bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of C‐terminal domain phosphorylation in RNA polymerase II transcription through the nucleosome
Authors: Liu Y. V. , Clark D. J. , Tchernajenko V. , Dahmus M. E. , Studitsky V. M. 
Published: March 2003

AbstractEnd‐initiated transcription of a 256 base‐pair (bp) template containing a single uniquely positioned nucleosome by yeast and calf thymus nuclear RNA polymerases II (pol II) was analyzed in vitro. The nucleosome‐specific pausing pattern is similar to the pattern observed in the case of transcription of the same nucleosome by yeast RNA polymerase III. However, the pausing pattern is clearly different from the patterns observed previously during transcription by promoter‐initiated and assembled pol II. This suggests that end‐initiated and promoter‐initiated RNA polymerases differ in the way they progress through the nucleosome. The rates of transcription through the nucleosome by pol II are significantly lower than the rates observed in the case of SP6 polymerase and RNA polymerase III. Using calf thymus pol II, we have investigated the possibility that phosphorylation of the C‐terminal domain (CTD) facilitates transcription through the nucleosome. The rates of transcription through the nucleosome by phosphorylated (IIO) and nonphosphorylated (IIA) forms of calf thymus pol II are very similar. This suggests that CTD phosphorylation is not sufficient to facilitate transcription through the nucleosome by end‐initiated pol II. © 2003 Wiley Periodicals, Inc. Biopolymers 68: 528–538, 2003
Structure and dynamics of nucleosomal DNA
Authors: Muthurajan Uma M. , Park Young‐Jun , Edayathumangalam R. S. , Suto Robert K. , Chakravarthy Srinivas , Dyer Pamela N. , Luger Karolin 
Published: March 2003

AbstractThe last five years have seen exciting advances in our understanding of the structure of the nucleosome core particle, the basic repeating unit in all eukaryotic chromatin. A picture emerges in which nucleosomal DNA, while distorted and compacted fivefold by tight interactions with the histone octamer core, is at the same time highly dynamic and adaptable. Here, we summarize the salient features from recent structural studies of nucleosome core particles (both published and unpublished) that concern the structure and dynamics of nucleosomal DNA, and the nature of protein–DNA interactions. Current mechanisms for chromatin remodeling and nucleosome sliding are discussed in light of new structural evidence. Finally, techniques to study nucleosome stability and ultimately dynamics are introduced. © 2003 Wiley Periodicals, Inc. Biopolymers 68: 547–556, 2003
Mechanisms for nucleosome mobilization
Authors: Flaus Andrew , Owen‐Hughes Tom 
Published: March 2003

AbstractNucleosomes are the ubiquitous and fundamental packaging for eukaryotic genomes, and are the substrate for many processes in the nucleus. Nucleosomes are not static entities but can readily be moved by thermal energy and ATP‐dependent chromatin remodeling complexes in a process known as sliding or shifting. We summarize from a mechanical perspective the twist defect and bulge diffusion mechanisms proposed as the most likely pathway for nucleosome mobilization. We then consider the elastic properties of DNA and how this affects the potential for each mechanism, concentrating on kinetic aspects of twist diffusion and possible planar bulge sizes and summarize the experimental evidence reflecting on each. Either, or both, mechanisms could occur, and careful experimentation focusing on their uniquely distinguishing features will be required to determine their relative contributions to chromatin dynamics. © 2003 Wiley Periodicals, Inc. Biopolymers 68: 563–578, 2003
Comparison of the conformation and electrostatic surface properties of magainin peptides bound to sodium dodecyl sulfate and dodecylphosphocholine micelles
Authors: Hicks Rickey P. , Mones Erin , Kim Hanah , Koser Brandon W. , Nichols Daniel A. , Bhattacharjee Apurba K. 
Published: March 2003

AbstractThe role played by noncovalent interactions in inducing a stable secondary structure onto the sodium dodecyl sulfate (SDS) and dodecylphosphocholine (DPC) micelle‐bound conformations of (Ala8,13,18)magainin 2 amide and the DPC micelle bound conformation of magainin 1 were determined. Two‐dimensional NMR and molecular modeling investigations indicated that (Ala8,13,18)magainin 2 amide bound to DPC micelles adopts a α‐helical secondary structure involving residues 2–16. The four C‐terminal residues converge to a lose β‐turn structure. (Ala8,13,18)magainin 2 amide bound to SDS miscelles adopts a α‐helical secondary structure involving residues 7–18. The C‐ and N‐terminal residues exhibited a great deal of conformational flexibility. Magainin 1 bound to DPC micelles adopts a α‐helical secondary structure involving residues 4–19. The C‐terminal residues converge to a lose β‐turn structure. The results of this investigation indicate hydrophobic interactions are the major contributors to stabilizing the induced helical structure of the micelle‐bound peptides. Electrostatic interactions between the polar head groups of the micelle and the cationic side chains of the peptides define the positions along the peptide backbone where the helical structures begin and end. Published 2003 Wiley Periodicals, Inc. Biopolymers 68: 459–470, 2003
Conformational analysis of endomorphin‐2 by molecular dynamics methods
Authors: Leitgeb Balázs , Ötvös Ferenc , Tóth Géza 
Published: March 2003

AbstractEndomorphin‐2 (EM2, H–Tyr–Pro–Phe–Phe–NH2) is a highly potent and selective μ‐opioid receptor agonist. A conformational analysis of EM2 was carried out by simulated annealing (SA) and molecular dynamics (MD) methods. Molecular modeling was conducted on both neutral (N‐terminal NH2) and charged (N‐terminal NH) molecules. Based on the results of NMR investigations showing an equilibrium mixture of cis and trans Tyr1–Pro2 peptide bonds for EM2 in solution, simulations were performed with restrained cis‐Pro and trans‐Pro peptide bonds, too. A separate SA study with unrestrained Pro peptide bonds was also conducted. Preferred conformational states are presented in Ramachandran plots. The g(+), g(‐), and trans populations of the aromatic amino acid residue side chains were determined in χ1 space. The distances between the N‐terminal N atom and the other backbone N and O atoms, and the distances between the centers of the aromatic rings and the Pro2 ring, were determined. The energy distribution of the structures obtained by SA was calculated. The preferred secondary structural elements were different kinds of β‐turns, an inverse γ‐turn located in the N‐terminal region, and regular and inverse γ‐turns located in the C‐terminal region. These turns were stabilized by intramolecular H‐bonds and bifurcated H‐bonds. © 2003 Wiley Periodicals, Inc. Biopolymers 68: 497–511, 2003
Experimental studies of direction of arrivals using a smart antenna testbed in wireless communication systems
Authors: Jeng Shiann‐Shiun , Lin Hsin‐Piao , Tsung Chen‐Wan 
Published: March 2003

AbstractThis paper presents some preliminary results from experimental studies on space‐division‐multiple‐access (SDMA) for wireless communications. A smart antenna system utilizing direction‐of‐arrival (DOA)‐based beamforming techniques can enhance signal quality by reducing co‐channel interference from mobiles located at angles spatially distinct from the base station. Adopting both smart uplink and downlink beamforming, a communication system with an antenna array can increase the cell coverage of a base station and significantly boost capacity compared with conventional antenna systems. However, successful implementation of DOA‐based beamforming techniques depends on the DOA characteristics. This paper presented the feasibility of direction finding and DOA variation with respect to frequency. Furthermore, the angle spread was studied for selected environments. The results demonstrate the feasibility of applying proposed smart antenna system utilizing DOA‐based beamforming algorithm for increasing channel capacity and improving system performance in frequency‐division‐duplex (FDD) wireless communication systems. Copyright © 2003 John Wiley & Sons, Ltd.
Identification and characterization of Grainyhead‐like epithelial transactivator (GET‐1), a novel mammalian Grainyhead‐like factor
Authors: Kudryavtseva Elena I. , Sugihara Tod M. , Wang Ning , Lasso Ronan J. , Gudnason Janus F. , Lipkin Steven M. , Andersen Bogi 
Published: March 2003

AbstractLMO‐4 is an LIM‐only factor that is highly expressed in many epithelial cells, including those of the epidermis and hair follicles. Because LMOs may function by interacting with DNA‐binding proteins, we have used the yeast two‐hybrid system to screen mouse skin libraries for LMO‐4–interacting DNA‐binding proteins. In this screen, we isolated a novel LMO‐4–interacting factor highly related to the Drosophila gene Grainyhead. Grainyhead is epidermally expressed and carries out important functions in cuticular formation in the fly embryo. With the identification of this novel mammalian Grainyhead‐like gene, referred to as Grainyhead‐like epithelial transactivator 1 (GET‐1), the known members of the mammalian Grainyhead‐like gene family are extended to six, falling into two classes based on sequence homology. Of interest, the expression pattern of GET‐1 is similar to that of Drosophila Grainyhead with highest expression in the somatic ectoderm/epidermis, but GET‐1 is additionally expressed in epithelial cells of gastrointestinal, genitourinary, and respiratory tracks. The GET‐1 protein localizes to the nucleus and binds to at least one Grainyhead DNA‐binding site. The GET‐1 DNA‐binding domain maps to a region containing homology to the Drosophila Grainyhead DNA‐binding domain. GET‐1 homodimerizes in solution by means of a short C‐terminally located domain that is homologous to other Grainyhead‐like genes. A short domain located between amino acids 100 and 190, which bears no homology to known transactivation domains, is sufficient to confer transactivation to the heterologous GAL4 DNA‐binding domain. In addition, GET‐1 appears to contain repression domains consistent with the observation that Grainyhead and other mammalian Grainyhead‐like genes can act both as activators and repressors. These data suggest that GET‐1 is a transcriptional regulator that may perform important functions in epithelial tissues of mammals. Developmental Dynamics 226:604–617, 2003. © 2003 Wiley‐Liss, Inc.
Alternative splicing of papilin and the diversity of Drosophila extracellular matrix during embryonic morphogenesis
Authors: Kramerova Irina A. , Kramerov Andrei A. , Fessler John H. 
Published: March 2003

AbstractPapilins are extracellular matrix proteins that share a particular, common order of types of protein domains. They occur widely, from nematodes to man, and can differ in the number of repeats of a given type of domain. Protein variety is increased by differential splicing of pre‐mRNA. We report that Drosophila, which has a compact genome, expresses three splice variants of papilin during embryogenesis in developmentally defined patterns. These isoforms have different numbers of Kunitz and IgC2 domains. The papilin isoforms are expressed in specific cell types and contribute to different extracellular matrices in gastrulation folds, early mesoderm, heart formation, basement membranes, and elaboration of the excorporeal peritrophic membrane that lines the gut. This finding indicates an unexpectedly broad spectrum of different pericellular matrices in Drosophila embryos. Such papilin‐containing matrices have developmental as well as functional significance, as we previously showed that both suppression of papilin synthesis and ectopic overexpression lethally disrupt organogenesis. Developmental Dynamics 226:634–642, 2003. © 2003 Wiley‐Liss, Inc.
Apparent mitochondrial asymmetry in Xenopus eggs
Authors: Volodina Natalia , Denegre James M. , Mowry Kimberly L. 
Published: March 2003

AbstractCell polarity is manifest along the animal/vegetal axis in eggs of the frog, Xenopus laevis. Along this axis, maternal cytoplasmic components are asymmetrically distributed and are thought to underlie specification of distinct cell fates. To ascertain the molecular identities of such cytoplasmic components, we have used a monoclonal antibody that specifically stains the vegetal hemisphere of Xenopus eggs. The antigenic protein Vp67 (vegetal protein of 67 kDa) was identified through purification and cloning as a Xenopus homolog of the mitochondrial protein dihydrolipoamide acetyltransferase, a component of the pyruvate dehydrogenase complex. The identification of Vp67 as a mitochondrial protein could indicate that populations of mitochondria are asymmetrically distributed in Xenopus eggs. Developmental Dynamics 226:654–662, © 2003 Wiley‐Liss, Inc.
Spontaneous mutation in mice provides new insight into the genetic mechanisms that pattern the seminal vesicles and prostate gland
Authors: Marker Paul C. , Dahiya Rajvir , Cunha Gerald R. 
Published: March 2003

AbstractThe seminal vesicles and prostate gland are anatomically adjacent male sex‐accessory glands. Although they arise from different embryonic precursor structures and express distinct sets of secretory proteins, these organs share common features in their developmental biology. A key shared developmental feature is the elaboration of complex secretory epithelia with tremendous surface area from simple precursor structures with juxtaposed epithelial and mesenchymal cells. In this study, new insight into the nature of the biological processes that underlie glandular morphogenesis is achieved by analyzing the phenotypes present in mice that harbor a spontaneous mutation, seminal vesicle shape (svs), previously identified for causing altered seminal vesicle morphology in adults. An examination of seminal vesicle development in svs mice provides the first evidence that the concurrent processes of epithelial branching and epithelial infolding are distinct processes under separate genetic control. It also provides the first direct evidence that the thickness and topology of the smooth muscle layer in the seminal vesicles are determined by interaction with the glandular epithelium during the branching process. In addition, the seminal vesicle phenotype in svs mice is shown to phenocopy the morphologic form present in certain other mammals such as the guinea pig, raising the possibility that the svs mutation is the sort of variant that arises during evolution. By also including an investigation of the prostate gland, this study also identifies previously unrecognized phenotypes in svs prostates, including increased gland size and dramatically reduced levels of branching morphogenesis. Finally, this study advances the goal of identifying the svs gene by mapping the svs mutation relative to known molecular markers and testing Fgfr2 as a candidate gene. The finding that the svs mutation maps to a genomic region syntenic to a region frequently deleted in human prostate tumors, together with the prostatic phenotype present in svs mice, further raises the interesting possibility that the svs mutation will identify a candidate prostate tumor suppressor gene. Developmental Dynamics 226:643–653, 2003. © 2003 Wiley‐Liss, Inc.
Origin of directionality in the fish stripe pattern
Authors: Shoji Hiroto , Mochizuki Atsushi , Iwasa Yoh , Hirata Masashi , Watanabe Tsuyoshi , Hioki Syozo , Kondo Shigeru 
Published: March 2003

AbstractThe formation of stripe patterns in animal skin has been explained by the reaction‐diffusion (RD) system, a hypothetical chemical reaction proposed by A. Turing. Although animal stripes usually have directionality, the RD model alone cannot explain how the direction is specified. To investigate the mechanism regulating the direction of stripes, we studied stripe pattern formation in two species of Genicanthus during sexual conversion. These species share almost identical morphologic properties, except for their stripe direction. In both species, spots transiently arise at random positions and then combine and rearrange to form directional stripes. Computational analysis has shown that diffusion anisotropy is very effective at specifying the direction of stripes formed by the RD system. Model simulations reproduce the transient dynamics of directional pattern formation observed in fish as well as the resulting stripes. In cases where the magnitude and direction of diffusion anisotropy of the substances are identical, the resulting stripes are not directional. However, if they differ, stripes become directional. As only a small difference in anisotropy is required for this effect, any kind of structure with directional conformation might cause a marked change in stripe direction. Scales are the most likely candidate structure for generating anisotropic interactions in skin. Developmental Dynamics 226:627–633, 2003. © 2003 Wiley‐Liss, Inc.
Hes1 but not Hes5 regulates an astrocyte versus oligodendrocyte fate choice in glial restricted precursors
Authors: Wu Yuanyuan , Liu Ying , Levine Edward M. , Rao Mahendra S. 
Published: March 2003

AbstractTo determine the role of Hes genes in the differentiation process of neuroepithelial (NEP) cells to glial restricted precursor cells (GRPs) and subsequently GRPs to oligodendrocytes and astrocytes, we have examined the effects of Hes1 and Hes5 on glial differentiation. We find that both Hes1 and Hes5 are expressed by GRPs and that Hes1 can drive GRPs to an astrocyte cell fate at the expense of oligodendrocyte differentiation. Overexpression of Hes1 in GRPs results in the up‐regulation of the astrocyte markers glial fibrillary acidic protein and CD44 and the down‐regulation of oligodendrocyte markers myelin proteolipid protein/DM20, GalC, and CNPase. Transcription factors involved in oligodendrocyte differentiation, such as Nkx2.2, Olig1, and Mash1, are also down‐regulated in Hes1‐overexpressing cells. The effect of Hes1 on gliogenesis is stage‐specific as Hes1 does not direct NEP cells to an astrocytic fate. In contrast to Hes1, Hes5 does not promote astrocyte differentiation. Instead, it inhibits both astrocyte and oligodendrocyte differentiation. Overexpression of Notch1 has an effect on gliogenesis similar to that of Hes1 and the mRNA levels of Hes1 are up‐regulated in cells overexpressing Notch1, suggesting that Notch1 could be an upstream activator of Hes1. Developmental Dynamics 675–689, 2003. © 2003 Wiley‐Liss, Inc.
Appearance of neurons and glia with respect to the wavefront during colonization of the avian gut by neural crest cells
Authors: Connor Paul J. , Focke Paul J. , Noden Drew M. , Epstein Miles L. 
Published: March 2003

AbstractThe original article to which this Erratum refers was published in Developmental Dynamics 226:91–98Developmental Dynamics(2000) 226(1) 91–98
Performance evaluation of TCP throughput with consideration of lower‐layer protocols for wireless cellular networks
Authors: Miyoshi Masahiro , Sugano Masashi , Murata Masayuki 
Published: March 2003

AbstractWe propose an analytical method for performance evaluation of TCP in a wireless cellular network, where the slotted ALOHA protocol is adopted as the data link layer. By using our method, we show that improving throughput at the data link layer level does not necessarily lead to TCP throughput improvement. Furthermore, we evaluate TCP throughput by considering communication errors on the radio link. When we introduce FEC as an error correcting method, we show that TCP throughput can be improved by selecting an appropriate error correction code with careful consideration of the overhead and the error correction capability according to the quality of the wireless channel. © 2003 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 86(8): 29–39, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecja.10086
Development of tabular broadband antenna for UHF‐TV
Authors: Okano Yoshinobu 
Published: March 2003

AbstractA tabular loop antenna is proposed that can be matched to the characteristic impedance of a coaxial cable without using complex parasitic elements or expensive matching elements while maintaining the broadband character and superior gain of the loop antenna. Specifically, modification of the aperture shape inside the loop is attempted without changing the external shape. In this way, the control of the input impedance becomes possible and the bandwidth for VSWR ≤ 2 can reach about 40% at the center frequency of 620 MHz for UHF‐band TV. An antenna with a unidirectional radiation pattern with a reflector was fabricated for trial and was studied both by experiments and by FDTD analysis. It was confirmed that the bandwidth for VSWR ≤ 2 reaches about 50% at 620 MHz. Further, with regard to the dynamic gain, a stable gain of 7.6 to 8.2 dBi was attained for the entire UHF band. This antenna will be useful for ground wave digital broadcasting. © 2003 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 86(8): 1–8, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecja.10112
A method of SCR improvement with a two‐dimensional weighted moving average filter
Authors: Kouya Satoshi , Miwa Susumu 
Published: March 2003

AbstractThere have been different methods to suppress radar clutter depending on its amplitude distribution. This paper describes a two‐dimensional weighted moving average filter and a two‐dimensional moving filter for clutter having a k‐distribution, both with weighted samples of a reflected signal from an illuminated surface. A genetic algorithm is used for the weighting, since its optimum value is obtained in a relatively short time. To simulate various field conditions, two kinds of data were used: data of reflected waves from objects in the green belt of an airport, and composite data of reflected waves from objects in clear weather (no clutter) and reflected waves from a field on a rainy day. The two‐dimensional weighted moving average improves the signal‐to‐clutter ratio significantly: by 0.5 to 2.3 dB compared with a two‐dimensional moving average without weighting; and by 0.9 to 3.7 dB compared with no averaging treatment. © 2003 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 86(8): 58–67, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecja.1172
A transmission mode detector for OFDM systems
Authors: Nogami Hiroshi , Tsuruga Sadao , Morinaga Norihiko 
Published: March 2003

AbstractDigital terrestrial TV broadcasting systems employing orthogonal frequency division multiplexing (OFDM), such as DVB‐T in Europe, accept more than one transmission mode in terms of the carrier spacing (or the effective symbol duration) and the guard interval. When the transmission mode is not uniquely fixed and previously unknown, a receiver set has to detect the transmission mode so as to demodulate the OFDM signal properly.In this paper, we propose a detection scheme for the transmission mode, where the transmission mode can be detected for a relatively short observation time with no demodulation of the OFDM signal. The proposed technique uses the wide sense cyclostationarity of the OFDM signal, that is, the averaged product (correlation) of the OFDM signal and itself delayed by the time of the effective symbol duration is a periodical signal with a period of the transmission symbol duration. Then the proposed technique detects the transmission mode by discrimination of the period through what we will call the spectrum emphasis filters, which basically consist of IIR filters.Computer simulation has been conducted to evaluate the detection performance of the proposed technique for the OFDM system which accepts eight transmission modes (1/4, 1/8, 1/16, and 1/32 guard intervals for both the 2k‐FFT and 8k‐FFT systems). The results show that the detection error rate of 1 × 10−2 or less is attained around the carrier‐to‐noise power ratio of 3 dB in the additive white Gaussian noise channel with the observation time being only four times the maximum transmission symbol duration among the eight modes. © 2003 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 86(8): 79–94, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecja.1174