bluuebunny/crossref_metadata_2025_split huggingface dataset:
Specific arrest of spermatogenesis caused by apoptotic cell death in transgenic mice
Authors: Suzuki Misao , Abe Koichiro , Yoshinaga Kazuya , Obinata Masuo , Furusawa Mitsuru , Abe Kuniya 
Published: November 2003

Background:
The c‐myc protooncogene has been implicated in the control of cell proliferation, differentiation and/or apoptosis in various cellular systems. However, the role of c‐myc in germ cell lineage is largely unknown.
Results:
We have produced transgenic mouse lines carrying the rat c‐myc protooncogene under the control of human metallothionein promoter (hMT‐c‐myc). It was found that the male transgenic mice were sterile. In contrast, all of the female transgenic mice were completely fertile and transmitted the transgene to the next generation. However, male transgenic mice from the female transgenic founders were also found to be sterile. This sterility was due to a defect in spermatogenic cell differentiation, since virtually no sperm were seen within the seminiferous tubules or the cauda epididymis. Histological examination revealed that germ cell death occurred approximately 7 days after birth and, consequently, spermatogenesis was arrested at an early stage in meiotic division in the transgenic mice. Moreover, this germ cell death was found to be caused by apoptosis.
Conclusion:
We conclude that an excess level of c‐myc expression in differentiating spermatogenic cells is responsible for the apoptotic death of germ cell, and that a decrease in c‐myc level would be an obligatory step for the completion of normal spermatogenesis.
Inhibition of ligand induced promoter occupancy in vivo by a dominant negative RXR
Authors: Blanco Jorge C.G. , Dey Anup , Leid Mark , Minucci Saverio , Park Byung‐Kiu , Jurutka Peter W. , Haussler Mark R. , Ozato Keiko 
Published: November 2003

Background: Retinoid X receptors (RXRs) heterodimerize with other nuclear hormone receptors and control ligand mediated transcription. To address how RXRs function as heterodimers, we investigated activities of truncated RXRα and RXRβ that lack ≈ 20 conserved C‐terminal amino acids.Results: The truncated RXRs formed heterodimers and bound to respective DNA elements in vitro. By transient reporter assays we found that these RXRs act as dominant negative receptors and inhibit ligand dependent transcription by the retinoic acid receptor (RAR) and vitamin D receptor. P19 embryonal carcinoma cells stably expressing the truncated RXRβ (termed ΔC2) were deficient in activating the endogenous RARβ gene and an RA responsive reporter. To study the dominant negative activity of ΔC2 further, genomic footprinting analysis was performed for the RARβ2 promoter. In control P19 clones, the RA responsive element (RARE) and other elements in the promoter were protected after RA treatment. However, in ΔC2 clones RA‐induced protection was markedly inhibited at all elements.Conclusions: These results indicate that the C‐terminal region of RXR is required for full RARE occupancy in vivo, a RA dependent process that leads to the recruitment of other factors to the promoter and the subsequent transcriptional activation. Thus, RXRs play an integral role in ligand dependent transcription.
Communication between homologous chromosomes: genetic alterations at a nuclease‐hypersensitive site can alter mitotic chromatin structure at that site both in cis and in trans
Authors: Keeney Scott , Kleckner Nancy 
Published: November 2003

Background:  In vegetatively growing diploid strains of the yeast Saccharomyces cerevisiae, homologous chromosomes appear to be paired via multiple interstitial interactions, likely as a regular feature of the diploid lifestyle. We have previously suggested that this pairing is guided by direct physical interactions between intact DNA duplexes in nuclease‐hypersensitive regions and that homology is sensed directly at the DNA level. Results:  As a first test of this idea we have examined the level of DNase I sensitivity at a prominent nuclease‐hypersensitive site in mitotic chromatin in strains that are either homozygous or heterozygous for a pair of alleles at this site. We find that the degree of nuclease sensitivity at this site on a given (maternal or paternal) chromosome can vary depending upon whether the homologue carries the same allele or the different allele. The data are suggestive that nuclease sensitivity is higher in the former case than in the latter, as though nuclease hypersensitivity might be increased when the two alleles match as compared to when they do not. Conclusions:  Formally, these observations suggest that homologous chromosomes can communicate via a mechanism that senses the status of the assayed nuclease‐hypersensitive site with resultant changes in chromatin structure at that site. The observed pattern of effects is fully compatible with direct physical interactions between homologues at nuclease‐hypersensitive regions, but alternative scenarios also can be envisioned. Since DNase I hypersensitive sites occur in many important regions of chromosomes, homology‐dependent interactions involving such regions could potentially affect diverse processes including gene expression (e.g. transvection), chromosome organization, domain structure, and/or DNA replication patterns.
The 12/23 rule is enforced at the cleavage step of V(D)J recombination in vivo
Authors: Bockheim Steen Sharri , Gomelsky Larissa , Roth David B. 
Published: November 2003

Background: V(D)J recombination is initiated by the introduction of double‐stranded breaks (DSB) adjacent to recombination signal sequences (RSS). Each RSS contains a conserved heptamer and a conserved nonamer element separated by a 12 or 23 nucleotide spacer. In vivo, efficient recombination requires one RSS of each spacer length, although it has been unclear whether this ‘12/23 rule’ regulates cleavage, joining, or both. Results: We describe a novel system that permits semiquantitative detection of DSB at RSS derived from V(D)J recombination substrates transfected into cultured cells. This approach provides a powerful new tool for analysis of the cleavage and joining steps of V(D)J recombination in vivo. In this study, substrates containing either a consensus 12/23 RSS pair or various deviations from the consensus were used to investigate the requirements for cleavage. The results show that both a 12‐spacer and a 23‐spacer RSS are required for efficient cleavage. Truncated RAG‐1 and RAG‐2 proteins, while capable of cleaving at isolated RSS in cell‐free systems, also require a 12/23 RSS pair for efficient cleavage in vivo. Conclusions: These results suggest that the 12/23 rule is enforced at or prior to cleavage and support a synapsis model for V(D)J recombination. Detection of rare cleavage events in substrates containing a single RSS or a pair of RSS with the same spacer length provide evidence for an inefficient, single RSS cleavage pathway that may contribute to aberrant V(D)J rearrangements in vivo.
Escherichia coli RNase HI inhibits murine leukaemia virus reverse transcription in vitro and yeast retrotransposon Ty1 transposition in vivo
Authors: Ma Wu‐Po , Crouch Robert J. 
Published: November 2003

Background: Reverse transcription, which converts an RNA genome into double‐stranded DNA, requires both the polymerase and RNase H activities of reverse transcriptase (RT). In vitro, poorly processive RT dissociates from partially copied RNA–DNA hybrids, that are usually extended by a second RT molecule. Despite similar structures, RNase HI of Escherichia coli can degrade RNA–DNA hybrids that are resistant to RNase H of RT. E. coli RNase HI is used to determine the accessibility to and requirement for RNA–DNA hybrids in reverse transcription in vivo and in vitro. Results: In the presence of E. coli RNase HI, reverse transcription yields incomplete cDNA molecules due to degradation of RNA–DNA hybrids. Delivery of E. coli RNase HI to Ty1 particles via fusion to the capsid protein can reduce retrotransposition by more than 99%, also indicating inhibition of DNA synthesis in vivo. Conclusion: Inhibition of both reverse transcription in vitro and retrotransposition in vivo by E. coli RNase HI indicates that the poor processivity of RT exposes RNA–DNA hybrids critical for reverse transcription to degradation. Targeting a cellular RNase H to HIV may help define the site(s) of RNA–DNA hybrids that are susceptible to non‐retroviral RNase H and may be useful for gene therapy to inhibit retroviral replication.
The highly conserved DAD1 protein involved in apoptosis is required for N‐linked glycosylation
Authors: Makishima Tomoko , Nakashima Torahiko , Nagata‐Kuno Kazue , Fukushima Kohtaro , Iida Hiroshi , Sakaguchi Masao , Ikehara Yukio , Komiyama Sohtaro , Nishimoto Takeharu 
Published: November 2003

Background: The tsBN7 cell line is one of the temperature‐sensitive mutants for cell proliferation which have been isolated from the BHK21 cell line derived from the golden hamster. It has a mutation in the DAD1 gene encoding a 12.5 kDa highly conserved protein through evolution, and enters apoptosis at the restrictive temperature due to this mutation. Results: DAD1 was recovered in light membrane fractions after differential centrifugation. It could not be released from the membrane, even by carbonate extraction, without a detergent. Upon digestion with proteinase K, both N and C terminal portions—but not the middle portions of DAD1—were released from the membrane. Thus, DAD1 appears to be an integral membrane protein in which both termini are located in the cytosol. DAD1 was localized in the endoplasmic reticulum. In accordance with a similarity to the yeast protein Ost2p, which is a subunit of the oligosaccharyltransferase, at the restrictive temperature, loss of DAD1 function caused a defect of N‐linked glycosylation in tsBN7 cells resulting in apoptosis. However, tunicamycin, which is known to inhibit N‐linked glycosylation did not induce apoptosis in either tsBN7 or BHK21 cells. Conclusion: tsBN7 cells have a defect in N‐linked glycosylation caused by the loss of DAD1.
Gin4 of S. cerevisiae is a bud neck protein that interacts with the Cdc28 complex
Authors: Okuzaki Daisuke , Tanaka Seiji , Kanazawa Hiroshi , Nojima Hiroshi 
Published: November 2003

Background:A number of proteins make up the Cdc28 complex in Saccharomyces cerevisiae, and regulate CDK activity. The cell cycle regulator Nik1 (Hsl1) is a protein kinase that interacts with the Cdc28 complex. The growth inhibitor Gin4 is structurally similar to Nik1 and may play a redundant role in the regulation of the cell cycle. We investigated the functions of Gin4 with respect to those of Nik1.Results: GIN4 was not essential for growth, and cells deficient in the GIN4 gene displayed no obvious defects in cell cycle regulation. The Δgin4 Δnik1 strain was temperature sensitive and showed an abnormal cell shape and FACS profile at permissive temperatures. GFP‐fused Gin4 was localized at the bud‐neck from late G1 to the M phase. Overproduction of the C‐terminal portion of Gin4 was toxic for cell growth, and this domain was required for the bud‐neck localization of Gin4‐GFP. High copy expression of Gin4‐GFP disturbed the bud‐neck localization of Gin4 in the abnormally elongated cells. Cytokinesis was defective in the Δgin4 cdc28 double mutants. The GST‐Gin4 fusion protein physically associates with the Cdc28 complex.Conclusions:Gin4 is a bud‐neck protein. GIN4 and NIK1 have distinct but partially overlapping functions. The major function of GIN4 is to ensure proper mitotic progression and cytokinesis.
A nested set of C‐terminal deletions of the α subunit of Escherichia coli RNA polymerase define regions concerned with assembly, proteolysis, stabilization and transcriptional activation in vivo
Authors: Zou Chao , Thomas Mark S. , Keen Jennifer , Glass Robert E. 
Published: November 2003

Background
: The α subunit of eubacterial RNA polymerase comprises an N‐terminal assembly domain and a mobile C‐terminal domain which provides an activation contact site for class I transcription activators. One particular C‐terminal α mutant, rpoA341, impairs the response of Escherichia coli RNA polymerase to several activators, including MelR.
Results
: The in vivo properties of a set of C‐terminally truncated α variants were investigated. Derivatives of 230 amino acids or longer were assembled into functional RNA polymerase. However, derivatives greater than 271 residues in length were sensitised to proteolysis near K271. Deletion of only 13 C‐terminal amino acids impaired the response to CRP at a class I promoter whereas the complete removal of the α C‐terminal domain did not prevent complementation of MelR‐dependent PmelAB activity in the rpoA341 mutant.
Conclusions
: Our results refine the C‐terminal limit of the α assembly domain to between residues 221 and 230. The 13 extreme C‐terminal amino acids are exposed in the holoenzyme and participate in the protection of an otherwise proteolytically sensitive bond near K271. Their presence is also essential for transcription activation at class I CRP‐dependent promoters. The rpoA341‐mediated substitution, K271E, does not define an activation contact site for MelR.
Expression and distribution of ZO‐3, a tight junction MAGUK protein, in mouse tissues
Authors: Inoko Akihito , Itoh Masahiko , Tamura Atsushi , Matsuda Miho , Furuse Mikio , Tsukita Shoichiro 
Published: November 2003

AbstractBackground:  Three related MAGUK proteins, ZO‐1, ZO‐2 and ZO‐3, are concentrated at the cytoplasmic surface of tight junctions. However, in contrast to ZO‐1/ZO‐2, our knowledge of the expression and distribution of ZO‐3 is still fragmentary, partly due to a lack of antibodies that specifically distinguish ZO‐3 from ZO‐1 and ZO‐2.Results:  We generated one pAb and one mAb that specifically recognized ZO‐3 on Western blotting. The immunofluorescence signals obtained with these antibodies completely disappeared from ZO‐1/ZO‐2‐positive tight junctions in the liver of ZO‐3‐deficient mice, indicating that the antibodies can be used to localize ZO‐3 in various tissues by immunofluorescence microscopy. Immunofluorescence microscopy with these antibodies revealed that ZO‐3 was concentrated at tight junctions in various types of epithelium, but not in endothelium or at cadherin‐based cell‐cell adhesion sites (spot adherens junctions of fibroblasts and intercalated discs of cardiac muscle cells), where ZO‐1 and ZO‐2 are concentrated.Conclusions:  We conclude that ZO‐3 is expressed in a more epithelium‐specific manner than ZO‐1 and ZO‐2. These observations provide for a better understanding of the functions of tight junction‐associated MAGUKs.
New digital linear filters for Hankel J0 and J1 transforms
Authors: Guptasarma D. , Singh B. 
Published: November 2003

The numerical evaluation of certain integral transforms is required for the interpretation of some geophysical exploration data. Digital linear filter operators are widely used for carrying out such numerical integration.It is known that the method of Wiener–Hopf minimization of the error can be used to design very efficient, short digital linear filter operators for this purpose. We have found that, with appropriate modifications, this method can also be used to design longer filters. Two filters for the Hankel J0 transform (61‐point and 120‐point operators), and two for the Hankel J1 transform (47‐point and 140‐point operators) have been designed. For these transforms, the new filters give much lower errors compared to all other known filters of comparable, or somewhat longer, size. The new filter operators and some results of comparative performance tests with known integral transforms are presented.These filters would find widespread application in many numerical evaluation problems in geophysics.
Effects of anelasticity on reflection and transmission coefficients
Authors: Nechtschein S. , Hron F. 
Published: November 2003

It is known that the reflection and transmission coefficients used in the zeroth order approximation of asymptotic ray theory (ART) are identical to those obtained for the plane wave impinging on a plane interface separating two perfectly elastic half‐spaces. We have used ART to compute reflection and transmission coefficients for two viscoelastic media separated by a plane interface. Our method is different from the plane‐wave approach because the ART approach requires only a local application of the boundary conditions both for the eikonal and the ray amplitudes.Several types of viscoelastic media were studied. For a given model, the elastic case was emulated by setting all the quality factors Q equal to each other. Several anelastic cases were computed by keeping the same velocities and densities while changing the Qs. The quality factor is a relatively difficult parameter to measure exactly. Hence elastic coefficients are used in most synthetic seismogram computations, and the quality factors are chosen from experimental measurements or simply estimated.From these computations, amplitude and phase differences between elastic coefficients and coefficients for dissipative media are observed in some cases. These differences show the importance of knowing the exact values of Q. Incorrect Q values can lead to unrealistic moduli and to noticeable phase differences of these viscoelastic coefficients.
A hexagonal sampling grid for 3D recording and processing of 3D seismic data
Authors: Bardan Virgil 
Published: November 2003

3D seismic data are usually recorded and processed on rectangular grids, for which sampling requirements are generally derived from the usual 1D viewpoint. For a 3D data set, the band region (the region of the Fourier space in which the amplitude spectrum is not zero) can be approximated by a domain bounded by two cones. Considering the particular shape of this band region we can use the 3D sampling viewpoint, which leads to weaker sampling requirements than does the 1D viewpoint; i.e. fewer sample points are needed to represent data with the same degree of accuracy. The 3D sampling viewpoint considers regular nonrectangular sampling grids.The recording and processing of 3D seismic data on a hexagonal sampling grid is explored. The acquisition of 3D seismic data on a hexagonal sampling grid is an advantageous economic alternative because it requires 13.4% fewer sample points than a rectangular sampling grid. The hexagonal sampling offers savings in data storage and processing of 3D seismic data.A fast algorithm for 3D discrete spectrum evaluation and trace interpolation in the case of a 3D seismic data set sampled on a hexagonal grid is presented and illustrated by synthetic examples. It is shown that by using this algorithm the hexagonal sampling offers, approximately, the same advantage of saving 13.4% in data storage and computational time for 3D phase‐shift migration.
Growth and reproduction of aphids and levels of free amino acids in Scots pine and Norway spruce in an open‐air fumigation with ozone
Authors: HOLOPAINEN JARMO , KAINULAINEN PIRJO , OKSANEN† JARI 
Published: November 2003

To estimate the susceptibility of conifer seedlings to aphids under future tropospheric ozone levels, Scots pine (Pinus sylvestris L.) and Norway spruce (Picea abies (L.) Karst.) seedlings were exposed to ambient and elevated ozone levels in an open‐air exposure system. Growth and reproduction of the aphids Schizolachnus pineti and Cinara pinea on Scots pine and Cinara pilicornis on Norway spruce were monitored. Levels of free amino acids in foliage and young shoots were used as indicators of host plant quality. In elevated treatment plots the ozone doses were between 1.2 and 1.7 times the dose in ambient plots in 1990–93. Half of the seedling material in 1992–93 was subjected to nitrogen fertilization treatment to evaluate the effects of increased N deposition.In 1990, population density of S. pineti on pine did not differ between ambient and elevated ozone treatments during growing season, but remained higher in the elevated ozone plot than in the ambient plot at the end of the growing season. This was associated with elevated levels of glutamic acid in foliage. In August 1992, the numbers of S. pineti were consistent between the two ambient ozone plots, but deviated highly between the two ozone‐fumigated plots. Glycine concentration in pine foliage was elevated by ozone, but free amino acid concentrations were not related to aphid performance. In 1993, ozone and nitrogen did not significantly affect the relative growth rate (RGR) of S. pineti or C. pinea nymphs on Scots pine, but glutamic acid concentration in foliage was increased by nitrogen fertilization. On Norway spruce, fecundity of C. pilicornis females was higher in elevated ozone treatment, but RGR of nymphs was not affected in 1992. In 1993, RGR of C. pilicornis nymphs was increased by nitrogen fertilization in June, but not affected by ozone. Nitrogen fertilization increased the levels of total free amino acids, aspartic acid, glutamic acid and proline in elongating shoots of Norway spruce, and ozone reduced the concentrations of valine and γ‐butyric acid.Our results suggest that availability of nitrogen from soil has a stronger impact on the concentrations of free amino acids in conifer seedlings than ozone. Some episodes of high ozone concentration may increase free amino acids in foliage. Aphid response to ozone was extremely variable, in agreement with previous laboratory experiments. The expected 20–70% increase in ambient concentrations of tropospheric ozone may in some occasions enhance aphid performance on Scots pine and Norway spruce seedlings, but in most cases the ozone effect on the susceptibility of conifer seedlings to sucking insect pests is not important.
Microbial decomposition at elevated CO2 levels: effect of litter quality
Authors: BALL ANDREW 
Published: November 2003

The decomposition of senesced plant litter represents an important intermediate step in the cycling of nutrients between above‐ and below‐ground systems. The rate of decomposition of plant litter is sensitive to fluctuations in a number of parameters, including environmental conditions, and particularly to changes in the quality of the litter. Increased C: N ratios of litter are thought to be one possible consequence of growth of plants under elevated [CO2]. This response is likely to reduce the rate of decomposition of the litter.Evidence from the growth of plants in both pot and field studies suggests that growth of C3 plants in elevated atmospheric [CO2] (600–700 μmol mol–1) may lead to a significant increase in either/both the C: N and the lignin: N ratios of litter. Short‐term decomposition of litter from plants showing this response in elevated [CO2] has confirmed that decomposition occurs at a significantly lower rate. The limited studies of both the response of C4 plants to elevated [CO2] and the subsequent degradability of the senescent litter suggest that no differences in litter quality or degradability occur. In terms of litter quality the response of plants therefore appears to be dependent upon photosynthetic type; the C:N and lignin:N ratios of litter from C3 plants exposed to elevated [CO2] are increased, leading to lower degradation rates, while the nutrient ratios and degradation rates of litter from C4 plants grown in elevated [CO2] remain unchanged.To date, very few ecosystem studies of decomposition have been carried out. Further work is required at the ecosystem level to determine whether the effects observed in laboratory, pot and field studies are also observed in long‐term, complex ecosystem studies. Clearly if these results are repeated at the ecosystem level then significant changes in the cycling of C and N in important terrestrial ecosystems may occur as a results of elevated [CO2].