bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of foliar nitrogen in light harvesting and shade tolerance of four temperate deciduous woody species
Authors: NIINEMETS Ü.
Published: November 2003

1. Distribution of leaf chlorophyll (Chl), nitrogen and non‐structural carbohydrates (NSC, ethanol‐soluble sugars and starch) in leaves along a natural light gradient was studied in saplings of four deciduous woody species: Acer platanoides, Padus avium, Populus tremula and Quercus robur (from most shade tolerant to intolerant).

2. Leaf dry mass per area (LMA) increased linearly with increasing relative irradiance (RI) in all species and therefore it may be considered as a species‐specific estimate of long‐term light conditions.

3. Decreasing irradiance enhanced chlorophyll synthesis, and consistently resulted in highest Chl per leaf dry mass in low‐light environments. Chl content per leaf area was correlated negatively with RI in A. platanoides and was independent of RI in three other species.

4. Leaf nitrogen content per leaf area (Na) increased linearly with LMA in all species, and with RI in all except A. platanoides.

5. The slopes and intercepts of Na vs LMA relationships were negatively correlated. Moreover, it appeared that the slope decreased and the intercept increased with increasing species shade tolerance. Thus, average nitrogen content per mass (Nm) increases and maximum concentrations of leaf nitrogen shift towards more open habitats with decreasing shade tolerance. Distribution of foliar nitrogen in this way is likely to contribute to greater photosynthetic potentials at higher irradiances in shade‐intolerant species. Inversely, more tolerant species have greater concentrations of foliar nitrogen at low irradiance — an investment pattern, which provides resources to enhance the capacity of light harvesting in light‐limited conditions.

6. NSC per leaf dry mass was positively related to relative irradiance and the slope of this relationship was highest for shade‐intolerant species, which have intrinsically higher photosynthetic capacities. Nevertheless, the conclusions were robust and were not significantly biased by using the parameters expressed either on a total or on a NSC‐free dry mass.

7. The analysis was further extended by including a number of other species from several independent studies. Examination of both sets of data resulted in identical conclusions. Based on this evidence it may be concluded that the variability in leaf nitrogen concentration in relation to irradiance plays a central role in species shade tolerance.
The effects of novel and stressful environments on trait distribution
Authors: HOLLOWAY G. J. , CROCKER H. J. , CALLAGHAN A.
Published: November 2003

1. Ecotoxicology seeks to blend the disciplines of toxicology and ecology to provide a means of assessing the risk that natural populations of organisms are exposed to when confronted by an environmental stress, such as a pollutant. The LC50 of a compound is usually used to assess this risk with little or no consideration of the importance of the variation about the mean.

2. Several populations of the Rice Weevil, Sitophilus oryzae, were examined that had been bred on toxic (Yellow Split‐pea) or non‐toxic (Wheat) foodstuffs, or transferred between the two. The goal was to establish the effect of stress on the levels of activity of two detoxification enzyme systems, esterases and glutathione‐S‐transferases, and the variation about the mean enzyme activity.

3. Populations kept on their original foodstuffs showed similar levels of enzyme activity irrespective of whether they bred on toxic or non‐toxic foods. When transferred to a novel food stuff there was a small increase in enzyme activity, perhaps reflecting induction, but transfer to a more toxic food did not produce a greater increase in activity than transfer to a non‐toxic food.

4. Populations on their original foodstuff showed similar levels of variation about the mean, but the variation about the mean increased considerably following transfer to a novel food. There was some evidence that this increase was greater when the transfer was to the more toxic food.

5. The increase in variation following transfer was largely due to a small number of individuals showing particularly high levels of enzyme activity. The consequence of the generation of this type of distribution in response to an environmental stress is discussed.
The influence of thermoregulation on behavioural recovery from exercise in a lizard
Authors: WAGNER E. L. , GLEESON T. T.
Published: November 2003

1. Past work on the thermal preferences of Dipsosaurus dorsalis (Biard & Giard) has indicated that intense, exhaustive exercise causes these lizards to select a body temperature (33·5 °C) which is cooler than their preferred activity temperature of 40°C during the first 1–2 h of exercise recovery.

2. In order to test the hypothesis that the thermal regime selected by exhausted D. dorsalis is beneficial to the process of exercise recovery, lizards were forced to undergo both exhaustive and sprinting exercise at their preferred body temperature of 40°C. The peak speeds attained and the total distances travelled by these animals during these two different exercise protocols were measured and the animals were then forced to undergo a second bout of either sprinting or exhaustive exercise, following a 30–330 min recovery at either 20°C, 40°C or under a variable thermal regime which duplicated that selected by animals following exercise.

3. Animals recovering at a constant 40°C regained their ability to repeat exhaustive activity in less than 85 min, while animals recovering under the other two thermal regimes required between 85 and 100 min of recovery to be able to repeat this activity. Animals recovering at both 40°C and under the variable thermal regime regained their ability to repeat sprint behaviour within 60 min of recovery, while animals recovering at 20°C required more than 100 min of recovery to be able to repeat sprint behaviour.

4. These results formed the basis of the conclusion that the post‐exercise behaviour selected by D. dorsalis retards the rate at which the animals recover their ability to repeat exhaustive exercise when compared with recovery at a constant 40°C but does not retard their ability to repeat sprint exercise.
The probabilities of supercoil removal and decatenation by yeast DNA topoisomerase II
Authors: Roca Joaquim , Wang James C.
Published: November 2003

Background:  In yeast a single type II DNA topoisomerase is involved in both the removal of DNA supercoils and the unlinking of intertwined pairs of newly replicated chromosomes or plasmids; in bacteria, two type II enzymes, DNA gyrase and DNA topoisomerase IV, function separately in the passage of DNA segments in cis and in trans. To deduce the molecular characteristics of these enzyme‐mediated reactions, the efficiencies of supercoil removal and decatenation by the yeast enzyme upon the addition of a nonhydrolysable ATP analogue were determined.

Results:  The probability that a bound enzyme transports a DNA segment in cis increases with positive or negative supercoiling of the DNA, and transport is nearly quantitative at high degrees of supercoiling. The relative probabilities of transporting a contiguous and noncontiguous DNA segment by a yeast enzyme bound to one member of a singly linked pair of 3.6‐kb rings were calculated from the observed efficiency of decatenation. When the enzyme‐bound ring is highly supercoiled, transport of a noncontiguous segment is more probable than a contiguous one.

Conclusion:  A DNA‐bound yeast enzyme has no intrinsic bias in its selection of a contiguous or noncontiguous DNA segment for transport, and the selection is determined by DNA conformations. For the singly linked dimeric catenane studied, a high degree of supercoiling of the enzyme‐bound DNA does not make supercoil removal more favourable than decatenation. In the case of bacterial gyrase, however, wrapping of a DNA segment around the enzyme is expected to strongly favour the transport of a contiguous segment.
Roles of multiple promoter elements of the proliferating cell nuclear antigen gene during Drosophila development
Authors: Yamaguchi Masamitsu , Hirose Fumiko , Matsukage Akio
Published: November 2003

The expression of genes involved in DNA replication is closely correlated with the proliferating state of cells and is repressed with the progression of differentiation during development. Promoter regions of the Drosophila proliferating cell nuclear antigen (PCNA) gene and the DNA polymerase α gene contain a common 8‐base pair promoter element (DRE: DNA replication‐related element). The examination of a common expression mechanism for DNA replication‐related genes, which is regulated positively by growth signals and negatively by differentiation signals would be of interest.  We generated PCNA‐LacZ fusion genes in which the 5′‐flanking sequence of the PCNA gene has been mutated. An examination of the expression of these fusion genes, introduced into flies by germ‐line transformation, led to the identification of another distinct regulatory element, URE (upstream regulatory element), within the region from –168 to –119 with respect to the transcription initiation site. During embryogenesis, the region containing the DRE sequence (–108 to –91) greatly stimulated the PCNA gene minimal promoter (–86 to +130), when it was placed upstream of the promoter in both normal and reverse orientations. Addition of the URE sequence further stimulated the promoter activity twofold. During larval stages, both DRE and URE were indispensable to the promoter activity, since neither of the sequences alone activated the minimal promoter. Demonstration of β‐galactosidase activity indicated URE plays an essential role in various larval tissues such as salivary gland and imaginal disc. While the minimal promoter region alone directed maternal expression of lacZ in ovaries of adult females, both DRE and URE further stimulated promoter activity.  These results show several elements of the PCNA gene promoter play roles during Drosophila development.
The major pathways of protein translocation across membranes
Authors: Ito Koreaki
Published: November 2003

The initial events in the localization of cell surface proteins include targeting of precursor molecules to the membrane and subsequent translocation across the membrane. The translocation reaction is mediated through a series of molecular interactions involving a number of protein factors. The trimeric SecY/Sec61 core complex, which is conserved throughout evolution, provides a proteinaceous pathway for translocation. The driving force for translocation is provided by the dynamic motion of the SecA ATPase in prokaryotes and by polypeptide elongation through the ribosome‐Sec61 junction in eukaryotes.
Compartmentalized distribution of the proteins controlling the prespore‐specific transcription factor σF of Bacillus subtilis
Authors: Lewis Peter J. , Magnin Thierry , Errington Jeffery
Published: November 2003

Background: Differential gene expression during sporulation in the prespore and mother cell of Bacillus subtilis is dependent on the correct timing and localization of the activity of specific transcription (σ) factors. The first σ factor activated is σF, which directs gene expression specifically in the prespore compartment. Release of σF activity is tightly controlled through a series of complex interactions involving an anti‐σ factor, SpoIIAB, an anti‐anti‐σ factor SpoIIAA and a phosphoprotein phosphatase SpoIIE. In vitro studies have shown that SpoIIAB binds to σF, preventing transcription of the σF regulon, and that it can also phosphorylate SpoIIAA, thereby inactivating it. However, non‐phosphorylated SpoIIAA can displace σF from SpoIIAB. The SpoIIE phosphatase provides a means of reactivating SpoIIAA‐P.

Results: We have directly determined the cellular distibutions of σF, SpoIIAB, SpoIIAA‐P and SpoIIAA during sporulation, using recently developed immunofluorescence methods. While σF activity is restricted to the prespore, the protein is present in both compartments. As development proceeds the σF signal disappears. The anti‐σ factor SpoIIAB is also distributed throughout both cells and rapidly disappears from both cellular compartments soon after σF becomes active. Disappearance of SpoIIAB seems to be closely associated with the activation of the second prespore‐specific σ factor σF. The distribution of phosphorylated SpoIIAA closely mimics that of SpoIIAB, being non‐compartmentalized and disappearing soon after σF activation occurs. Significantly, the active, non‐phosphorylated form of the anti‐anti‐σ factor, SpoIIAA, accumulates in the prespore just before σF becomes active.

Conclusion: These results support the hypothesis that the accumulation of SpoIIAA within the prespore is the single most important requirement for activation of σF.
Genetic interactions between CDC7 and CDC28: growth inhibition of cdc28‐1N by Cdc7 point mutants
Authors: Ohtoshi Akihira , Arai Ken‐ichi , Masai Hisao
Published: November 2003

Background: Cdc7 kinase of Saccharomyces cerevisiae, a nuclear phosphoprotein, regulates initiation of chromosomal DNA replication. Overexpression of kinase‐negative Cdc7 point mutants (T281E, D182N and D163N) arrests the cell cycle of the wild‐type Saccharomyces cerevisiae cells at the G1/S boundary. This is caused by titration of a regulatory protein, Dbf4, from the wild‐type Cdc7, which leads to inactivation of its kinase activity.

Results: We report here that kinase‐negative Cdc7 mutants, when overexpressed in cdc28‐1N(ts) at a permissive temperature, not only inhibit DNA replication by inactivating the wild‐type Cdc7 but may also disturb coordination between DNA replication and cell division. Suppression of growth inhibition under this condition requires co‐expression of both Dbf4 and Cdc28, whereas Dbf4 alone can counteract the growth inhibition in the wild‐type cells. In cdc28‐1N(ts), co‐expression of the wild‐type Dbf4 rescues only the G1/S defect and results in accumulation of those cells with less than 1C DNA as well as 2C DNA. On the other hand, co‐expression of Cdc28 alone leads to increase of those cells arrested at the G1/S boundary, as found typically in the wild‐type. We also report that overexpression of T281A, a ‘weak’ allele of Cdc7, causes growth arrest in cdc28‐1N(ts) cells, but not in the CDC28 wild‐type cells. This suggests that T281A is inactive in cdc28‐1N(ts) and is consistent with the idea that Cdc28 activates Cdc7 by phosphorylation.

Conclusion: We conclude that two essential serine‐threonine kinases, Cdc28 and Cdc7, genetically inter‐act for initiation of the S phase and possibly for G2/M progression and/or S phase checkpoint control.
Fas‐induced apoptosis, and diseases caused by its abnormality
Authors: Nagata Shigekazu
Published: November 2003

Homeostasis of multicellular organisms is controlled not only by proliferation and differentiation of cells but also by cell death. Physiological cell death mostly proceeds by apoptosis, a process which includes condensation and segmentation of the nuclei and cytoplasm, and often extensive fragmentation of chromosomal DNA into nucleosome units. Molecular and cellular characterization of Fas, a cell‐surface protein recognized by cytotoxic monoclonal antibodies, has led to its definition as a receptor for a Fas ligand (FasL). FasL binds to Fas, which results in target cell apoptosis. A family of cysteine proteases seems to be sequentially activated during the Fas‐mediated apoptosis. The phenotypes of the loss‐of‐function mutants of Fas and FasL indicate that this system is involved in T cell‐mediated cytotoxicity, in down‐regulation of immune responses, and probably in the turnover of senescent cells. Malfunction of the Fas system causes hyperplasia in peripheral lymphoid organs and the liver, accelerating autoimmune diseases and tumorigenesis, whereas exaggeration of the system leads to tissue disruption.
Complete growth inhibition of Escherichia coli by ribosome trapping with truncated cspA mRNA at low temperature
Authors: Jiang Weining , Fang Li , Inouye Masayori
Published: November 2003

Background: CspA, the major cold‐shock protein of Escherichia coli, is transiently induced upon temperature downshift and considered to play an important role in low‐temperature adaptation.

Results: Overproduction of truncated cspA mRNAs retaining translational ability was found to completely block cell growth at low temperatures. This effect was termed ‘low‐temperature antibiotic effect of truncated cspA expression (LACE)’. In contrast to the significant reduction of polysomes in normal cells upon cold shock, cells under LACE maintained a high polysome profile, producing only truncated cspA products. Growth inhibition of cells under LACE was suppressed when CspA was overproduced together with the truncated cspA mRNA.

Conclusion: LACE is caused by the overproduction of a truncated cspA mRNA in the absence of CspA production, which in turn traps all the cellular ribosomes in a non‐adaptive form incapable of forming initiation complexes with other cellular mRNAs. LACE may provide a novel approach to the development of a new antibiotic.
A single point mutation of hamster aminoacyl‐tRNA synthetase causes apoptosis by deprivation of cognate amino acid residue
Authors: Fukushima Kohtaro , Motomura Seiichi , Kuraoka Akio , Nakano Hitoo , Nishimoto Takeharu
Published: November 2003

Background:
We have isolated a series of temperature‐sensitive mutants for cell‐proliferation from the BHK21 cell line derived from the golden hamster (Nishimoto & Basilico 1978; Nishimoto et al. 1982). Using these mutants as a recipient of DNA‐mediated gene transfer, we have been cloning human genes which complement these ts mutants.

Results:
Cultures of tsBN269 cells, a temperature‐sensitive mutant of the BHK21 cell line, underwent apoptosis at 39.5 °C, a nonpermissive temperature. The gene complementing the tsBN269 cells was cloned and found to encode lysyl‐tRNA synthetase. Indeed, tsBN269 cells were found to have a single cytosine to a thymine point mutation at the first nucleotide of codon 542 in hamster lysyl‐tRNA synthetases. Due to this mutation, the activity of lysyl‐tRNA synthetase was reduced—even at 33.5 °C, a permissive temperature. Consistent with these findings, while supplementation with lysine permitted tsBN269 cells to grow at a nonpermissive temperature, the deprivation of lysine caused apoptosis in tsBN269 cells, even at 33.5 °C. Cycloheximide inhibited the apoptosis caused by lysine starvation at 33.5 °C, but not at 39.5 °C. We also found that another hamster temperature‐sensitive mutant, tsBN250, which is defective in histidyl‐tRNA synthetase, entered apoptosis with the deprivation of histidine.

Conclusion:
Our data suggested that the defect in aminoacyl‐tRNA synthetase turned on the cascade of apoptosis that was already present in the cells.
DNA nicking by Escherichia coli topoisomerase IV with a substitution mutation from tyrosine to histidine at the active site
Authors: Yokochi Tomoki , Kato Jun‐ichi , Ikeda Hideo
Published: November 2003

Background:

Escherichia coli topoisomerase IV is a type II topoisomerase composed of ParC and ParE subunits and plays a major role in the decatenation of replicated molecules. The reaction with type II topoisomerases involves the cutting through transesterification between an active‐site tyrosine and a DNA phosphodiester bond and a rejoining of cleaved DNA.

Results:
To genetically analyse the mechanism of this reaction, we isolated dominant‐negative topoisomerase IV mutants. In one of them, the parC10 mutant, there was a substitution by histidine of the active‐site tyrosine. Purified mutant topoisomerase IV did not show normal DNA cutting activity but retained DNA nicking activity, even in the absence of ATP. The DNA ends of the product were not covalently bound to the ParC subunits, suggesting that the DNA is not cut via transesterification but by hydrolysis.

Conclusions:
We have shown genetically that the 120th tyrosine residue is important for the DNA cutting step in the topoisomerase reaction. The 120th amino acid residue, tyrosine or histidine, appears to be activated and the histidine residue forces the hydrogen‐bonded water to attack the phosphoryl group of the DNA in hydrolysis, while the tyrosine residue directly attacks the phosphoryl group during transesterification.
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.
Differentiation of T‐helper lymphocytes: selective regulation by members of the STAT family of transcription factors
Authors: Schindler Ulrike , Hoey Timothy , McKnight Steven L.
Published: November 2003

Interleukin‐4 (IL‐4) and interleukin‐12 (IL‐12) control the differentiation of T‐helper cells. Here we summarize studies which investigate the mechanism by which these cytokines selectively reprogramme gene expression in T‐lymphocytes. Cytokine stimulation leads to the phosphorylation of specific tyrosine residues within the intracellular domain of the corresponding cytokine receptor. These phosphotyrosines serve as docking sites for latent, cytoplasmic transcription factors known as signal transducers and activators of transcription (Stat) proteins. Receptor/Stat interaction is mediated by the src homology 2 (SH2) domain of the corresponding Stat protein. Although Stat binding to the intracellular domain of the cytokine receptor strongly depends on the phosphotyrosine residue, the recruitment of a specific Stat protein is dictated by amino acid residues C‐terminal to the phosphotyrosine. Specific docking sites within individual cytokine receptors have been identified for almost all Stat proteins. The direct coupling between cytokine receptor and transcription factor helps to explain how different cytokines elicit distinct patterns of gene expression.
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 ontogenesis of the steroidogenic tissues
Authors: Morohashi Ken‐ichirou
Published: November 2003

Based on the common function of steroid hormone‐producing tissues and homologous regulation by the hypothalamo‐pituitary axis, the adrenal cortex and the gonads have been suggested to have an intimate ontogenic relationship. This assumption is also supported by the findings of common transcription factors implicated in the differentiation of both types of tissue and further supported by concomitant defects in such tissues due to the disruption of a single gene. Similarly, simultaneous anomalies in those tissues are also observed in some diseases caused by mutations of the genes encoding those transcription factors. A recent immunohistochemical study with one of the transcription factors, Ad4BP/SF‐1, definitely demonstrated the presence of a particular cell population designated the ‘adreno‐genital primordium (AGP)’ which gives rise to both the adrenal cortex and the gonads. In the process of differentiation from the AGP to the mature adrenal cortex and the gonads of the two sexes, several interesting issues can be raised as to the next targets for the study. To address these issues it is important to elucidate the upstream regulatory mechanisms and downstream target genes of such transcription factors as WT1, SRY, SOX9 and DAX1, in addition to Ad4BP/SF‐1, all of which are implicated in steroidogenic tissue differentiation.
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

Background:  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.
Insects in amber
Authors: ROSS ANDREW J.
Published: November 2003

Amber is fossilized resin that has exquisitely preserved many insects that otherwise would not be represented in the fossil record. The insects and other inclusions give us an insight into what terrestrial life and the environment was like millions of years ago.
The detection of King Xerxes' Canal by the use of shallow reflection and refraction seismics — Preliminary results
Authors: Karastathis V.K. , Papamarinopoulos St. P.
Published: November 2003

Shallow reflection and refraction seismic studies were carried out in Greece in the eastern leg of the Chalkidiki peninsula, in order to test the validity of reports in history books which describe a legendary canal built by the engineers of King Xerxes during the major Persian invasion of Europe through Greece in the 5th century B.C.  In the narrowest part of the Athos peninsula, where it is 2 km wide, an 85 m profile was topographically defined almost centrally between the two coastlines. The position of this profile was based on palaeogeographical, geomorphological and topographic studies and observations. A sledgehammer was used as the seismic source for the shallow target. Despite the presence of significant urban and coherent noise, a final stacked section was produced by a suitable choice of acquisition and processing parameters.  Both the reflection and refraction seismic studies illustrated clearly the existence of a channel‐like structure of trapezoid cross‐section, almost midway between the two opposite sides of the peninsula.
Seismic inversion for coal‐seam thicknesses: trials from the Belvoir coalfield, England
Authors: Gang Tian , Goulty N.R.
Published: November 2003

We have applied generalized linear inversion to high‐quality seismic reflection data from the Coal Measures in the East Midlands of England. The purpose was to test whether accurate values for coal‐seam thicknesses could be obtained to benefit longwall coal‐mining and coal‐bed methane production. A seismic line intersecting two logged boreholes was chosen so that an objective evaluation of the results could be made, and inversion was carried out after careful reprocessing of the line with post‐stack migration. As coal‐seams are thin beds in the seismic bandwidth, it was necessary to assume that acoustic impedance values are constant. Of the ten coal‐seams in the sequence, only two were found to be major contributors to the reflection response at the boreholes, but inversion runs were carried out independently for two seams and four seams. It was found that keeping the wavelet fixed was the best strategy when inverting for the interface two‐way times at the seam boundaries. However, all the strategies tested showed inconsistent variations in seam thicknesses which were geologically implausible. We conclude that significant improvements need to be made in acquisition and processing techniques for inversion to give useful results in this application.
A compact representation of magnetotelluric responses for two‐layer models
Authors: Szarka László
Published: November 2003

In this paper the locations where ρapp = ρ1 and ϕ = π/4 and where these parameters reach an extreme value in two‐layer magnetotelluric (MT) sounding curves are summarized in an extremely compact form. The key parameters over two‐layer models with conductivities σ1, σ2 and upper layer thickness h are the real S and α, where S is the conductivity contrast and α is the distance between the observation site and the conductivity interface, normalized to the half skindepth in the first layer. If the impedance components, various resistivity definitions ( ρRe Z, ρIm Z and ρ|Z|, based on different parts of the complex impedance Z ) and the magnetotelluric phase ϕ are derived as a function of S and α, then the conditions for the apparent resistivity ρapp and the phase ϕ are that they either satisfy ρapp = ρ1 and ϕ = π/4 or attain extreme values which can be given in terms of simple algebraic equations between S and α. All equations are valid for observation sites at any depth 0 ≤ z ≤ h in the first layer. The set of equations, presented in a tabular form, may make it possible to determine a layer boundary from the short period part of the sounding curves, in particular the ρRe Z and the ϕMT curves.
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.
Self‐potential global tomography including topographic effects
Authors: Patella Domenico
Published: November 2003

This paper is an extension of a previous study, in which the principles of self‐potential ground surface tomography were outlined. The new arguments which are here set forth are the proper accounting for the topographic effects and a robust approach to global 3D tomography. The 2D case is initially considered in order to facilitate a full understanding of the new method. In order to gauge the topographic distortions, the concepts of slope effect and surface regularization are introduced, as suitable means to compute point by point correction factors of the measured self‐potential data, prior to the recognition of the tomographic images of the primary and induced electric sources underground. The tomographic approach is then developed by introducing again the concepts of the scanning function and of the charge occurrence probability function, which were amply dealt with in the previous paper. The new approach to 3D global tomography means here the composition of charge occurrence probability functions related to any two orthogonal surface components of the natural electric field, in order to account fully for the total surface component of the self‐potential field and hence to elicit the greatest amount of information. Two field examples are presented to show the full effectiveness of the proposed method. They refer, respectively, to a near‐surface investigation for archaeological purposes and to a very deep investigation in an active volcanic area.
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.