six subsequent extraction steps, the present study assessed the variations in P sorption and desorption properties of the newly born wetland soils in Yellow River Delta. It is found that the P sorption isotherms were nonlinear and the amount of P sorption reached a steady state as P initial concentration added increased in the studied soils. Though the capacity of P retention differed strongly among the studied zone, the soils can protect the aquatic ecosystem from excessive P input to a certain extent degree. From the desorption experiments, it is found that the newly sorbed P was easily desorbed in higher initial added concentration and the desorption P significantly decreased with successive extraction in all samples. The release of P from soil proposed a significant contribution to the water quality and eutrophication of coastal zone. Correlation and regression analyses showed that the amorphous and free Fe/Al oxides, correlated with clay content in the studied soils, were the crucial chemical factors ascribed to the soil P retention and release capacity.
Expression of kisspeptins in the brain and pituitary of the european sea bass (Dicentrarchus labrax)
Authors: Escobar Sebastián , Felip Alicia , Gueguen Marie‐Madeleine , Zanuy Silvia , Carrillo Manuel , Kah Olivier , Servili Arianna 
Published: August 2012

AbstractKisspeptins are now considered key players in the neuroendocrine control of puberty and reproduction, at least in mammals. Most teleosts have two kiss genes, kiss1 and kiss2, but their sites of expression are still poorly documented. As a first step in investigating the role of kisspeptins in the European sea bass, a perciform fish, we studied the distribution of kiss1 and kiss2‐expressing cells in the brain of males and females undergoing their first sexual maturation. Animals were examined at early and late in the reproductive season. We also examined the putative expression of estrogen receptors in kiss‐expressing cells and, finally, we investigated whether kisspeptins are expressed in the pituitary gland. We show that kiss1‐expressing cells were consistently detected in the habenula and, in mature males and females, in the rostral mediobasal hypothalamus. In both sexes, kiss2‐expressing cells were consistently detected at the level of the preoptic area, but the main kiss2 mRNA‐positive population was observed in the dorsal hypothalamus, above and under the lateral recess. No obvious sexual differences in kiss1 and kiss2 mRNA expression were detected. Additional studies based on confocal imaging clearly showed that most kiss1 mRNA‐containing cells of the mediobasal hypothalamus strongly express ERα and slightly express ERβ2. At the pituitary level, both sexes exhibited kiss1 mRNA expression in most FSHβ‐positive cells and never in LHβ‐positive cells. J. Comp. Neurol. 521:933–948, 2013. © 2012 Wiley Periodicals, Inc.
Stat3 defines three populations of müller glia and is required for initiating maximal müller glia proliferation in the regenerating zebrafish retina
Authors: Nelson Craig M. , Gorsuch Ryne A. , Bailey Travis J. , Ackerman Kristin M. , Kassen Sean C. , Hyde David R. 
Published: August 2012

AbstractWe analyzed the role of Stat3, Ascl1a, and Lin28a in Müller glia reentry into the cell cycle following damage to the zebrafish retina. Immunohistochemical analysis was employed to determine the temporal and spatial expression of Stat3 and Ascl1a proteins following rod and cone photoreceptor cell apoptosis. Stat3 expression was observed in all Müller glia, whereas Ascl1a expression was restricted to only the mitotic Müller glia. Knockdown of Stat3 protein expression did not affect photoreceptor apoptosis, but significantly reduced, without abolishing, the number of proliferating Ascl1a‐positive Müller glia. Knockdown of Ascl1a protein also did not change the extent of photoreceptor apoptosis, but did yield significantly fewer Müller glia that reentered the cell cycle relative to the stat3 morphant and significantly decreased the number and intensity of Stat3‐expressing Müller glia. Finally, introduction of lin28a morpholinos resulted in decreased Müller glia expression of Stat3 and Ascl1a, significantly reducing the number of proliferating Müller glia. Thus, there are three populations of Müller glia in the light‐damaged zebrafish retina: 1) Stat3‐expressing Ascl1a‐nonexpressing nonproliferating (quiescent) Müller glia; 2) Stat3‐dependent Ascl1a‐dependent proliferating Müller glia; and 3) Stat3‐independent Ascl1a‐dependent proliferating Müller glia. Whereas Ascl1a and Lin28a are required for Müller glia proliferation, Stat3 is necessary for the maximal number of Müller glia to proliferate during regeneration of the damaged zebrafish retina. J. Comp. Neurol. 520:4294–4311, 2012. © 2012 Wiley Periodicals, Inc.
Anatomical basis of sun compass navigation II: The neuronal composition of the central complex of the monarch butterfly
Authors: Heinze Stanley , Florman Jeremy , Asokaraj Surainder , el Jundi Basil , Reppert Steven M. 
Published: August 2012

AbstractEach fall, eastern North American monarch butterflies in their northern range undergo a long‐distance migration south to their overwintering grounds in Mexico. Migrants use a time‐compensated sun compass to determine directionality during the migration. This compass system uses information extracted from sun‐derived skylight cues that is compensated for time of day and ultimately transformed into the appropriate motor commands. The central complex (CX) is likely the site of the actual sun compass, because neurons in this brain region are tuned to specific skylight cues. To help illuminate the neural basis of sun compass navigation, we examined the neuronal composition of the CX and its associated brain regions. We generated a standardized version of the sun compass neuropils, providing reference volumes, as well as a common frame of reference for the registration of neuron morphologies. Volumetric comparisons between migratory and nonmigratory monarchs substantiated the proposed involvement of the CX and related brain areas in migratory behavior. Through registration of more than 55 neurons of 34 cell types, we were able to delineate the major input pathways to the CX, output pathways, and intrinsic neurons. Comparison of these neural elements with those of other species, especially the desert locust, revealed a surprising degree of conservation. From these interspecies data, we have established key components of a conserved core network of the CX, likely complemented by species‐specific neurons, which together may comprise the neural substrates underlying the computations performed by the CX. J. Comp. Neurol. 521:267–298, 2013. © 2012 Wiley Periodicals, Inc.
The Influence of H2O Content in Solvents {Water + Carbinol} and {Water + Ethanol} on the Deposition Mechanism of AZO Films Synthesized by Cold‐wall AACVD
Authors: Zhao Lin , Qin Xiu Juan , Shao Guang Jie , Wang Na 
Published: August 2012

AbstractUsing binary mixtures {x water + (1‐x) carbinol} and {x water + (1‐x) ethanol} as solvents for the precursor solutions, Al‐doped ZnO films are synthesized by cold‐wall, aerosol‐assisted (AA)CVD. The behavior of aerosol droplets influenced by H2O content in the precursor solution is discussed. It is found that as H2O content increases, the coagulation of the droplets is promoted by an increase in both the surface tension of the precursor solution and initial droplet mass. The coagulation reduces the amount of usable reactants that deposit on the substrate. As a result, the film thickness decreases with the increase in surface tension of the precursor solution and initial droplet mass. Transmittances in the visible range are also reduced by those micrometer‐sized grains that precipitate from large coagulate droplets. Film cannot be synthesized once the surface tension of the precursor solution exceeds 25.00 × 10−3 N · m−1 and the initial droplet mass exceeds 4.474 × 10−15 kg in both systems {x water + (1‐x) carbinol} and {x water + (1‐x) ethanol}.
Effects of Nordic walking on cardiovascular risk factors in overweight individuals with type 2 diabetes, impaired or normal glucose tolerance
Authors: Fritz T. , Caidahl K. , Krook A. , Lundström P. , Mashili F. , Osler M. , Szekeres F. L. M. , Östenson C. G. , Wändell P. , Zierath J. R. 
Published: August 2012

AbstractBackgroundPhysical activity remains a valuable prevention for metabolic disease. The effects of Nordic walking on cardiovascular risk factors were determined in overweight individuals with normal or disturbed glucose regulation.MethodsWe included 213 individuals, aged 60 ± 5.3 years and with body mass index (BMI) of 30.2 ± 3.8 kg/m2; of these, 128 had normal glucose tolerance (NGT), 35 had impaired glucose tolerance (IGT) and 50 had type 2 diabetes mellitus (T2DM). Participants were randomized to unaltered physical activity or to 5 h per week of Nordic walking with poles, for a 4‐month period. Dietary habits were unaltered. BMI, waist circumference, blood pressure, glucose tolerance, clinical chemistry, maximal oxygen uptake (peak VO2) and self‐reported physical activity (questionnaire) were assessed at the time of inclusion and after 4 months. The participants in the exercise‐intervention group kept a walking diary.ResultsIn the NGT exercise group, self‐reported physical activity increased markedly, and body weight (−2.0 ± 3.8 kg), BMI (−0.8 ± 1.4 kg/m2) and waist circumference (−4.9 ± 4.4 cm) (mean ± SD) decreased. Exercise power output (12.9 ± 9.9 W) and peak VO2 (2.7 ± 2.8 mL/kg/min) increased in the IGT exercise group. More cardiovascular risk factors were improved after exercise intervention in people with NGT compared with those with IGT or T2DM. Exercise capacity improved significantly in all three groups of participants who reported at least 80% compliance with the scheduled exercise.ConclusionsNordic walking improved anthropometric measurements and exercise capacity. However, unsupervised Nordic walking may not provide a sufficient increase in exercise intensity to achieve ultimate health‐promoting benefits on the cardiovascular parameters assessed in this study, particularly for those with disturbed glucose regulation. Copyright © 2012 John Wiley & Sons, Ltd.
Testing transpiration controls by quantifying spatial variability along a boreal black spruce forest drainage gradient
Authors: Angstmann Julia L. , Ewers Brent E. , Barber Jarrett , Kwon Hyojung 
Published: August 2012

ABSTRACTOne of the biggest challenges in predicting ecohydrologic fluxes is scaling from easily measured variables to more difficult, often emergent patterns and processes. This is especially true in spatially heterogeneous systems such as black spruce (Picea mariana)‐dominated boreal forests containing excessive and low soil moisture conditions. Traditional hypotheses suggest that transpiration is controlled by hydraulic responses to vapor pressure deficit (D) and soil moisture; however, these may potentially be misinformed because of omission of soil drainage gradients. Thus, we predict that 1) spatial heterogeneity in tree transpiration along a soil drainage gradient is positively correlated withD, 2) sap flux (JS) and leaf‐level transpiration (EL) are higher and whole‐tree transpiration (EC) lower in the poorly drained than well‐drained stands, and 3) spatial heterogeneity ofECis regulated primarily by tree‐related covariates such as sapwood and leaf area and secondarily by environmental covariates including peat and moss depth. With the use of 122 black spruce sap flux measurements, the range of autocorrelation (inverse of spatial variation) decreased from 20 m at lowD(<0.7 kPa) to 2 m at middayDvalues (>0.9 kPa).JSandELwere significantly greater andECless in poorly drained than well‐drained stands; controlled primarily by tree‐related covariates (sapwood and leaf area) representing long‐term growth conditions and secondarily by soil moisture and spatially sampledDreflecting shorter‐term environmental variation. Quantification of spatial heterogeneity informs predictive models of the distance at which homogeneity can no longer be assumed and will improve mechanistic predictions of transpiration at multiple spatial scales. Copyright © 2012 John Wiley & Sons, Ltd.
Studies of the Electronic Properties of N‐Heterocyclic Carbene Ligands in the Context of Homogeneous Catalysis and Bioorganometallic Chemistry
Authors: Kumar Anuj , Ghosh Prasenjit 
Published: August 2012

AbstractN‐heterocyclic carbenes (NHCs) have been dominating the world of homogeneous catalysis in an unprecedented manner in the last two decades. Understanding the underlying reasons behind catalysis with NHC ligands has thus become of significant interest. Subscribing to this view, we strive to identify the key attributes of N‐heterocyclic carbene ligands through a combination of experimental and computational studies. Rational catalyst design, by appropriate functionalization of N‐heterocyclic carbene ligands to investigate their utility in a host of catalytically relevant transformations of interest to contemporary organic synthesis, is thus central to our efforts. From this perspective, a variety of C–C and C–N bond forming reactions, namely, the Suzuki–Miyaura, Sonogashira, and Hiyama cross‐couplings, the base‐free Michael additions, the alkene and alkyne hydroaminations, the formation of β‐enaminones from 1,3‐dicarbonyl compounds and primary amines, and the environmentally important ring‐opening polymerizations (ROP) of L‐lactides, which produce biodegradable polylactide polymers from renewable resources, have been studied. The metal–carbene interaction in these catalysts has been probed with the aid of computational studies, which suggest that strong σ‐donor N‐heterocyclic carbene ligands bind tightly to the metal center and thereby impart the much needed stability to these catalysts. Even going beyond catalysis, we investigated the potential of N‐heterocyclic carbene complexes in biomedical applications particularly for their antimicrobial and anticancer properties.