bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of transcription factors by mass spectrometry and the role of SELDI‐MS
Authors: Forde Cameron E. , McCutchen‐Maloney Sandra L. 
Published: March 2003

Abstract

I.
Introduction
419

II.
Genomics, Proteomics, and MS
420

III.
Regulatory Networks and the Traditional Study of Transcription Factors
421

IV.
Identification of Transcription‐Factor Complexes
422

V.
Structural Characterization of Transcription Factors
423

VI.
Determination of Binding Sites and Stoichiometry of Binding
423

VII.
Post‐Translational Modifications
426

VIII.
Assessing Metal Binding and Activity
427

IX.
Affinity Capture and Identification of Transcription Factors Using MS
429

X.
Role of SELDI‐MS to Characterize Transcription Factors
430

XI.
Other Applications of SELDI‐MS
433

XII.
Conclusion and Future Prospects
434

Acknowledgments
434

References
434

Over the last decade, much progress has been made in the field of biological mass spectrometry, with numerous advances in technology, resolution, and affinity capture. The field of genomics has also been transformed by the sequencing and characterization of entire genomes. Some of the next challenges lie in understanding the relationship between the genome and the proteome, the protein complement of the genome, and in characterizing the regulatory processes involved in progressing from gene to functional protein. In this new age of proteomics, development of mass spectrometry methods to characterize transcription factors promises to add greatly to our understanding of regulatory networks that govern expression. However, at this time, regulatory networks of transcription factors are mostly uncharted territory. In this review, we summarize the latest advances in characterization of transcription factors by mass spectrometry including affinity capture, identification of complexes of DNA‐binding proteins, structural characterization, determination of protein–DNA and protein–protein interactions, assessment of modification sites and metal binding, studies of functional activity, and the latest chip technologies that use SELDI‐MS that allow the rapid capture and identification of transcription factors. © 2003 Wiley Periodicals, Inc., Mass Spec Rev 21:419–439, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mas.10040
Inhibition of proteasome‐dependent degradation of Wee1 in G2‐arrested Hep3B cells by TGFβ1
Authors: Hashimoto Osamu , Ueno Takato , Kimura Rina , Ohtsubo Motoaki , Nakamura Toru , Koga Hironori , Torimura Takuji , Uchida Sanae , Yamashita Katsumi , Sata Michio 
Published: March 2003

AbstractTransforming growth factor β1 (TGFβ1)‐induced G2 arrest was observed when a proliferation inhibitory function of the retinoblastoma protein (Rb) was compromised, but the mechanism underlying the G2 arrest was poorly characterized compared with that of G1 arrest. In the present study, we characterized G2 arrest induced by TGFβ1 (1 ng/mL) in the Rb‐negative hepatoma cell line (Hep3B) and compared with G1 arrest in the Rb‐positive hepatoma cell line (Huh7). Activities of cyclin‐dependent kinases (CDK) 2 and cell division cycle (CDC) 2 were markedly decreased at 24 h, the time when cell‐cycle arrest became apparent in both cell lines. However, considerable amounts of inactive CDC2‐cyclinB1 complexes were present in the nucleus of G2‐arrested Hep3B but were not present in G1‐arrested Huh7. The inhibitory phosphorylation of CDC2 on Tyr‐15 was significantly elevated at 12–24 h, and its levels gradually declined during G2 arrest in Hep3B. In particular, augmentation of CDK inhibitors p21cip1 and p27kip1 and Wee1 kinase and diminution of CDC25C phosphatase coincided with induced Tyr‐15 phosphorylation and inhibition of CDC2. Wee1 in Hep3B was unstable and was degraded in a proteasome‐dependent manner, but it became substantially stabilized within 6 h of TGFβ1 treatment. Moreover, a Wee1 inhibitor, PD0166285, abrogated the TGFβ1‐induced G2 arrest in Hep3B. These findings suggest that TGFβ1 induced G2 arrest in Hep3B at least in part through stabilization of Wee1 and subsequent increase in Tyr‐15 phosphorylation and inhibition of CDC2. © 2003 Wiley‐Liss, Inc.
Mutational analysis of Ctnnb1 and Apc in tumors from rats given 1,2‐dimethylhydrazine or 2‐amino‐3‐methylimidazo[4,5‐f]quinoline: Mutational ‘hotspots’ and the relative expression of β‐catenin and c‐jun
Authors: Blum Carmen A. , Tanaka Tomoko , Zhong Xiaoying , Li Qingjie , Dashwood Wan‐Mohaiza , Pereira Clifford , Xu Meirong , Dashwood Roderick H. 
Published: March 2003

AbstractThere is growing interest in β‐catenin and its role in various human cancers. We recently reported that 2‐amino‐3‐methylimidazo[4,5‐f]quinoline (IQ)‐ and 1,2‐dimethylhydrazine (DMH)‐induced colon tumors in the rat contain mutations in Ctnnb1, the gene for β‐catenin, but the mutation spectrum was influenced by postinitiation exposure to chlorophyllin (CHL) and indole‐3‐carbinol (I3C) [Blum et al., Carcinogenesis 2001;22:315–320]. The present paper describes a follow‐up study in which all of the target organs for IQ‐ and DMH‐induced tumorigenesis were screened; Ctnnb1 mutations were found in 44 of 119 DMH‐induced colon tumors, six of 13 IQ‐induced colon tumors, 28 of 81 DMH‐induced small intestine tumors, none of five IQ‐induced small intestine tumors, four of 106 IQ‐induced liver tumors, none of 14 DMH‐induced Zymbal's gland tumors, none of 24 IQ‐induced Zymbal's gland tumors, and none of 29 IQ‐induced skin tumors. In tumors from rats given carcinogen alone, or carcinogen plus CHL or I3C, Ctnnb1 mutations frequently substituted amino acids adjacent to Ser33, a critical Ser/Thr residue in the glycogen synthase kinase‐3β regulatory domain of β‐catenin. However, substitution of critical Ser/Thr residues themselves was detected in only three of 24 (12.5%) of the tumors from rats given carcinogen alone, compared with 23 of 58 (40%) of the tumors from rats given carcinogen and treated postinitiation with I3C or CHL (P < 0.02). More than 50 of the colon tumors with wild‐type β‐catenin were examined further for their Apc status; the overall frequency of Apc mutations was <10%, and these genetic changes occurred exclusively in the ‘Mutation Cluster Region’ of Apc. A subset of colon tumors also was examined for expression of β‐catenin and c‐jun; these proteins were overexpressed in all tumors containing Ctnnb1 mutations, but the expression was highest in tumors with Ctnnb1 mutations affecting Thr41 and Ser45 residues in the glycogen synthase kinase‐3β region of β‐catenin. Thus, Ctnnb1 mutations occurred more frequently than Apc mutations in colon and small intestine tumors of the rat, and certain mutations upregulated β‐catenin/T‐cell factor target genes more effectively than others, perhaps influencing the response to phytochemicals administered postinitiation. © 2003 Wiley‐Liss, Inc.
The phytochemical profile and identification of main phenolic compounds from the leaf exudate of Aloe secundiflora by high‐performance liquid chromatography–mass spectroscopy
Authors: Rebecca Waihenya , Kayser Oliver , Hagels Hansjörg , Zessin Karl‐H , Madundo Mtambo , Gamba Nkwengulila 
Published: March 2003

AbstractThe phytochemical profile of Aloe secundiflora (Aloeaceae) and the identity of eight major compounds, including the two main constituents, have been determined from the leaf exudate of this ethnoveterinary used species from Kenya and Tanzania. Analytical HPLC‐MS studies of the exudate have revealed that ­it comprises a mixture of phenolic compounds, mainly anthrones (aloenin, aloenin B, isobarbaloin, barbaloin and other aloin derivatives), chromones and phenylpyrones with a low content of polysaccharides and aliphatic compounds. The high percentage of anthrones in the exudate could provide a first line of evidence for the use of the plant in ethnoveterinary practices. Copyright © 2003 John Wiley & Sons, Ltd.
Analysis of carbohydrates and amino acids in vegetable waste waters by ion chromatography
Authors: Arienzo Michele , De Martino Antonio , Capasso Renato , Di Maro Antimo , Parente Augusto 
Published: March 2003

AbstractHigh‐performance anion exchange chromatography coupled with pulsed amperometric detection was used for the quantitative determination of total and free sugars in olive oil mill waste waters (OMWW). Automated amino acid ion chromatography was employed to analyse total and free amino acids in the same OMWW. Sugars were analysed in samples pre‐purified by means of a three‐step purification procedure involving: (i) methanol precipitation of OMWW; (ii) dialysis of the obtained solid and liquid fractions; and (iii) chromatographic purification on RP18 phase followed by Amberlite resin. The amino acids were determined directly in samples obtained from the first two steps performed for sugar analysis. The analysis carried out with the reported methodologies allowed the quantitative determination of total sugars and amino acids and the differentiation between their free and bound forms. The sugars determined were arabinose, fructose, galactose, glucose, rhamnose, xylose, galacturonic and glucuronic acids, and the amino acids were Asp, Glu, Thr, Ser, Pro, Gly, Ala, Val, Met, Ile, Leu, Tyr, Phe, Lys, His, Arg and Cys. Asn, Gln, and Trp were not detected. The technological, biotechnological and environmental advantages arising from this analytical methodology applied to OMWW are briefly discussed. Copyright © 2003 John Wiley & Sons, Ltd.
On‐line identification of unstable catalpol derivatives from Jamesbrittenia fodina by LC‐MS and LC‐NMR
Authors: Cogne A.‐L. , Queiroz E. F. , Wolfender J.‐L. , Marston A. , Mavi S. , Hostettmann K. 
Published: March 2003

AbstractLC‐UV‐MS analysis of the methanol extract of Jamesbrittenia fodina O. M. Hilliard (Scrophulariaceae) revealed the presence of cinnamic ester derivatives. Two isomeric pairs of these constituents were detected, but could not be isolated. In order to identify these unstable compounds, LC‐1H‐NMR spectra were obtained for each individual isomer and standard NMR measurements were performed in‐mixture. The spectra clearly demonstrated that the fractions consisted of mixtures of cis and trans cinnamoyl catalpol glycoside esters. Copyright © 2003 John Wiley & Sons, Ltd.
Composition of volatiles of banana cultivars from Madeira Island
Authors: Nogueira J. M. F. , Fernandes P. J. P. , Nascimento A. M. D. 
Published: March 2003

AbstractThe composition of the volatiles of banana fruit from various cultivars grown on Madeira Island has been determined. Using GC‐MS, the volatiles were shown to be complex mixtures of several classes of components, mainly esters, alcohols, aldehydes, ketones and acids. The average contents of the total volatiles from cultivars “Dwarf Cavendish”, “Giant Cavendish”, “Robusta” and “Williams” were 93.0, 116.5, 157.3 and 157.0 mg/kg, respectively. The ester and alcoholic fractions appear to play a decisive role in the organoleptic characteristics of banana fruit, presenting a substantial content ranging from 57.2 to 89.8 mg/kg and 19.0 to 47.7 mg/kg, respectively, in all cultivars from Madeira Island studied. 3‐Methyl butyl butanoate ester was the major constituent. Copyright © 2003 John Wiley & Sons, Ltd.
Identification of lipophilic flavones and flavonols by comparative HPLC, TLC and UV spectral analysis
Authors: Greenham Jenny , Harborne Jeffrey B. , Williams Christine A. 
Published: March 2003

AbstractThe identification of lipophilic flavones and flavonols using a combination of high performance liquid chromatography, thin layer chromatography and UV spectral analysis is discussed. Data are provided for the flavones, apigenin, luteolin and tricetin and twelve of their methyl ethers, 8‐hydroxyluteolin, 6‐hydroxyluteolin and scutellarein and fourteen of their methyl ethers, and some 6,8‐dihydroxyapigenin and 6,8‐dihydroxyluteolin derivatives. Data for some forty two flavonols with extra 6‐ and/or 8‐hydroxylation, mostly 6‐hydroxykaempferol and quercetagetin derivatives, are also presented. The remaining compounds analysed include fourteen 5‐deoxyflavones, four 5‐methoxyflavones and five 5‐deoxyflavonols plus further 5‐hydroxylated flavones and flavonols without B‐ring oxidation or with 2′‐, 5′‐ or 6′‐hydroxylation. Copyright © 2003 John Wiley & Sons, Ltd.
Reactions of 1,2,5‐thiadiazole 1,1‐dioxide derivatives with nitrogenated nucleophiles. Part 1—Addition of amines and amides to 3,4‐diphenyl‐1,2,5‐thiadiazole 1,1‐dioxide
Authors: Caram José Alberto , Aimone Silvia Lucía , Mirífico María Virginia , Vasini Enrique Julio 
Published: March 2003

AbstractThe addition reactions of some amides and aromatic amines to a CN double bond of 3,4‐diphenyl‐1,2,5‐thiadiazole 1,1‐dioxide (1) were studied in aprotic solvent solutions [N,N‐dimethylformamide (DMF) and acetonitrile (MeCN)]. Equilibrium constants for the reactions of 1 with acetamide, 2‐fluoroacetamide, butyramide, benzamide, aniline and 3‐aminopyridine were measured using a previously reported cyclic voltammetric (CV) method. Aliphatic amines gave unstable solutions, probably owing to reactions of anionic species derived from 1. Other N nucleophiles tested (formamide, succinimide, thioacetamide and cyanamide) yielded different products that have not yet been characterized. DMF, N,N‐dimethylacetamide (DMA) and N‐methylacetamide did not react. The addition thiadiazoline produced in the reaction of acetamide with 1 was characterized by IR and 1H and 13C RMN NMR spectroscopy as a prototype compound. For this system, the equilibrium constant could also be measured by a standard UV–VIS method and was found to be in agreement with the value obtained by CV. The reaction of 1 with urea produced a bicyclic product, identified as 3a,6a‐diphenyltetrahydroimidazo[4,5‐c]‐1,2,5‐thiadiazol‐5‐one 2,2‐dioxide. Copyright © 2003 John Wiley & Sons, Ltd.
Algorithmic, geometric and graphs issues in wireless networks
Authors: Li Xiang‐Yang 
Published: March 2003

AbstractWe present an overview of the recent progress of applying computational geometry techniques to solve some questions, such as topology construction and broadcasting, in wireless ad hoc networks. Treating each wireless device as a node in a two‐dimensional plane, we model the wireless networks by unit disk graphs in which two nodes are connected if their Euclidean distance is no more than one. We first summarize the current status of constructing sparse spanners for unit disk graphs with various combinations of the following properties: bounded stretch factor, bounded node degree, planar, and bounded total edges weight (compared with the minimum spanning tree). Instead of constructing subgraphs by removing links, we then review the algorithms for constructing a sparse backbone (connected dominating set), that is, subgraph from the subset of nodes. We then review some efficient methods for broadcasting and multicasting with theoretic guaranteed performance. Copyright © 2003 John Wiley & Sons, Ltd.
Robust position‐based routing in wireless ad hoc networks with irregular transmission ranges
Authors: Barrière Lali , Fraigniaud Pierre , Narayanan Lata , Opatrny Jaroslav 
Published: March 2003

AbstractSeveral papers considered the problem of routing inad hocwireless networks using the positions of the mobile hosts. Perimeter routing1,2gives an algorithm that guarantees delivery of messages in such networks without the use of flooding of control packets. However, this protocol is likely to fail if the transmission ranges of the mobile hosts vary because of natural or man‐made obstacles. It may fail because either some connections are not considered, which effectively results in a disconnection of the network, or because some crossing connections are used, which could misdirect the message. In this paper, we describe a robust routing protocol, a variant of perimeter routing, which tolerates up to 40% of variation in the transmission ranges of the mobile hosts. More precisely, our protocol guarantees message delivery in a connected ad hoc wireless network without the use of message flooding whenever the ratio of the maximum transmission range to the minimum transmission range is at most √2. Copyright © 2003 John Wiley & Sons, Ltd.
Forward‐node‐set‐based broadcast in clustered mobile ad hoc networks
Authors: Wu Jie , Lou Wei 
Published: March 2003

AbstractA taxonomy of broadcast protocols in mobile ad hoc networks (MANETs) is given where protocols are classified into four groups: global, quasi‐global, quasi‐local, and local. The taxonomy also divides protocols based on the nature of algorithms: probabilistic and deterministic. The locality of maintenance also plays an important role in evaluating the protocol. An important objective in designing a broadcast protocol is to reduce broadcast redundancy to save scarce resources such as energy and bandwidth and to avoid the broadcast storm problem. This objective should be achieved without introducing excessive overhead and time delay, measured by sequential rounds of information exchanges. This is done by choosing a small forward node set that forms a connected dominating set (CDS) to carry out a broadcast process. In this paper, a clustered network model is proposed in which each node is a clusterhead in the clustered architecture. Clusterheads are connected by carefully selecting non‐clusterhead nodes locally at each clusterhead to connect clusterheads within the 2.5‐hop coverage, a novel notion proposed in this paper. Information of neighbor clusterheads is piggybacked on the broadcast packet to further reduce each forward node set. It is shown that this approach is quasi‐local with locality of maintenance. In addition, this approach has a constant approximation ratio to the minimum connected dominating set (MCDS) and generates a small forward node set in the average case. Comparisons are also done through simulation with representative protocols from each of the four groups of protocols based on the proposed taxonomy. We also simulate the proposed broadcast protocol in a dynamic network and analyze its performance. Copyright © 2003 John Wiley & Sons, Ltd.
Constructing optimal virtual cellular networks for nonuniformly distributed base stations
Authors: Fan Guangbin , Zhang Jingyuan 
Published: March 2003

AbstractIn a cellular network, the cell size varies from area to area, and the base stations may not be uniformly distributed. For example, in a well‐populated city, the cell size may be smaller than that in a rural area. It is harder to study the performance of a nonuniform cellular network. By imposing a virtual uniform cellular network on the nonuniform cellular network, some performance issues of the nonuniform network can be studied using the imposed virtual one. In the imposed virtual cellular network, each virtual cell cannot contain more than one base station. This paper has proposed algorithms to construct optimal virtual cellular networks for nonuniformly distributed base stations. The constructed virtual cellular networks are optimal in the sense that their corresponding uniform cell sizes reach the largest possible. The main advantage of constructing the optimal virtual cellular network is that the number of virtual cells required to cover the service area is minimized. The algorithm works for mesh networks as well as for honeycomb networks. On the basis of a novel concept, referred to as the projection locus, both kinds of optimal virtual cellular networks can be constructed in O(nlog n) time for n nonuniformly distributed base stations. Copyright © 2003 John Wiley & Sons, Ltd.
Admission control in TD‐CDMA networks
Authors: Mišić Jelena , Tang Yat‐Kwan , Mišić Vojislav B 
Published: March 2003

AbstractQuality of service (QoS) at the call or flow level in Time Division Code Division Multiple Access (TD‐CDMA) networks is an important topic that has not yet received much attention. In this paper, we propose a two‐tier admission and scheduling policy. The scheduling policy is comprised of two procedures, theUser Prioritizer Procedure(UPP) andPacket Allocator Procedure(PAP). TheUPPis used to determine the serving priority of users. The task ofPAPis to allocate packets to a time slot without violating the outage probability by invoking the tier 1 and tier 2 admission control. The tier 1 admission keeps the probability of violating the Bit Error Rate (BER) limits for new call arrivals below a specified threshold. The tier 1 admission allocates bandwidth for newly arrived calls on the basis of the outage probability threshold. The tier 2 admission reserves bandwidth in all surrounding sectors for future handoff events, which minimizes the probability that the handoff call from one sector will cause an outage condition in the target sector. The performance of the proposed policy is evaluated through simulations in the presence of voice and data traffic types. We show that the proposed scheme can provide satisfactory quality for a call or data flow during its lifetime. Copyright © 2003 John Wiley & Sons, Ltd.
The use of the simulated annealing algorithm for channel allocation in mobile computing
Authors: Zomaya Albert Y. , Smith Aidan , Seredynski Franciszek 
Published: March 2003

AbstractA mobile network is a distributed communication system that uses radio signals as its information medium. Since the popularization of mobile networks, the rate of connectivity has soared and the subsequent load on the networks is much more significant than original projections. Hence, resource management becomes an important issue when designing mobile networks. This work concentrates on the most important resource available to mobile networks, that is, the limited allocated bandwidth. With the given amount of bandwidth, the network is expected to meet a minimum quality of service, to provide subscribers with access to the network. As the network is based on a cellular design, the way to improve utilization of the bandwidth is to reuse frequencies or channels. However, this reuse comes at a cost. The allocation of reused channels must be subject to the avoidance of interference between allocated channels. This is known as the channel allocation problem (CAP). It will be shown that the problem can be formalized into an optimization problem, for which there are many solution methodologies. In order to meet the demands of solution quality and algorithm efficiency, the decision of which method to use is critical. Biologically inspired techniques provide effective search strategies that enable the discovery of near optimal solutions. They are ideal for problems with large and complex solution spaces such as the CAP. However, the performance of these algorithms in terms of solution quality and efficiency varies greatly with the problems to which they are applied. Copyright © 2003 John Wiley & Sons, Ltd.