bluuebunny/crossref_metadata_2025 huggingface dataset:
Non‐structural carbohydrate accumulation and use in an understorey rain‐forest shrub and relevance for the impact of leaf herbivory
Authors: MARQUIS R. J. , NEWELL E. A. , VILLEGAS A. C.
Published: November 2003

1.
Piper arieianum, an evergreen, understorey shrub of lowland moist forests of Central and South America, exhibits marked seasonal variation in reproductive activity even though climatic variation is low at the study site. Despite a lack of climatic seasonality, previous experimental leaf removal suggested that carbohydrate accumulation is seasonal, occurring prior to flowering.

2. We first tested the hypothesis that carbohydrates necessary for reproduction are accumulated prior to flowering, rather than during or after. By measuring non‐structural carbohydrate production in the form of glucose and starch we found that the concentration of these reserves is greatest 1–3months before flowering, decreasing by 50% during peak fruit maturation.

3. The hypothesis that reproduction was the cause of this decrease in carbohydrate reserves was then tested by comparing reserves in plants that were prevented from flowering with those that flowered and produced fruit naturally. As predicted, reserves declined more in flowering than in non‐flowering plants. A smaller decline in reserves of non‐flowering plants was accompanied by greater stem and leaf production, suggesting that stored carbohydrates are also required for growth.

4. Because concentrations of non‐structural carbohydrates were similar in roots, stems and leaves, and because the greatest amount of plant biomass is in stems for plants of a range of sizes, stems appear to be the main storage site of carbohydrate reserves in this plant species.

5. These results, together with previous studies, demonstrate that the impact of leaf herbivory on seed production in P. arieianum depends on the timing of that herbivory relative to the accumulation and use of non‐structural carbohydrates.
An optimum body size for mammals? Comparative evidence from bats
Authors: JONES K. E. , PURVIS A.
Published: November 2003

1. The distribution of body sizes among mammalian species has been modelled by Brown, Marquet & Taper (1993), who suggest that reproductive power (the rate at which energy from the environment is channelled into offspring production) is maximized at a size of 100 g, and the observed size distribution among species reflects the way reproductive power depends on size. The model makes a testable prediction about life‐history allometries: namely, that components of reproductive power should not scale linearly with body size but should change sign at the optimum size.

2. A large set of life‐history data from a single clade of small mammals, the bats (Order: Chiroptera), was analysed to test this key prediction. The analyses in this study offer no support for the idea that allometries of reproductive power change sign in bats, either at 100 g or at any other size. Furthermore the life‐history allometries of bats, which are mostly below the 100 g optimum, were broadly the same as in mammalian taxa larger than the optimum size.

3. These findings together contradict a key prediction of Brown et al.’s (1993) model to explain the skewed body size distribution across mammalian species.
Geographic variation in ‘costs of reproduction’ in the scincid lizard Lampropholis guichenoti
Authors: QUALLS F. J. , SHINE R.
Published: November 2003

1. A major focus of life‐history research has been the analysis of reproductive effort (RE). However, while clearly defined in theory, RE has proved very difficult to measure. Consequently, researchers have looked for indices that estimate the components of RE. Uncritical use of indices of reproductive investment, such as measures of costs of reproduction, without verification of the underlying assumptions of the link between these traits, may lead to spurious conclusions. In this paper, the common assumption that the physical burden of the clutch impairs locomotor ability in gravid reptiles is examined.

2. Two neighbouring populations of Australian scincid lizards (Lampropholis guichenoti) are similar in adult body sizes, body shapes and reproductive output (egg sizes, clutch sizes, relative clutch masses).

3. Despite morphological and reproductive similarities, the effects of pregnancy on maternal locomotor ability (running speeds, as measured in a laboratory raceway) differed dramatically between the two populations.

4. Lizards from the two populations ran at similar speeds when nongravid (i.e. after egg‐laying), but pregnancy significantly reduced running speeds in one population and increased them in the other. Thus, superficial similarities in body size and reproductive output masked a strong divergence in the locomotor ‘costs’ of reproduction.

5. Caution is advised if using simple measures of reproductive output (e.g. relative clutch mass) as indices of reproductive effort, or to generalize results even among conspecific populations.
Dissection of fission yeast microtubule associating protein p93Dis1: regions implicated in regulated localization and microtubule interaction
Authors: Nakaseko Yukinobu , Nabeshima Kentaro , Kinoshita Kazuhisa , Yanagida Mitsuhiro
Published: November 2003

Background: Fission yeast microtubule associating protein (MAP) p93Dis1 functions for sister chromatid separation: dis1 mutants fail to separate chromosomes, while the spindle elongates but without cyclin destruction. p93Dis1 localizes along microtubules in interphase cytoplasm, but shifts to the spindle pole body (SPB) and spindle microtubules upon the entry into mitosis. In this study, regions of p93Dis1 were dissected to examine their role.

Results: Nitrocellulose filter blotting shows that recombinant Dis1 binds to bovine brain microtubules in vitro. A basic central region rich in S, T and P is essential for this association. However, the whole p93Dis1 with N‐ and C‐termini containing a conserved repeat motif and heptad repeats, respectively, is necessary for normal microtubule association in vivo. The N‐truncated region also binds to microtubules but only to the portions near the SPBs. Overproduction phenotypes indicate that p93Dis1 greatly affects spindle formation and cell morphogenesis. The central region is essential but, by itself, not sufficient for generating such effects.

Conclusions: We propose that p93Dis1 consists of three regions which carry distinct properties for localization: the N‐region for cell cycle dependent localization, the central region for direct microtubule association, and the C‐region for SPB and nuclear localization. The essential role of p93Dis1 is carried out in the C‐region, while the N‐region acts as a regulator.
Rab3A small GTP‐binding protein in Ca2+‐dependent exocytosis
Authors: Takai Yoshimi , Sasaki Takuya , Shirataki Hiromichi , Nakanishi Hiroyuki
Published: November 2003

There exists a small GTP‐binding protein (G protein) superfamily, consisting of more than 50 members, from yeast to mammal. The Rab family belongs to this superfamily and is implicated in intracellular vesicle trafficking. Rab3A small G protein is a member of the Rab3 subfamily which belongs to this Rab family. The regulators and downstream targets of Rab3A have been isolated, and evidence is accumulating that Rab3A and these Rab3A‐interacting proteins are involved in Ca2+‐dependent exocytosis, particularly in neurotransmitter release from nerve terminals.
Enhancer analysis of the mouse HNF‐3β gene: regulatory elements for node/notochord and floor plate are independent and consist of multiple sub‐ elements
Authors: Sasaki Hiroshi , Hogan Brigid L. M.
Published: November 2003

Background:  Axial pattern formation in vertebrate embryos depends on signals from the node and, later, from the notochord and floor plate. Previous studies have shown that HNF‐3β, a member of the winged‐helix transcription factor family, plays key roles in the development of all three organizing centres.

Results:  Enhancer analysis of HNF‐3β has therefore been performed using lacZ reporter gene constructs in transgenic mouse embryos. This has led to the identification of independent node/notochord and floor plate enhancers, at positions far upstream (−15 to −14 kb) and downstream (+6 to +11 kb) of the transcription start site, respectively. The node/notochord enhancer activity has been localized to a 520 bp fragment. Floor plate gene expression requires a combination of two separate fragments of the enhancer. Deletion analysis of one of these fragments (400 bp) has identified subregions required for the initiation and the maintenance of floor plate expression, and for the suppression of ectopic expression within the neural tube.

Conclusion:  We conclude that HNF‐3β gene expression in the node/notochord and in the floor plate are controlled through different enhancers, which consist of positive and negative elements.
The master control gene for morphogenesis and evolution of the eye
Authors: Gehring Walter J.
Published: November 2003

The human Aniridia, the murine Small eye, and the eyeless mutations of Drosophila affect homologous (Pax‐6) genes that contain both a paired‐ and a homeobox. By ectopic expression of these genes, functional eyes can be induced on the legs, wings, and antennae of the fly, indicating that eyeless (Pax‐6) is the master control gene for eye morphogenesis. The finding of Pax‐6 from flatworms to humans suggests that eyeless is a universal master control gene and that the various types of eyes in the various animal phyla may have evolved from a single prototype.
A one‐hybrid system for detecting RNA–protein interactions
Authors: Wilhelm James E. , Vale Ronald D.
Published: November 2003

Background : mRNA translation, stability, and localization are controlled by regulatory proteins that bind to specific RNA motifs. Since biochemical isolation of such proteins has often proven to be difficult, a genetic system for studying RNA–protein interactions would be of great utility in the identification of novel RNA binding proteins and in understanding how these proteins recognize particular RNA sequences.  The bacteriophage lambda gene product N protein is a sequence specific RNA binding protein that when bound to its target sequence allows RNA polymerase to ignore transcription termination signals. The fact that the binding of N protein to RNA is directly coupled to gene expression suggests that N protein could be used to develop a general system for studying RNA–protein interactions.

Results : Our results show that fusion of the RNA binding protein, R17, to N causes antitermination in a β‐galactosidase reporter construct that has the R17 binding site substituted for the normal N target sequence. This system can both detect low affinity interactions as well as discriminate between binding events with equilibrium dissociation constants from 10−5 to 10−8 m. The differences in antitermination activity with various mutant binding sites can be reliably detected by colony colour on X‐Gal plates as well as by liquid culture assay.

Conclusions: We have demonstrated that N protein can cause antitermination through a heterologous RNA–protein interaction and that the system is capable of detecting RNA–protein interactions of differing affinities. This approach may also be useful in screening libraries for proteins that bind to novel RNA regulatory elements. Our results are also consistent with a model of N protein function in which binding to the nascent transcript increases the effective concentration of N in the vicinity of RNA polymerase leading to antitermination.
Molecular anatomy of the β′ subunit of the E. coli RNA polymerase: identification of regions involved in polymerase assembly
Authors: Luo Jianying , Sharif Karim A. , Jin Ruzhong , Fujita Nobuyuki , Ishihama Akira , Krakow Joseph S.
Published: November 2003

Background: The E. coli RNA polymerase is a multisubunit enzyme, which is present in two different forms: the catalytic competent core enzyme (α2ββ ′) and the promoter selective holoenzyme (α2ββ ′σ). Correct assembly of individual subunits into core or holoenzyme is essential for the function of this enzyme.

Results: Mutant β ′ proteins truncated near the centre or at the C‐terminus were able to form stable core enzyme‐like complexes under reconstitution conditions. Mutant β ′ proteins lacking the region between amino acids 201–477 failed to form holoenzyme complexes while retaining the ability to form core enzyme complexes. Furthermore, free β ′ subunit interacted with free σ subunit to form a stable β ′σ subassembly. Removal of amino acids 201–477 from the β ′ subunit strongly interfered with this interaction.

Conclusion: Our results suggest that the N‐terminal region of the β ′ subunit is involved in the assembly of core enzyme. The region between amino acids 201 and 477 on β ′ may be directly or indirectly involved in the interaction between the β ′ subunit and the σ subunit.
Molecular assembly of RNA polymerase II from the fission yeast Schizosaccharomyces pombe: subunit–subunit contact network involving Rpb5
Authors: Miyao Takenori , Yasui Kiyoshi , Sakurai Hitomi , Yamagishi Masahiro , Ishihama Akira
Published: November 2003

Background: Eukaryotic RNA polymerase II is composed of more than 10 polypeptide chains. The minimum and essential subunits for RNA synthesis have not yet been identified. Toward this ultimate goal, we analysed the topological arrangement of the putative subunits. Here we report a subunit–subunit contact network involving subunit 5 of the fission yeast Schizosaccharomyces pombe RNA polymerase II.

Results: The rpb5+ gene encoding subunit 5 of RNA polymerase II was cloned from the fission yeast Schizosaccharomyces pombe. The polypeptide predicted from DNA sequence of the rpb5+ gene consists of  210 amino acids with a calculated molecular weight of 23 914. The homology of the amino acid sequence is 55% and 43% with Saccharomyces cerevisiae RPB5 and human hRPB25, respectively. Far‐Western blot analysis of S. pombe RNA polymerase II using 32P‐labelled recombinant Rpb5 fused to glutathione S‐transferase (GST) as a probe, indicated that Rpb5 binds strongly to membrane‐immobilized Rpb1, Rpb2 and Rpb3 and weakly to Rpb5 and a 15‐kDa subunit (Rpb8 or Rpb11). In agreement with this result, the 32P‐labelled Rpb3 probe showed a strong binding signal against Rpb5 in addition to Rpb1 and Rpb2. The existence of Rpb5–Rpb3 contact was supported by detection of complexes formed between these two proteins synthesized in vitro using protein‐immobilized beads.

Conclusion: Rpb3 and Rpb5, the putative subunits of RNA polymerase II, associate each other to form binary complexes. These two subunits also bind to the two large subunits, Rpb1 and Rpb2, independently.
Regulation of IFN‐α/β genes: evidence for a dual function of the transcription factor complex ISGF3 in the production and action of IFN‐α/β
Authors: Harada Hisashi , Matsumoto Masahito , Sato Mitsuharu , Kashiwazaki Yasuo , Kimura Tohru , Kitagawa Motoo , Yokochi Taeko , Sok‐Pin Tan Rosemary , Takasugi Tomohiro , Kadokawa Yuzo , Schindler Chris , Schreiber Robert D. , Noguchi Shigeru , Taniguchi Tadatsugu
Published: November 2003

Background: Efficient production of interferons (IFNs) in virally infected cells is an essential aspect of the host defence. The transcription factor complex ISGF3 (IFN‐stimulated gene factor 3) was originally identified as a critical mediator of the IFN signal; it is formed upon IFN receptor (IFNR) stimulation and binds to ISREs (IFN‐stimulated response elements) to activate IFN‐inducible genes. It has recently been shown that the DNA binding component of ISGF3, p48 (ISGF3γ) also binds to virus‐inducible elements in the IFN‐α/β genes, suggesting a potential new role of p48 in IFN production.

Results: Primary cells from mice with a targeted disruption of the p48 gene show severe defects in virus‐induced IFN‐α/β gene expression. A similar defect was also observed in cells lacking type I IFNR or Stat1, further demonstrating the role of IFN signalling in the induction of these IFN genes. ISGF3 in fact binds to the virus‐inducible elements within the IFN‐α/β promoters. We also provide evidence showing that these elements are additionally controlled by an unidentified factor(s) which presumably triggers the primary phase of IFN gene induction.

Conclusions: Our results demonstrate that the IFN signal transducing complex ISGF3 plays a crucial role in IFN production and suggest that ISGF3 may participate directly in the activation of IFN‐α/β promoters. This dual function of ISGF3 may insure the efficient operation of this cytokine system in the host defence.
Roles of cysteine residues of DsbB in its activity to reoxidize DsbA, the protein disulphide bond catalyst of Escherichia coli
Authors: Kishigami Satoshi , Ito Koreaki
Published: November 2003

Background: DsbA, a periplasmic protein, catalyses the disulphide bond formation of other cell surface proteins in E. coli. Reoxidation of DsbA for catalytic turn over is assured by DsbB, a membrane protein with four essential cysteine residues facing the periplasm. We and others previously reported that the reactive Cys30 residue of DsbA forms a mixed disulphide with DsbB in the absence of its partner Cys33 residue.

Results: Under the medium condition in which the DsbA mutant lacking Cys33 forms a mixed disulphide only with DsbB, we examined cysteine mutants of epitope‐tagged DsbB for their ability to form the complex. It was shown that Cys104 of DsbB is absolutely required while other three cysteines are also required for maximum interaction. Examination of the redox states of cysteines in wild‐type and mutant DsbB suggested that Cys104 and Cys130 form a disulphide bond which will be transferred to DsbA. In agreement with this notion, DsbB mutants lacking one of the N‐terminally located cysteines retain weak DsbB activity in vivo. The primary role of the N‐terminally located thioredoxin‐like motif of DsbB is probably to reoxidize Cys104 and Cys130

Conclusions: We propose the following reaction cycle. DsbB is initially oxidized (State A in Summary Figure). Disulphide interaction between Cys30 of DsbA and Cys104 of DsbB should then trigger the recycling reaction of DsbA (State B), allowing over all electron transfer from newly secreted protein via DsbA (Cys30/Cys33) to DsbB in which intrachain electron flow from Cys104/Cys130 (State C) to Cys41/Cys44 (State D) may occur.
Vertebrate non‐receptor protein–tyrosine kinase families
Authors: Neet Kellie , Hunter Tony
Published: November 2003

Many non‐receptor protein–tyrosine kinases (PTKs) function as subunits of receptors, either receptors with or without intrinsic PTK catalytic activity of their own. There are currently at least 33 known vertebrate genes that encode non‐receptor PTKs. These can be divided into nine families: Abl, Fes/Fer, Syk/Zap70, Jak, Tec, Fak, Ack, Src, and Csk. Four additional non‐receptor PTKs (Rlk/Txk, Srm, Rak/Frk, and Brk/Sik) do not appear to belong to any of the defined families. Here we review current knowledge of the general roles of non‐receptor PTKs, as well as the characteristic features and functions of each family and its family members.
Localization of mouse Rad51 and Lim15 proteins on meiotic chromosomes at late stages of prophase 1
Authors: Ikeya Tomoatsu , Shinohara Akira , Sato Shusei , Tabata Satoshi , Ogawa Tomoko
Published: November 2003

Background: In meiosis, eukaryotic chromosomes show a series of morphological changes, during which chromosomes synapse and recombine. To understand the mechanisms of the morphological changes and recombination of chromosomes, we examined stage‐specific localization of the Rad51 and Lim15 proteins on the chromosomes in meiotic prophase 1. These proteins are homologous with the RecA protein and have general properties of searching and pairing of homologous DNA sequences. We used mouse chromosomes whose small sizes allow us to identify the locations of these proteins on the entire structures of the chromosomes.

Results: In the leptotene and zygotene stages, the Rad51 protein was present on chromatin loops of mouse testis chromosomes then the protein left the loops. In the pachytene stage, the Rad51 protein was present almost exclusively along the core of the synaptonemal complexes (SC). When the stage proceeded to diplotene, the protein was present in the synaptic regions of chromosomes, in particular, in the chiasma regions. The protein was not present on separated homologous SC cores. On the other hand, the Lim15 protein that was found on chromatin loops in early prophase 1, was present almost exclusively at both ends of the SC cores throughout the late stages of prophase 1.

Conclusion: The Rad51 and Lim15 proteins are present in chromatin loops when chromosomes form SC. The proteins may promote pairing of homologous DNA sequences that would lead formation of SC. The Rad51 protein in the SC cores may be involved in chiasma formation in late stages. The Lim15 protein, instead, may be involved in recombination in the telomeric region or in cohesion of sister chromatids for segregation.
The directionality of RuvAB‐mediated branch migration: in vitro studies with three‐armed junctions
Authors: Hiom Kevin , Tsaneva Irina R. , West Stephen C.
Published: November 2003

Background:  The Escherichia coli RuvA and RuvB proteins promote the branch migration of 4‐way (Holliday) junctions during genetic recombination. The active complex is a tripartite structure in which RuvA protein is bound to the crossover and is sandwiched between two hexameric rings of RuvB. Branch migration requires ATP hydrolysis and occurs as the DNA passes through each RuvB ring.

Results:  In this work, we have investigated the mechanism by which RuvAB catalyses the branch migration of a three‐armed (Y) junction. Using synthetic DNA structures, we observed the formation of DNA products, a partial duplex DNA molecule and a single‐stranded oligonucleotide, indicative of a branch migration reaction that occurred with unique polarity. Analysis of the RuvAB‐junction complex by DNase footprinting showed that RuvA bound asymmetrically to the junction and targeted a single hexameric RuvB ring to one arm of DNA.

Conclusion:  Branch migration of a three‐armed junction occurs in a unidirectional manner that is determined by the assembly of a single RuvB ring onto one arm of the DNA. The asymmetry of the complex and observed directionality of branch migration indicate that strand passage occurs as the DNA is pulled into the RuvB ring structure, a reaction likely to be coupled with DNA unwinding.
Architectural flexibility in lambda site‐specific recombination: three alternate conformations channel the attL site into three distinct pathways
Authors: Segall Anca M. , Nash Howard A.
Published: November 2003

Background:  In the phage lambda life cycle, the Integrase (Int) protein carries out recombination between two different sets of DNA substrates: attP and attB in integration, attL and attR in excision. In each case, the partners are very different in structure from each other and the recombination reaction between them is effectively irreversible. For comparison, we have studied the recombination mediated by Int between two identical attL sites. Both in vitro and in vivo, recombination between two attL sites can be mediated inefficiently by Int alone. But, while IHF can stimulate recombination 5–10‐fold in vivo (to the level of excision and integration), this stimulation is not observed under standard conditions in vitro

Results:  We find that IHF can stimulate the in vitro recombination between two attLs that are modified to be defective in one of the high affinity binding sites for Int, P′1. With such substrates, the efficiency of IHF‐stimulated recombination is comparable to that seen in vivo. The requirements for this reaction distinguish it from other lambda recombination pathways, as does the performance of several mutant Int proteins. Recombination of attL sites on intracellular plasmids suggests that this pathway is effective in vivo, but that some unknown factor or condition permits it to operate on wild‐type as well as mutated attL sites.

Conclusions:  The recombination pathway described in this work apparently uses a unique attL architecture, one which requires bending by IHF and is inhibited by Int bound at the P′1 site. In addition to demonstrating the architectural flexibity of the lambda system, this pathway should be a valuable resource for separating the basic requirements of strand exchange chemistry from the features which impart directionality.
Subcellular localization of proteins governing the proteolytic activation of a developmental transcription factor in Bacillus subtilis
Authors: Resnekov Orna , Alper Scott , Losick Richard
Published: November 2003

Background: Spore formation in Bacillus subtilis takes place in a sporangium consisting of two compartments called the forespore and the mother cell. Late in development, when the forespore is wholly contained within the mother cell, gene transcription is coordinated between the compartments by an intercellular signal transduction pathway. This pathway operates at the level of proteolytic processing of the proprotein precursor (pro‐σK) to the mother‐cell transcription factor σK. The conversion of pro‐σK to σK is governed by the putative processing enzyme SpoIVFB and its negative regulator SpoIVFA, which are produced in the mother cell.

Results: We used fluorescence microscopy in conjunction with antibodies against SpoIVFA and SpoIVFB and a fusion of SpoIVFB to the Green Fluorescent Protein from Aquorea victoria to visualize these proteins in the sporangium. Both proteins were found to co‐localize with the forespore region of the sporangium, a finding consistent with the idea that SpoIVFA and SpoIVFB, which are inferred to be integral membrane proteins, are located in the mother cell membrane that surrounds the forespore.

Conclusions:  We conclude that SpoIVFA and SpoIVFB are situated at the boundary between the forespore and the mother cell, at which location SpoIVFB could be activated by a signalling protein produced in the forespore.
Molecular evolution of retinal and nonretinal opsins
Authors: Yokoyama Shozo
Published: November 2003

Vision and the circadian rhythms of various biological functions are triggered by phototransduction. The retinal and nonretinal (pineal gland‐specific) opsins are traced back to a single common ancestor. Evolutionary analyses of these opsins identify amino acid changes that are potentially important in the regulation of wavelength absorption of photosensitive molecules—visual pigments. Such theoretical predictions can now be tested experimentally using site‐directed mutagenesis; expressing the mutagenized opsins in tissue culture cells, reconstituting with 11‐cis retinal, and measuring the absorption spectra of the regenerated visual pigments.
Random and imprinted monoallelic expression
Authors: Watanabe Daisuke , Barlow Denise P.
Published: November 2003

This review has surveyed the current literature on random and imprinted monoallelic expression from the unusual perspective of considering that these two forms of monoallelic expression (MAE) may be regulated by similar mechanisms. The true extent of genes which show MAE is not yet known. Imprinted MAE is thought to involve 0.1–0.2% of mammalian genes, while the number of genes in the random MAE category cannot at present be predicted since very few genes have been examined with assays that distinguish parental transcripts in single cells. The perspective adopted in this review is speculative since only one gene (XIST) is known which displays both random and imprinted MAE. However, a recent report that H19 may also show random allelic expression, suggests that MAE should be further investigated as a gene regulation mechanism in mammals.
Upstream and downstream of erythroid transcription factor GATA‐1
Authors: Yamamoto Masayuki , Takahashi Satoru , Onodera Ko , Muraosa Yasushi , Engel James Douglas
Published: November 2003

All mature blood lineages in the peripheral circulation are derived from pluripotent haematopoietic stem cell. Progressive lineage‐restriction of this stem cell is executed, in part, by the interplay and cross‐talk between a host of lineage‐restricted as well as ubiquitous transcription factors. To elucidate the regulatory mechanisms underlying the erythroid gene regulation, it is essential to understand how individual transcription factors contribute to the regulation of specific target genes, and how these erythroid transcription factor genes are regulated in turn. These key issues of mammalian development have been addressed by examining the activities controlling the prototype transcription factor, GATA‐1. The transcriptional regulation of GATA‐1 has been intensively investigated, thereby leading to the identification of its developmental stage‐specific regulatory sequences. Loss‐of‐function mutant animals, combined with specific marking of the primitive and definitive erythroid lineages have also shed new insight into how GATA‐1 activity is required in vivo at specific developmental stages. Procedures have also been developed for ascertaining whether or not the GATA‐1 protein actually binds in vivo to regulatory GATA motifs in candidate target genes. Application of a similar multifaceted approach should enable investigators to examine the physiological roles that any transcription factor might play in vivo during the differentiation of any well defined cell lineage.
Proto‐oncogene of int‐3, a mouse Notch homologue, is expressed in endothelial cells during early embryogenesis
Authors: Shirayoshi Yasuaki , Yuasa Yoshihiro , Suzuki Takashi , Sugaya Kimihiko , Kawase Eihachiro , Ikemura Toshimichi , Nakatsuji Norio
Published: November 2003

Background: Notch and its homologues are key regulatory receptors of the cell fate decision in various developmental processes. The int‐3 oncogene was originally identified as a frequent target in Mouse Mammary Tumour Virus (MMTV)‐induced mammary tumours and has been regarded as a Notch homologue, based on its similarity to the intracellular domain of Notch. Studies with int‐3 transgenic mice have suggested that the int‐3 transgene affects the differentiation capacity of stem cells and leads to neoplastic proliferation in epithelial cells. However, the exact nature and the in vivo expression pattern of the int‐3 proto‐oncogene are unknown. The function of gene products in embryogenesis is also not clear.

Results: We isolated cDNA clones corresponding to the proto‐oncogene of int‐3 and analysed its overall structure. The predicted amino acid sequence of the int‐3 proto‐oncogene contains the conserved motif found in Notch family receptors. Therefore, we name Notch‐4 for the int‐3 proto‐oncogene. However, Notch‐4 has fewer EGF repeats and shows less similarity to Notch, compared with other mammalian Notch homologues. In embryogenesis, the expression of Notch‐4 was detected in endothelial cells of blood vessels forming tissues such as the dorsal aorta, intersegmental vessels, yolk sac vessels, cephalic vessels, heart, vessels in branchial arches, and capillary plexuses. In these tissues, Notch‐4 expression coincided with flk‐1, the major regulatory gene of vasculogenesis and angiogenesis. We also found that Notch‐4 expression was up‐regulated in vitro during the differentiation of endothelial cells from embryonic stem cells (ES cells).

Conclusion: The endothelial cell specific expression pattern of Notch‐4, as well as its structural similarity of Notch, suggest that Notch‐4 is an endothelial cell specific homologue of Notch and it may play a crucial role in vasculogenesis and angiogenesis.
Caenorhabditis elegans RBX1 is essential for meiosis, mitotic chromosomal condensation and segregation, and cytokinesis
Authors: Sasagawa Yohei , Urano Takeshi , Kohara Yuji , Takahashi Hideyuki , Higashitani Atsushi
Published: November 2003

Background:  The RING‐H2 finger protein RBX1 (ROC1/HRT1) is a common subunit of SKP1‐CDC53/CUL1‐F‐box (SCF), other cullins and von Hippel‐Lindau (VHL) tumour suppressor E3 ubiquitin ligase complexes. RBX1 protein sequences are highly conserved in various species, including yeasts, Drosophila melanogaster, mice and humans. In Saccharo‐myces cerevisiae, RBX1 is essential for the G1/S transition.

Results:  Caenorhabditis elegans RBX1 is strongly expressed in early embryos and in the gonad, including meiotic cells. Depletion of RBX1 by RNA‐mediated interference (RNAi) caused pronounced defects in the first meiotic division. Several irregular phenotypes were identified in embryos that escaped from meiotic arrest: defects in mitotic chromosomal condensation and segregation, abnormal chromosome bridges, giant nuclei, abnormal cortical protrusion, multinucleate cells and defects in germ cell proliferation. Moreover, histone H3 phosphorylation at Ser10 and Ser28 was significantly reduced in these embryos. The histone H3 phosphorylation defect of embryos was rescued by the additional depletion of protein phosphatase 1 (GLC7α/β) by RNAi.

Conclusion:  These results indicate that the RBX1 protein participates in diverse functions relevant to chromosome metabolism and cell cycle control.
Double‐stranded DNA binding properties of Saccharomyces cerevisiae DNA polymerase ɛ and of the Dpb3p‐Dpb4p subassembly
Authors: Tsubota Toshiaki , Maki Satoko , Kubota Hajime , Sugino Akio , Maki Hisaji
Published: November 2003

Background:  DNA polymerase ɛ (Pol ɛ) of Saccharomyces cerevisiae participates in many aspects of DNA replication, as well as in DNA repair. In order to clarify molecular mechanisms employed in the multiple tasks of Pol ɛ, we have been characterizing the interaction between Pol ɛ and DNA.

Results:  Analysis of the four‐subunit Pol ɛ complex by gel mobility shift assay revealed that the complex binds not only to single‐stranded (ss) DNA but also equally well to double‐stranded (ds) DNA. A truncated polypeptide consisting of the N‐terminal domain of Pol2p catalytic subunit binds to ssDNA but not to dsDNA, indicating that the Pol2p C‐terminal domain and/or the auxiliary subunits are involved in the dsDNA‐binding. The dsDNA‐binding by Pol ɛ does not require DNA ends or specific DNA sequences. Further analysis by competition experiments indicated that Pol ɛ contains at least two distinct DNA‐binding sites, one of which binds exclusively to ssDNA and the other to dsDNA. The dsDNA‐binding site, however, is suggested to also bind ssDNA. The DNA polymerase activity of Pol ɛ is inhibited by ssDNA but not by dsDNA. Furthermore, purification of the Pol ɛ auxiliary subunits Dpb3p and Dpb4p revealed that these proteins form a heterodimer and associate with dsDNA.

Conclusions:  Pol ɛ has multiple sites at which it interacts with DNA. One of these sites has a strong affinity for dsDNA, a feature that is not generally associated with DNA polymerases. Involvement of the Dpb3p‐Dpb4p complex in the dsDNA‐binding of Pol ɛ is inferred.
Stone runs in the Falkland Islands
Authors: ROSENBAUM MIKE
Published: November 2003

Large parts of the Falkland Islands are covered by conspicuous stone stripes. Their appearance is believed to be the result of partial vegetation cover developing on solifluction‐transported rock.
Loess: The Yellow Earth
Authors: Smalley Ian , Rogers Chris
Published: November 2003

A wind‐deposited silt forming large deposits in China and middle America, loess is the basis of much grade‐one agricultural land.
Azimuthal variation in AVO response for fractured gas sands
Authors: Sayers Colin M. , Rickett James E.
Published: November 2003

Natural fractures in reservoirs play an important role in determining fluid flow during production, and hence the density and orientation of fractures is of great interest. In the presence of aligned vertical fractures, the reflection amplitude at finite offset varies with azimuth. The effect of natural fractures on the azimuthal AVO response from a gas‐sandstone reservoir encased within shale is investigated. A simple expression for the difference in P‐wave reflection coefficient from the top of the reservoir parallel and perpendicular to the strike of the fractures is obtained in terms of the normal and tangential compliances, ZN and ZT, of the fractures. This expression is valid for small anisotropy and material contrasts and is compared with the results of numerical modelling. For a given value of ZT, the azimuthal variation in reflection coefficient at moderate offsets is found to increase with decreasing ZN/ZT. For gas‐filled open fractures ZN/ZT ≈ 1, but a lower ratio of ZN/ZT may result from the presence of cement or clay within the fractures, or from the presence of a fluid with non‐zero bulk modulus. For ZN/ZT = 1 and moderate offsets, the variation with offset of the reflection coefficient from the top of the fractured unit is dominated by the contrast in Poisson's ratio between the gas sand and the overlying shale, the effect of fractures only becoming noticeable as the critical angle for the unfractured sandstone is approached. However, for reflections from the base of the fractured unit, the variation in reflection amplitude with azimuth is much greater at conventional seismic offsets than for the reflection from the top. Azimuthal variations in the strength of the reflection from the top of the reservoir depend only on the variation in reflection coefficient, whereas the raypath is also a function of azimuth for reflections from the base of the fractured unit, leading to stronger, more visible, variations of AVO with azimuth. It follows that an azimuthal variation in AVO due to fractures in the overburden may be misinterpreted as due to the presence of aligned fractures in the reservoir.
Spectral factorization technique for estimation of an ARMA operator for multichannel deconvolution of seismic data
Authors: Pathak R.K. , Sengupta S. , Sinha S.
Published: November 2003

A new spectral factorization method is presented for the estimation of a causal as well as a causally invertible ARMA operator from the correlation sequence of seismic traces. The method has been implemented for multichannel deconvolution of seismic traces with the aim of exploiting the trace‐to‐trace correlation that exists within seismograms. A layered earth model with a small reflectivity sequence has been considered, and the seismic traces have been considered as the output of a linear system driven by white noise reflection coefficient sequences.  The present method is the concatenation of three algorithms, namely Kung's method for state variable (F,G,H) realization using a singular value decomposition (SVD) algorithm, Faurre's technique for computation of the strong spectral factor and Leverrier's algorithm for ARMA representation of the spectral factor. The inverted ARMA operator is used as a recursive filter for deconvolution of seismic traces. In the example shown, two traces with a covariance sequence of 160 ms length have been considered for multichannel deconvolution of stacked seismic traces. The results presented, when compared with those obtained from a conventional deconvolution algorithm, have shown encouraging prospects.
Introduction to ground surface self‐potential tomography
Authors: Patella Domenico
Published: November 2003

A new approach to self‐potential (SP) data interpretation for the recognition of a buried causative SP source system is presented. The general model considered is characterized by the presence of primary electric sources or sinks, located within any complex resistivity structure with a flat air‐earth boundary. First, using physical considerations of the nature of the electric potential generated by any arbitrary distribution of primary source charges and the related secondary induced charges over the buried resistivity discontinuity planes, a general formula is derived for the potential and the electric field component along any fixed direction on the ground surface. The total effect is written as a sum of elementary contributions, all of the same simple mathematical form. It is then demonstrated that the total electric power associated with the standing natural electric field component can be written in the space domain as a sum of cross‐correlation integrals between the observed component of the total electric field and the component of the field due to each single constitutive elementary charge. By means of the cross‐correlation bounding inequality, the concept of a scanning function is introduced as the key to the new interpretation procedure. In the space domain, the scanning function is the unit strength electric field component generated by an elementary positive charge. Next, the concept of charge occurrence probability is introduced as a suitable function for the tomographic imaging of the charge distribution geometry underground. This function is defined as the cross‐correlation product of the total observed electric field component and the scanning function, divided by the square root of the product of the respective variances. Using this physical scheme, the tomographic procedure is described. It consists of scanning the section, through any SP survey profile, by the unit strength elementary charge, which is given a regular grid of space coordinates within the section, at each point of which the charge occurrence probability function is calculated. The complete set of calculated grid values can be used to draw contour lines in order to single out the zones of highest probability of concentrations of polarized, primary and secondary electric charges. An extension to the wavenumber domain and to three‐dimensional tomography is also presented and discussed. A few simple synthetic examples are given to demonstrate the resolution power of the new SP inversion procedure.
3D targeted multiple attenuation
Authors: Kneib G. , Bardan V.
Published: November 2003

Short‐period multiple reflections pose a particular problem in the North Sea where predictive deconvolution is often only partially successful. The targeted multiple attenuation (TMA) algorithm comprises computation of the covariance matrix of preflattened prestack or post‐stack seismic data, the determination of the dominating eigenvectors of the covariance matrix, and subtraction of the related eigenimages followed by reverse flattening. The main assumption made is that the flattened multiple reflections may be represented by the first eigenimage(s) which implies that the spatial amplitude variations of primaries and associated multiples are similar. This assumption usually limits the method to short‐period multiple reflections. TMA is applicable post‐stack or prestack to common‐offset gathers. It is computationally fast, robust towards random noise, irregular geometry and spatial aliasing, and it preserves the amplitudes of primaries provided they are not parallel to the targeted multiples. Application of TMA to 3D wavefields is preferable because this allows a better discrimination between primaries and multiples. Real data examples show that the danger of partially removing primary energy can be reduced by improving the raw multiple model that is based on eigenimages, for example by prediction filtering.
Seismic migration and velocity analysis
Authors: Maeland Einar
Published: November 2003

Migration using an erroneous velocity gives a curve along which the energy is smeared. Associated with this curve is the caustic enveloped by the normal rays. It is possible to compensate for an erroneous velocity by a simple modification of the imaging principle. Formulae are derived for the general case when the velocity changes laterally, and the position of the caustic suggests how to modify the imaging principle so as to obtain an estimate of the NMO velocity. A synthetic example is used to illustrate the results of the analysis.
Magnetotelluric inversion using regularized Hopfield neural networks
Authors: Zhang Yuanchou , Paulson K. V.
Published: November 2003

Hopfield neural networks are massive parallel automata that support specific models and are adept in solving optimization problems. They suffer from a ‘rough’ solution space and convergence properties that are highly dependent on the starting model or prior. These detractions may be overcome by introducing regularization into the network in the form of local feedback smoothing. Application of regularized Hopfield networks to over 50 optimization test cases has yielded successful results, even with uniform (minimal information) priors. In particular, the non‐linear, one‐ and two‐dimensional magnetotelluric inverse problems have been solved by means of these regularized networks. The solutions compare favourably with those produced by other methods. Such regularized networks, with either hardware or programmed, parallel‐computer implementation, can be extended to the problem of three‐dimensional magnetotelluric inversion. Because neural networks are natural analog‐to‐digital converters, it is predicted that they will be the basic building blocks of future magnetotelluric instrumentation.
3D FD resistivity modelling and sensitivity analyses applied to a highly resistive phonolitic body
Authors: Spitzer K. , Kümpel H.‐J.
Published: November 2003

A highly resistive phonolitic body near Sainerholz / Westerwald in Germany has been investigated for geological mapping using vertical electrical soundings in a Schlumberger configuration. Because of its explicitly three‐dimensional shape, conventional 1D and 2D interpretation techniques are not applicable. Therefore, a new 3D finite‐difference forward modelling algorithm has been applied to acquire information about its subsurface structure and to explain the observed data. This investigation focuses on two exposed soundings: one located near the centre of the body and the other close to its rim. For the interpretation, data from electromagnetic measurements on the lateral extension of the body are additionally taken into account as well as geological a priori information. A possible 3D conductivity model is presented and evidence for its validity is discussed using model studies and sensitivity analyses. The latter are carried out using a newly developed 3D FD sensitivity modelling code with which the total subsurface response can be decomposed. This permits the determination of the resolution of model parameters, indicating the contribution of different parts of the model to the overall response. The results emphasize the feasibility of 3D forward modelling in practice.
Modelling the effects of elevated atmospheric CO2 on crown development, light interception and photosynthesis of poplar in open top chambers
Authors: CHEN S.G. , IMPENS I. , CEULEMANS R.
Published: November 2003

An open‐top chamber experiment was carried out to examine the likely effects of elevated atmospheric [CO2] on architectural as well as on physiological characteristics of two poplar clones (Populus trichocarpa × P. deltoides clone Beaupré and P. deltoides × P. nigra clone Robusta). Crown architectural parameters required as input parameters for a three‐dimensional (3D) model of poplar structure, such as branching frequency and position, branch angle, internode length and its distribution pattern, leaf size and orientation, were measured following growth in ambient and elevated [CO2 ] (ambient + 350 μmol mol–1) treated open‐top chambers. Based on this information, the light interception and photosynthesis of poplar canopies in different [CO2] treatments were simulated using the 3D poplar tree model and a 3D radiative transfer model at various stages of the growing season. The first year experiments and modelling results showed that the [CO2] enrichment had effects on light intercepting canopy structure as well as on leaf photosynthesis properties. The elevated [CO2] treatment resulted in an increase of leaf area, canopy photosynthetic rate and above‐ground biomass production of the two poplar clones studied. However, the structural components responded less than the process components to the [CO2] enrichment. Among the structural components, the increase of LAI contributed the most to the canopy light interception and canopy photosynthesis; the change of other structural aspects as a whole caused by the [CO2] enrichment had little effect on daily canopy light interception and photosynthesis.