bluuebunny/crossref_metadata_2025_split huggingface dataset:
Position‐Specific Incorporation of Fluorescent Non‐natural Amino Acids into Maltose‐Binding Protein for Detection of Ligand Binding by FRET and Fluorescence Quenching
Authors: Iijima Issei , Hohsaka Takahiro 
Published: March 2009

AbstractFRETting about MBP: Position‐specific incorporation of fluorescent groups is a useful method for analysis of the functions and structures of proteins. Here we demonstrate that position‐specific incorporation of fluorescent non‐natural amino acids in response to expanded codons enables us to detect ligand‐binding activity of maltose‐binding protein (MBP) through fluorescence resonance energy transfer (FRET) and ligand‐dependent fluorescence quenching.magnified imagePosition‐specific incorporation of fluorescent groups is a useful method for analysis of the functions and structures of proteins. We have developed a method for the incorporation of visible‐wavelength‐fluorescent non‐natural amino acids into proteins in a cell‐free translation system. Using this technique, we introduced one or two BODIPY‐linked amino acids into maltose‐binding protein (MBP) to obtain MBP derivatives showing ligand‐dependent changes in fluorescence intensity or intensity ratio. BODIPY‐FL‐aminophenylalanine was incorporated in place of 15 tyrosines, as well as the N‐terminal Lys1, and the C‐terminal Lys370 of MBP. Fluorescence measurements revealed that MBP containing a BODIPY‐FL moiety in place of Tyr210 showed a 13‐fold increase in fluorescence upon binding of maltose. Tryptophan‐to‐phenylalanine substitutions suggest that the increase in fluorescence was the result of a decrease in the quenching of BODIPY‐FL by tryptophan located around the binding site. MBP containing a BODIPY‐558 moiety also showed a maltose‐dependent increase in fluorescence. BODIPY‐FL was then additionally incorporated in place of Lys1 of the BODIPY‐558‐containing MBP as a response to the amber codon. Fluorescence measurements with excitation of BODIPY‐FL showed a large change in fluorescence intensity ratio (0.13 to 1.25) upon binding of maltose; this change can be attributed to fluorescence resonance energy transfer (FRET) and maltose‐dependent quenching of BODIPY‐558. These results demonstrate the usefulness of the position‐specific incorporation of fluorescent amino acids in the fluorescence‐based detection of protein functions.
Analysis of the Indanomycin Biosynthetic Gene Cluster from Streptomyces antibioticus NRRL 8167
Authors: Li Chaoxuan , Roege Kathryn E. , Kelly Wendy L. 
Published: March 2009

AbstractMore than meets the I: The biosynthetic gene cluster for indanomycin was identified from Streptomyces antibioticus NRRL 8167. The framework of the indanomycins includes a tetrahydropyran and a central indane ring system. The final module of the indanomycin polyketide synthase possesses an unusual terminal module lacking an integrated thioesterase.magnified imageMetabolites that harbor a core indane scaffold are found to have diverse biological properties. Indanomycin and related pyrroloketoindanes are ionophores and have demonstrated antiparasitic, insecticidal, and antibacterial activities. To understand the biochemical mechanisms guiding formation of the central indane ring, the biosynthetic gene cluster for indanomycin was identified from Streptomyces antibioticus NRRL 8167 and sequenced to ∼80 kb; this revealed five genes encoding subunits of a polyketide synthase (PKS) and 18 other open reading frames. The involvement of this cluster in indanomycin biosynthesis was confirmed by deletion mutagenesis. The indanomycin PKS lacks the expected thioesterase at the carboxy terminus of the final module, and instead appears to house an incomplete module containing an unusual cyclase domain. These findings now enable additional detailed genetic and biochemical studies of the mechanisms guiding the generation of pyrroloketoindanes.
Synthesis of α‐Stereogenic Amides and Ketones by Enantioselective Conjugate Addition of 1,4‐Dicarbonyl But‐2‐enes
Authors: Jiang Zhiyong , Yang Yuanyong , Pan Yuanhang , Zhao Yujun , Liu Hongjun , Tan Choon‐Hong 
Published: March 2009

AbstractConstructing α‐stereogenic amides and ketones: The highly regioselective and enantioselective conjugate addition of 1,3‐dicarbonyl compounds to 1,4‐dicarbonyl but‐2‐enes has been developed with the chiral bicyclic guanidine as catalyst (ee values up to 97 %; see scheme).magnified imageIn the conjugate addition reaction of a α,β‐unsaturated compound, the new stereogenic center is created in the β‐position. In contrast, conjugate addition to 1,4‐dicarbonyl but‐2‐enes will generate an α‐stereogenic center with respect to one of the carbonyl groups, which informally, can be considered as an inversion of normal reactivity patterns or Umpolung. In this paper, we demonstrate that chiral bicyclic guanidine can catalyze the addition of 1,3‐dicarbonyl compounds to 1,4‐dicarbonyl but‐2‐enes [(E)‐4‐oxo‐4‐arylbutenamides and (E)‐4‐oxo‐4‐arylbutenones] with high regioselectivity and enantioselectivity (ee values up to 97 %).
Design of a Full‐Profile‐Matching Solution for High‐Throughput Analysis of Multiphase Samples Through Powder X‐ray Diffraction
Authors: Baumes Laurent A. , Moliner Manuel , Corma Avelino 
Published: March 2009

AbstractFinding a clear route to new structures: The design of an adaptable time warping (ATW) methodology (see figure) for automatically, quickly, and reliably deciphering X‐ray diffraction patterns is described.magnified imageFew solutions that aim to identify crystalline materials from the analysis of powder X‐ray diffraction (XRD) data have been reported to date. A careful inspection of the powder XRD data, and the corresponding highlight of specific failures when it has been used for the determination of the crystallographic phases of zeolites among mixtures, has allowed the creation of the recently proposed strategy: adaptable time warping (ATW). Herein, the design process is thoroughly detailed in a step‐by‐step manner, which allows a deep understanding of the motivations, improvements, and the resulting remarkable properties of our methodology. Because the use of high‐throughput (HT) techniques for the discovery or for increasing the breadth of the synthetic routes of new microporous crystalline structures makes the reliability of search–match methods a critical factor to be assessed, a meticulous evaluation of the reliability and the robustness is provided and supported by both empirical comparisons and mathematical proof. The results offered by our methodology, which clearly outperforms the well‐established solutions, open the way towards total automation of such a routine procedure, eliminating laborious and time‐consuming controls, preliminary treatments, and settings. Consequently, the proposed solution is of great interest and appears to be very promising, not only because of the numerous potential applications of XRD in materials science, but also the possible expansion of the solution to several other characterization techniques.
Scale‐up study of spouted beds using computational fluid dynamics
Authors: Béttega Rodrigo , Corrêa Ronaldo Guimarães , Freire José Teixeira 
Published: March 2009

AbstractThis work presents a numerical study of the hydrodynamic of spouted beds using computational fluid dynamics (CFD) simulation. Scaling relationships proposed by He et al. [He et al., Chem. Eng. Sci. 1997;52:329–339] for spouted bed systems based on similitude method are numerically investigated using CFD simulation. In the present work it is verified that the spouted bed scale‐up relationships of He et al. [He et al., Chem. Eng. Sci. 1997;52:329–339] produce good numerical results when all of the scale‐up relationships are satisfied. It is also verified the behaviour of the numerical results when the scaling procedure is applied in a practical condition. In this case, the properties of fluid and solid are kept constant, which is a real situation of a scale‐up procedure in a spouted bed used for drying of grains. In this work it is possible to verify that CFD simulation is a useful tool to evaluate similitude methods in spouted bed (multiphase flow) systems. The commercial package FLUENT 6.3.26 was used in all simulations.
Identification of the state of a wet spouted bed through time‐frequency analysis of pressure fluctuation time series
Authors: Oliveira W.P. , Souza C.R.F. , Lim C.J. , Grace J.R. 
Published: March 2009

AbstractThe feasibility of detecting instability in wet spouted beds via pressure fluctuation (PF) time‐series analyses was investigated. Experiments were carried out in a cylindrical Plexiglas column of diameter 150 mm with a conical base of internal angle 60°, an inlet orifice diameter of 25 mm and glass beads of diameter 2.4 mm. Transducers at several axial positions measured PF time series with incremental addition of aqueous sucrose solutions of different concentrations. Liquid addition affected the spouted bed dynamics, causing irregular spouting, increased voidage in the annulus, increased fountain height, irregular annulus height, channelling, agglomeration, and adhesion of particles to the column walls. Autocorrelations indicated the appearance of periodicities in the PF signals with increasing sucrose addition. Dominant peaks in power‐spectral density developed at low frequencies with changing system dynamics. The results indicate that PF signals furnish relevant information on system dynamics, useful for monitoring and control of spouted bed operations such as particle coating and drying of paste‐like materials.
Clinical Efficiency and Safety Analysis of Transcatheter Closure of Multiple Atrial Septal Defects in Adults
Authors: Song Zhi‐Yuan , He Guo‐Xiang , Shu Mao‐Qin , Hu Hou‐Yuan , Tong Shi‐Fei , Ran Bo‐Li , Liu Jian‐Ping , Li Yong‐Hua , Jing Tao 
Published: March 2009

AbstractBackgroundTranscatheter closure of atrial septal defects (ASDs) is currently a reliable alternative to surgery, even though challenging in patients with multiple ASDs.HypothesisThe aim of this study was to evaluate the clinical efficiency and safety of transcatheter closure in multiple ASDs.MethodsMultiple ASDs were diagnosed by transthoracic echocardiography (TTE) or transesophageal echocardiography (TEE). The occlusive condition and distance between 2 adjacent ASDs were measured by TTE examination. Then, the number and size of the occluder(s) was determined. TTE examinations were performed after transcatheter closure as follow‐up.ResultsThe transcatheter procedure was successful in 15 patients with multiple ASDs, using a single occluder in 9 patients and 2 occluders in the remaining 6 patients. Overall, 21 ASD occluders were implanted. During a follow‐up period of 6 mo to 5 y, a slight residual shunt was found in 1 patient without any symptoms; a moderate residual shunt was identified at the inferior vena cava and the occluder was removed by surgery 1 mo after procedure. Other complications, including endocarditis, arrhythmia, thromboembolism, and atrioventricular valve damage were not recorded in any of the 15 patients during the follow‐up period.ConclusionTranscatheter closure of multiple ASDs is safe and efficient. Two occluders are necessary for the distance of 2 ASDs more than 7 mm, and a single occluder is sufficient for those 7 mm or less. Copyright © 2009 Wiley Periodicals, Inc.
Kit and foxd3 genetically interact to regulate melanophore survival in zebrafish
Authors: Cooper Cynthia D. , Linbo Tor H. , Raible David W. 
Published: March 2009

AbstractWe have investigated the role of foxd3 activity in conjunction with signaling by the kit tyrosine kinase receptor in zebrafish black pigment cell (melanophore) development. As loss‐of‐function of these molecules individually has distinct effects on melanophore number, we have examined the phenotype of double mutants. Individuals with a null mutation in kit have fewer melanophores than wild‐type, with cells lost through death. When kit mutants are injected with foxd3 antisense morpholino oligonucleotides or crossed with a foxd3 zebrafish mutant, they have more melanophores than their uninjected or foxd3+ counterparts. Examination of foxd3 loss‐of‐function in two additional kit mutants that differentially alter kit‐dependent migration and survival indicates a change in melanophore number in survival mutants only. Consistently, TUNEL (terminal deoxynucleotidyl transferase–mediated deoxyuridinetriphosphate nick end‐labeling) analysis confirms a partial rescue of melanophores from cell death. Ectopic expression of foxd3 indicates that foxd3 promotes early melanophore death only when kit is inactive. Taken together, these data suggest a kit‐dependent role for foxd3 in the regulation of melanophore survival. Developmental Dynamics 238:875–886, 2009. © 2009 Wiley‐Liss, Inc.
Transcriptional control of Rohon‐Beard sensory neuron development at the neural plate border
Authors: Rossi Christy Cortez , Kaji Takao , Artinger Kristin Bruk 
Published: March 2009

AbstractRohon‐Beard (RB) mechanosensory neurons are among the first sensory neurons to develop, and the process by which they adopt their fate is not completely understood. RBs form at the neural plate border (NPB), the junction between neural and epidermal ectoderm, and require the transcription factor prdm1a. Here, we show that prior to RB differentiation, prdm1a overlaps extensively with the epidermal marker dlx3b but shows little overlap with the neuroectodermal markers sox3 and sox19a. Birthdating analysis reveals that the majority of RBs are born during gastrulation in zebrafish, suggesting that it is during this period that RBs become specified. Expression analysis in prdm1a and neurogenin1 mutant and dlx3b/dlx4b morpholino‐injected embryos suggests that prdm1a is upstream of dlx3b, dlx4b, and neurogenin1 at the NPB. mRNA for neurogenin1 or dlx3b/dlx4b can rescue the lack of RBs in prdm1a mutants. Based on these data, we suggest a preliminary gene regulatory network for RB development. Developmental Dynamics 238:931–943, 2009. © 2009 Wiley‐Liss, Inc.
Case studies of ends‐out gene targeting in Drosophila
Authors: Chen Haiyang , Ma Zhiguo , Liu Zhonghua , Tian Yuan , Xiang Yanhui , Wang Chao , Scott Matthew P. , Huang Xun 
Published: March 2009

AbstractEnds‐in and ends‐out gene replacement approaches have been successfully used to disrupt Drosophila genes involved in a variety of biological processes. These methods combine double‐strand breaks and homologous recombination to replace a targeted chromosome region with a designed DNA sequence. Unfortunately, these methods require large numbers of single animal crosses, making them both time consuming and labor intensive. Here, we designed a single complete targeting vector for use in a mass crossing ends‐out gene targeting study. Importantly, our gene targeting method included a balancer chromosome to block endogenous homologous chromosome pairing and to promote pairing between the foreign targeting DNA fragment and the targeted chromosome. This technique provided successful and efficient gene replacement, greatly facilitating the gene knockout procedure. genesis 47:305–308, 2009. © 2009 Wiley‐Liss, Inc.
Unexpected Thermal Reactivity of Phosphirano‐[1,2]thiaphosphole P–W(CO)5 Complexes
Authors: Maurer Stefan , Jikyo Tamaki , Maas Gerhard 
Published: March 2009

AbstractSpiro[fluorene‐9,6′‐[2]thia[1]phosphabicyclo[3.1.0]hex[3]enes] 7a–c have been obtained in one step from 3,5‐diaryl‐1,2‐thiaphospholes and 9‐diazofluorene or its 2,7‐dibromo derivative. The bicyclic phosphiranes are stable against water and resist attempts at sulfuration or selenation of the phosphorus atom. However, cleavage of the P–C ring fusion with hydrogen chloride followed by hydrolysis led to the monocyclic 2‐(9H‐fluoren‐9‐yl)‐2,3‐dihydro‐1,2‐thiaphosphole 2‐oxides 8a–c. Phosphiranes 7a–c also react to form the hexacarbonyltungsten‐(P–W) complexes 10a–c readily and in high yields. These complexes rearrange in toluene solution at 50–80 °C to form the spiro[fluorene‐9,2′‐[1]phospha[6]thiabicyclo[3.1.0]hex‐3‐ene]‐W(CO)5‐(P–W) complexes 11a–c, which are the first representatives of ring‐fused thiaphosphiranes. Compound 11a is readily desulfurated with tributylphosphane to form the highly oxygen‐sensitive spiro[fluorene‐9,2′‐[2H]phosphole] 13, which is reconverted into 11a upon treatment with sulfur. Bicyclic 1,3,2‐dithiaphospholanes 12a–c are formed as minor byproducts of the thermal isomerization of phosphiranes 10. Compound 10a slowly rearranges in solution to give 12a as the sole product. Compounds 12 may result from a formal [3+2] cycloaddition reaction of an α,β‐unsaturated thione, formed by partial decomposition of 10, with a dipolar valence isomer of 10 or 11, featuring aW(CO)5‐complexed thiocarbonyl‐phospha‐ylide dipole (R2C=S+–P–R). W(CO)5 complexation is not a prerequisite for the cycloaddition reaction: the uncomplexed phosphirano‐thiaphosphole 7a reacts with thiobenzophenone in the same way to form the bicyclic 1,3,2‐dithiaphospholane 18 in high yield. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
Monitoring changes in the volatile profile of cheese crackers during storage using GC–MS and PTR–MS
Authors: Pozo‐Bayón Maria‐Ángeles , Martín‐Álvarez Pedro J. , Reineccius Gary A. 
Published: March 2009

AbstractThe primary objective of this work was to determine the feasibility of using PTR–MS ion profiles to monitor changes in the volatile profile of cheese crackers during storage. This was done by obtaining PTR–MS ion profiles of cheese crackers during the early shelf‐life of the product (first 4 months of storage) and comparing these data to those obtained using a more traditional approach, i.e. purge and trap–GC–MS (PT–GC–MS). The PTR–MS profile of the samples was monitored for 47 ion masses, mainly corresponding to low molecular weight compounds or fragments of low mass. From the application of multivariate statistical analysis (cluster analysis, PCA, ANOVA) to the PTR–MS data of the samples of different storage times, it was shown that the age of the sample was an important factor for their classification. It was possible to differentiate two main groups of samples, the first group included samples of age <3 months (1, 1.5 and 2 months). This group had low ion intensities relative to the second group. The second group comprised samples of age ≥3 months (3 and 4 months) that showed higher ion intensities. PT–GC–MS data on the same samples found 38 volatile compounds, primarily aldehydes, that increased during storage. A good correlation was found between changes in some PTR–MS masses and major volatile compounds of crackers. The compounds that increased were generally products of autoxidation. It appears that a PTR–MS could be a useful tool for monitoring volatile changes during storage in cheese crackers. Copyright © 2009 John Wiley & Sons, Ltd.
Protein or amino acid deprivation differentially regulates the hepatic forkhead box protein A (FOXA) genes through an activating transcription factor-4–independent pathway #
Authors: Su Nan , Thiaville Michelle M. , Awad Keytam , Gjymishka Altin , Brant Jason O. , Yang Thomas P. , Kilberg Michael S. 
Published: March 2009

Abstract
The FOXA (forkhead box A) proteins (FOXA1, FOXA2, and FOXA3) play a critical role in the development of the liver, and they also regulate metabolism in adult hepatic tissue. The liver responds to changes in nutrient availability by initiating a number of stress signaling pathways. The present studies demonstrated that in mouse dams fed a low-protein diet hepatic expression of FOXA2 and FOXA3 messenger RNA, but not FOXA1, was induced. Conversely, fetal liver did not exhibit this regulation. Amino acid deprivation of HepG2 hepatoma cells also enhanced transcription from the FOXA2 and FOXA3 genes. In contrast, endoplasmic reticulum stress inhibited the expression of FOXA1, only slightly induced FOXA2, and had no effect on FOXA3. The FOXA2 and FOXA3 messenger RNA induction by amino acid deprivation did not require activating transcription factor 4, a critical component of the conventional amino acid response (AAR) pathway, but their induction was partially dependent on CCAAT/enhancer-binding protein β. Simultaneous knockdown of both FOXA2 and FOXA3 by small interfering RNA did not affect the activation of other amino acid responsive genes, suggesting that the FOXA proteins are not required for the known AAR pathway. Collectively, the results document that the hepatic FOXA family of genes are differentially regulated by amino acid availability. (Hepatology 2009.)
OX40 costimulation can abrogate Foxp3+ regulatory T cell‐mediated suppression of antitumor immunity
Authors: Kitamura Naomi , Murata Satoshi , Ueki Tomoyuki , Mekata Eiji , Reilly R. Todd , Jaffee Elizabeth M. , Tani Tohru 
Published: March 2009

AbstractRegulatory T cells (Tregs) play an important role in maintaining immunological tolerance that is one of the main obstacles to overcome for improving antitumor immunity. Recently, the Treg has been shown to constitutively express OX40 (CD134), which is a member of the TNF‐receptor family that is transiently expressed on effector T cells after TCR triggering, and through which the signal enhances effector T‐cell proliferation and memory T‐cell development. However, little is known about the role of OX40 costimulation to Tregs in tumor immunology. Here we show that OX40 signaling modulates the function of naturally occurring Tregs in vitro and in vivo. Foxp3 expression on Tregs was reduced by OX40 costimulation, but not by IL‐2 stimulation. Tregs suppressed the proliferation of naïve CD4+ CD25− T cells after TCR triggering, in contrast, OX40 costimulated Tregs that reduced Foxp3 expression reversed the suppressive function. In addition, Tregs inhibited the proliferation of TCR‐stimulated (primed) CD4+ T cells and naïve CD8+ T cells after TCR‐mediated activation, however, Tregs with OX40 costimulation lost their suppressive function. Interestingly, Tregs minimally suppressed the proliferation or the cytokine secretion of Ag‐specific CD8+ T cells after Ag‐restimulation. Furthermore, Tregs suppressive function to the antitumor effect was reversed by OX40 costimulation in vivo. Our data indicate that, in addition to controlling effector T‐cell function, OX40 costimulation directly controls Treg‐mediated suppression in tumor immunity. © 2009 UICC
ING2 is upregulated in colon cancer and increases invasion by enhanced MMP13 expression
Authors: Kumamoto Kensuke , Fujita Kaori , Kurotani Reiko , Saito Motonobu , Unoki Motoko , Hagiwara Nobutoshi , Shiga Hideaki , Bowman Elise D. , Yanaihara Nozomu , Okamura Shu , Nagashima Makoto , Miyamoto Kotaro , Takenoshita Seiichi , Yokota Jun , Harris Curtis C. 
Published: March 2009

AbstractInhibitor of growth 2 (ING2) is associated with chromatin remodeling and regulation of gene expression by binding to a methylated histone H3K4 residue and recruiting HDAC complexes to the region. The aim of our study is to investigate the regulation of ING2 expression and the clinical significance of upregulated ING2 in colon cancer. Here, we show that the ING2 mRNA level in colon cancer tissue increased to more than twice than that in normal mucosa in the 45% of colorectal cancer cases that we examined. A putative NF‐κB binding site was found in the ING2 promoter region. We confirmed that NF‐κB could bind to the ING2 promoter by EMSA and luciferase assays. Subsequent microarray analyses revealed that ING2 upregulates expression of matrix metalloproteinase 13 (MMP13), which enhances cancer invasion and metastasis. ING2 regulation of MMP13 expression was confirmed in both ING2 overexpression and knock down experiments. MMP13 expression was further induced by coexpression of ING2 with HDAC1 or with mSin3A, suggesting that the ING2‐HDAC1‐mSin3A complex members regulates expression of MMP13. In vitro invasion assay was performed to determine functional significance of ING2 upregulation. ING2 overexpressed cells exhibited greater invasive potential. Taken together, upregulation of ING2 was associated with colon cancer and MMP13‐dependent cellular invasion, indicating that ING2 expression might be involved with cancer invasion and metastasis. Published 2009 UICC.