bluuebunny/crossref_metadata_2025 huggingface dataset:
Tying synaptonemal complex initiation to the formation and programmed repair of DNA double-strand breaks
Authors: Henderson Kiersten A. , Keeney Scott
Published: March 2004

During meiosis, homologous chromosomes recombine and become closely apposed along their lengths within the synaptonemal complex (SC). In part because Spo11 is required both to make the double-strand breaks (DSBs) that initiate recombination and to promote normal SC formation in many organisms, it is clear that these two processes are intimately coupled. The molecular nature of this linkage is not well understood, but it has been proposed that SC formation initiates locally at the sites of ongoing recombination and in particular at the subset of sites that will eventually give rise to crossovers. To test this hypothesis, we examined further the relationship between DSBs and SC formation in
Saccharomyces cerevisiae
. SCs were monitored in a series of
spo11
missense mutants with varying DSB frequencies. Alleles that blocked DSB formation gave SC phenotypes indistinguishable from a deletion mutant, and partial loss-of-function mutations with progressively more severe DSB defects caused corresponding defects in SC formation. These results strongly correlate SC formation with Spo11 catalytic activity
per se
. Numbers of Zip3 complexes on chromosomes, thought to represent the sites of SC initiation, also declined when Spo11 activity decreased, but in a markedly nonlinear fashion: hypomorphic
spo11
alleles caused larger defects in DSB formation than in Zip3 complex formation. This nonlinear response of Zip3 closely paralleled the response of crossover recombination products. The quantitative relationship between Zip3 foci, SC formation, and crossing over strongly implicates crossover-designated recombination intermediates as the sites of SC initiation.
Proteomic mapping provides powerful insights into functional myelin biology
Authors: Taylor Christopher M. , Marta Cecilia B. , Claycomb Robert J. , Han David K. , Rasband Matthew N. , Coetzee Timothy , Pfeiffer Steven E.
Published: March 2004

Myelin is a dynamic, functionally active membrane necessary for rapid action potential conduction, axon survival, and cytoarchitecture. The number of debilitating neurological disorders that occur when myelin is disrupted emphasizes its importance. Using high-resolution 2D gel electrophoresis, mass spectrometry, and immunoblotting, we have developed an extensive proteomic map of proteins present in myelin, identifying 98 proteins corresponding to at least 130 of the ≈200 spots on the map. This proteomic map has been applied to analyses of the localization and function of selected proteins, providing a powerful tool to investigate the diverse functions of myelin.
Human IL-23-producing type 1 macrophages promote but IL-10-producing type 2 macrophages subvert immunity to (myco)bacteria
Authors: Verreck Frank A. W. , de Boer Tjitske , Langenberg Dennis M. L. , Hoeve Marieke A. , Kramer Matthijs , Vaisberg Elena , Kastelein Robert , Kolk Arend , de Waal-Malefyt René , Ottenhoff Tom H. M.
Published: March 2004

Macrophages (Mϕ) play a central role as effector cells in immunity to intracellular pathogens such asMycobacterium. Paradoxically, they also provide a habitat for intracellular bacterial survival. This paradoxical role of Mϕ remains poorly understood. Here we report that this dual role may emanate from the functional plasticity of Mϕ: Whereas Mϕ-1 polarized in the presence of granulocyte–Mϕ colony-stimulating factor promoted type 1 immunity, Mϕ-2 polarized with Mϕ colony-stimulating factor subverted type 1 immunity and thus may promote immune escape and chronic infection. Importantly, Mϕ-1 secreted high levels of IL-23 (p40/p19) but no IL-12 (p40/p35) after (myco)bacterial activation. In contrast, activated Mϕ-2 produced neither IL-23 nor IL-12 but predominantly secreted IL-10. Mϕ-1 required IFN-γ as a secondary signal to induce IL-12p35 gene transcription and IL-12 secretion. Activated dendritic cells produced both IL-12 and IL-23, but unlike Mϕ-1 they slightly reduced their IL-23 secretion after addition of IFN-γ. Binding, uptake, and outgrowth of a mycobacterial reporter strain was supported by both Mϕ subsets, but more efficiently by Mϕ-2 than Mϕ-1. Whereas Mϕ-1 efficiently stimulated type 1 helper cells, Mϕ-2 only poorly supported type 1 helper function. Accordingly, activated Mϕ-2 but not Mϕ-1 down-modulated their antigen-presenting and costimulatory molecules (HLA-DR, CD86, and CD40). These findings indicate that (i)Mϕ-1 and Mϕ-2 play opposing roles in cellular immunity and (ii) IL-23 rather than IL-12 is the primary type 1 cytokine produced by activated proinflammatory Mϕ-1. Mϕ heterogeneity thus may be an important determinant of immunity and disease outcome in intracellular bacterial infection.
Amniotic Sac Infection Syndrome Features Fetal Lung Neuroendocrine Cell Hyperfunction
Authors: Saad Aly G. , Heffelfinger Sue , Stanek Jerzy
Published: March 2004

Neuroendocrine cells (NEC) are abundant in fetal and neonatal lungs, but reduced in infants with hyaline membrane disease. Perinatal neuroendocrine cell hyperplasia (NCH) has been reported in the hypoplastic lung in diaphragmatic hernia, bronchopulmonary dysplasia, and Wilson-Mikity syndrome. Since we are unaware of any reports on NCH in fetal inflammatory conditions, this report addresses the NEC in fetuses with congenital pneumonia. Twenty-one fetuses/neonates with congenital pneumonia, autopsied between 1995 and 2001, were compared to 21 fetuses without a congenital infection matched for gestational age. Lung sections were immunostained for chromogranin, bombesin, calcitonin, and synaptophysin. Proportions of immunopositive cells lining 20 consecutive bronchioles calculated from digital images were significantly higher in the study than the control group for chromogranin (1.8 vs. 0.8%, P = 2.4E-06), calcitonin (1.2 vs. 0.7%, P = 0.005), and bombesin (1.1 vs. 0.7%, P = 0.005). There was no difference in synaptophysin (11.7% vs. 12.6%, P = 0.07). The absence of significant differences in the synaptophysin ratio excludes simple NCH in the study group. The synchronous increase in three neurohormones is indicative of NEC hyperfunction, due to either altered enzymatic inactivation by neutral endopeptidase, known to be reduced in adult lung inflammation, or by an increase in expression of the neurohormone genes. These data indicate that NEC hyperfunction may be responsible for the deranged fetal/neonatal lung function and circulatory adaptation, and contribute to the lethality of the amniotic sac infection syndrome.
Acute Lymphoblastic Leukemia with Hypereosinophilia: Report of a Case with 5q Deletion and Review of the Literature
Authors: Wynn Tung T. , Heerema Nyla A. , Hammond Sue , Ranalli Mark , Kahwash Samir B.
Published: March 2004

Peripheral blood eosinophilia as a presentation of acute lymphoblastic leukemia (ALL) has only rarely been reported. The eosinophilia is thought to be a nonneoplastic reaction to the neoplastic lymphoblasts. We present the case of a 5-year-old girl who developed peripheral hypereosinophilia with no circulating blasts prior to her diagnosis of B-cell lineage ALL. Cytogenetic study showed a hyperdiploid blast population with 5q deletion. Persistent peripheral hypereosinophilia should always be fully investigated, the possibility of a malignancy including ALL needs to be excluded, even in the absence of peripheral cytopenias and circulating blasts.
Concurrent Infantile Hemangioendothelioma and Mesenchymal Hamartoma in a Developmentally Arrested Liver of an Infant Requiring Hepatic Transplantation
Authors: Bejarano Pablo A. , Serrano Maria F. , Casillas Javier , Dehner Louis P. , Kato Tomoaki , Mittal Naveen , Rodriguez Maria M. , Tzakis Andreas
Published: March 2004

A newborn female underwent a surgical resection for a hepatic mass discovered prenatally by ultrasonography, and diagnosed pathologically as a mesenchymal hamartoma. Within 4 months after surgery, multiple cutaneous hemangiomas developed and a multinodular mass was detected in the liver. A liver biopsy showed an infantile hemangioendothelioma with type I features. An orthotopic liver transplant was performed due to the extensive nature of the hepatic involvement and progressive respiratory compromise. Virtually the entire liver was involved by a large infantile hemangioendothelioma. A multicystic mesenchymal hamartoma was also found on the left side. In addition, the uninvolved hepatic parenchyma had features recapitulating the fetal liver. This simultaneous involvement of the liver by a mesenchymal hamartoma and infantile hemangioendothelioma is unique. A review of the literature revealed only one incompletely characterized case with similar findings.
Patterns of species assemblages and geographical distributions associated with mandible size differences in coastal tiger beetles in Japan
Authors: Satoh Aya , Uéda Tetsuyuki , Enokido Yoshihiro , Hori Michio
Published: March 2004

Nine species of tiger beetle (Cicindelidae) occur in coastal habitats in Japan, with two to four species co‐occurring at each locality. To examine the patterns of coexistence and geographical distribution, the mandible size of co‐occurring species at 17 localities in Japan was examined, based on the assumption that competition for food is an important factor in determining these patterns. The interspecific overlap of mandible length was absent or very low in localities with two or three species, whereas it was more or less evident in localities with four species. For four large coastal species, the geographical distributions of two species with similar mandible lengths are either allopatric or parapatric, whereas those of two species with different mandible lengths largely overlap. These results strongly suggest that size‐assortment in mandible length is important in determining species assemblage and distribution in coastal tiger beetles in Japan.
Moth outbreaks in relation to oak masting and population levels of small mammals: an alternative explanation to the mammal‐predation hypothesis
Authors: Selås Vidar
Published: March 2004

The relationship between population outbreaks of the gypsy moth (Lymantria dispar) and oak masting in North America has been interpreted as an effect of reduced predation on moth pupae from small mammals after years of acorn failure. However, moth defoliation could be a consequence of high acorn production rather than of acorn failure, as all moth outbreaks in two time series presented by Liebhold et al. [Popul Ecol (2000) 42:257–266] were reported shortly after mast years. A similar pattern has been found for the green oak leaf roller moth (Tortrix viridana) in southern Norway. Because predation from small mammals should be less important for the latter species, I argue that the acorn‐moth relationships are most likely caused by mast‐induced changes in the chemical composition of oak leaves. Given the high number of eggs laid by each moth female, there is a huge potential for population growth in or shortly after a mast year if larval survival is no longer limited by low food quality.
Modeling temporal and spatial colony‐site dynamics in a long‐lived seabird
Authors: Martínez‐Abraín Alejandro , Oro Daniel , Forero Manuela G. , Conesa David
Published: March 2004

We studied the determinants of colony site dynamics in Audouin's gull,Larus audouinii, breeding in a small archipelago of the western Mediterranean. Data on island occupation were available for a series of 25 years, since first colonization of the archipelago in 1973. Group behavior was studied in relation to the components of dispersal: permanence or abandonment (extinction) on an island previously occupied and permanence or occupation (colonization) of another island. Generalized Linear Mixed Models (GLMMs) were used to identify the relative contribution of each explanatory variable to the probability of colony abandonment. Gulls showed a low probability (3%) of abandoning one of the islands (Grossa I.), especially when the colony was increasing in numbers from timeti‐1toti. However, the probability of abandoning Grossa increased up to 31% when the colony was declining. The probability of island abandonment was very high for all other islands (range 66–99%) when the colony was declining, but much lower (range 36–82%) when it was increasing. Hence, we suggest that island abandonment by Audouin's gull is at least a two‐step process. The first step (dispersal of a portion of the colony) probably takes place at random, as an evolutionary load typical of a species evolved in unstable habitats. The second step, a further loss of breeding pairs, seems to feedback on the first loss of members of the colony (public information), likely perceived as a loss of colony quality. Colonization of islands by gulls abandoning Grossa I. was marginally and negatively affected by the density of breeding yellow‐legged gulls, a predatory species. Results apply to conservation ecology since they highlight the need to protect not only occupied patches but also those empty at present.
Dimorphic migration, growth, and fecundity in a seasonally split population of Littorina brevicula (Mollusca: Gastropoda) on a boulder shore
Authors: Takada Yoshitake
Published: March 2004

Littorina brevicula (Philippi) is an abundant herbivorous gastropod species inhabiting intertidal zones of the north‐western Pacific and has internal fertilization with planktonic eggs and a larval stage. A population of L. brevicula on a shore in Amakusa, Japan, splits into an upper and a mid shore sub‐population during the mating season in winter, while all individuals occurred in the upper zone in summer. Transplant and recapture experiments have shown that snails from each sub‐population have a distinct pattern of seasonal migration, suggesting that the snail population consists of two behavioral morphs. To explore the relationship between migration pattern and life history characteristics in the snails of the two migration morphs, monthly quantitative samplings and a mark‐release and recapture survey were carried out for the population of L. brevicula over a 1‐year period. In autumn, some of the adults migrated downward to the mid shore and formed the lower sub‐population from October to April. Migration between the upper and lower sub‐populations was minimal from December to February, when L. brevicula copulate actively. The shell growth rates of the snails in the lower zone were slightly higher than those in the upper zone, but the shell width of females was not a good predictor of the number of mature ova they contained. The number of mature ova was not significantly different between the females of the two migration morphs. In addition, the mortality of marked snails did not differ significantly between the upper and lower zones. Thus, no evidence was obtained to indicate a difference in the reproductive fitness between the two migration morphs.
Land snails as a model to understand the role of history and selection in the origins of biodiversity
Authors: Davison A.
Published: March 2004

It is nearly 100 years since the first studies on variation in the shell patterns of land snails. Subsequently, snails have come to play an important role in our understanding of natural selection in the wild. In particular, snails have been an ideal model to understand the roles of history and selection in the origins of diversity. More recently, many studies have investigated the molecular genetic variation within snails. It is clear that snails are unusual, because some genes may vary by 10%–30% within a species. This molecular variation affords an excellent opportunity to further understand the action of natural selection in shaping the present‐day phenotypic diversity. In the first part of this review, I illustrate the distinction between the historical and selective interpretations using one of the best‐studied species, Cepaea nemoralis, and the example of “area effects.” In the second part, studies that have compared patterns of morphological and molecular variation (especially DNA) are examined.
The origins of postmating reproductive isolation: testing hypotheses in the grasshopper Chorthippus parallelus
Authors: Tregenza T. , Pritchard V. L. , Butlin R. K.
Published: March 2004

Although there are several well‐established hypotheses for the origins of postmating isolation during allopatric divergence, there have been very few attempts to determine their relative importance in nature. We have developed an approach based on knowledge of the differing evolutionary histories of populations within species that allows systematic comparison of the predictions of these hypotheses. In previous work, we have applied this methodology to mating signal variation and premating reproductive isolation between populations of the meadow grasshopper Chorthippus parallelus. Here we review the principles behind our approach and report a study measuring postmating isolation in the same set of populations. The populations have known and differing evolutionary histories and relationships resulting from the colonization of northern Europe following the last glaciation. We use a maximum‐likelihood analysis to compare the observed pattern of postmating isolation with the predictions of the hypotheses that isolation primarily evolves either as a result of gradual accumulation of mutations in allopatry, or through processes associated with colonization, such as founder events. We also quantify the extent to which degree of postmating isolation can be predicted by genetic distance. Our results suggest that although there is only a weak correlation between genetic distance and postmating isolation, long periods of allopatry do lead to postmating isolation. In contrast to the pattern of premating isolation described in our previous study, colonization does not seem to be associated with increased postmating isolation.
Ecological diversity and speciation in land snails of the genus Mandarina from the Bonin Islands
Authors: Chiba S.
Published: March 2004

Endemic land snails of the genus Mandarina of the oceanic Bonin Islands offer an example of habitat and character divergence among closely related species. The molecular phylogenies of Mandarina show that a divergence of arboreal, semiarboreal, and ground‐dwelling species has occurred repeatedly in different times, areas, and lineages. Ecological diversification is suggested to be important for the coexistence of Mandarina species based on the facts that sympatric species are typically highly differentiated ecologically and morphologically, and that species occupying similar habitats do not coexist. The ecological diversification of Mandarina has occurred without much genetic divergence compared with that of its mainland relatives. This suggests that morphological and ecological diversifications are accelerated in depauperate environments where there are fewer competitors and predators. Although the details of the reproductive isolation mechanisms are not understood and further examination is needed, the rapid evolution of prezygotic isolation is the main cause of speciation in Mandarina. In particular, ecological diversification may be an effective barrier to gene exchange between two species. Because of incomplete postmating isolation and the lower genetic divergence among species of Mandarina, breakdowns of reproductive isolation have frequently occurred as a result of habitat change. It is important to estimate the effect of hybridization on species diversification in future studies.
Ecology meets molecular genetics in Arabidopsis
Authors: Shimizu K. K.
Published: March 2004

Arabidopsis thaliana has been used as a model plant for molecular genetics studies. Recently, Arabidopsis has been utilized in an increasing number of ecological and evolutionary studies. These studies are beginning to explain three “black boxes” of ecology: the nature of the mutations responsible for phenotypic variation, female–male interactions in the pistil, and the genetic basis of speciation. Among the advances are the inclusive fitness of haploid gametophytes, the testing of the arms‐race model, morphological diversity, and reproductive isolation. Important methods include quantitative trait locus (QTL) mapping and molecular population genetics. Most significantly, natural variations of various aspects are now available via the taxonomic revision of its closely related species, and by the worldwide collection of accessions. Some conspicuous works using maize, Drosophila, and other species will be also discussed.
Scramble competition in Callosobruchus analis (Coleoptera: Bruchidae)
Authors: Mano H. , Toquenaga Y. , Fujii K.
Published: March 2004

Larvae of Callosobruchus analis have been used as model organisms of contest competition where only one adult can emerge from a bean irrespective of initial larval density. A new strain of C. analis found recently exhibited a higher rate of two‐adult emergence than a reference strain used in previous studies of larval competition. The higher rate of two‐adult emergence of the new strain to exhibit such behavior was investigated in terms of resource requirement examining elytron length and change in larval weight. The results showed the new strain had lower resource requirements than the reference strain. A lower encounter rate with opponents within a bean may prevent interference competition, as resource requirement becomes lower. We inferred that the new strain was not a scramble competitor but a contest competitor with small resource requirements. We also attempted to estimate the results of larval competition between the two strains, which differ in their resource requirement.
Estivation and hibernation of Pieris brassicae (L.) in southern Spain: synchronization of two complex behavioral patterns
Authors: Spieth H. R.
Published: March 2004

The large white butterfly, Pieris brassicae, has an unusually complex life‐history in its southernmost range in Western Europe. This complexity results (1) from two developmental rests, a short‐day induced hibernation and a long‐day induced estivation response, and (2) from the exceptionally early appearance of the first adult generation in January/February and a subsequent winter diapause in some of their progeny. It was found that in spring and autumn, different generations are faced with critical photophases which induce hibernation or estivation, with the consequence that in five out of six generations per year, only some develop directly whereas the others enter a dormancy phase. To assess the implications of this high number of optional responses on the generation succession, the development time was studied at various photoperiods and temperatures. The results showed that a threshold response determines the duration of estivation. With unchanged summer conditions (daylengths ≥15 h) estivation lasts on average 18–19 weeks, while with autumn conditions (daylengths ≤14 h) it lasts only 7 weeks. A change of photophases from ≥15 h to ≤14 h terminates estivation within about 3–5 weeks, slightly depending on the pupal exposure time in summer conditions. The duration of estivation is not affected by temperature or by the photophases experienced by the caterpillars. The winter diapause lasts 18–19 weeks on average with winter conditions (12°C/10.30 h light), but only 8–10 weeks with late spring conditions (21°C/15 h light). These results were used to assess the effects on the population phenology, with the finding that despite the different developmental pathways, a desynchronization of the generation succession is largely prevented. Estivation, hibernation, and direct development at different seasons are well adjusted to a common phenological pattern of a continuously reproducing population. This pattern of activity covers a cryptic dormant subpopulation, and could not have been deduced by field observations.
Herbivore abundance is independent of weather? A 20‐year study of a galling aphid Baizongia pistaciae (Homoptera: Aphidoidea)
Authors: Wool D.
Published: March 2004

The gall abundance of Baizongia pistaciae (L.) (Pemphiginae: Fordini) on marked Pistacia palaestina trees (Anacardiaceae) was monitored for 20 years at two natural sites in Israel (Carmel, in the center of the host distribution, and Beit Guvrin, near its southern limit), and in the botanical gardens of Tel Aviv University. Gall abundance varied between zero and 500 galls/tree and fluctuated from year to year. The analysis aimed at a diagnosis of the underlying causes of the temporal changes in gall abundance. Weather variables were expected to synchronize gall abundance on most trees on the same site. There was little indication of synchrony among trees in most years. Correlations of mean gall abundance with weather variables were low (<0.4, explaining <16% of the variation) and almost none were significant. The temporal pattern of gall abundance was analyzed for every tree separately (the “autecological” paradigm). There was no convincing evidence of self‐regulation (density‐dependence) in gall abundance on any tree, although the rate of change in abundance tended to decrease with increasing density on some trees. At one site (Carmel), significantly more abundance peaks (1 SD above the mean) occurred in “wet” years (precipitation above average) than in “dry” years. This pattern was not observed at the other sites. The biannual fluctuations in abundance, observed in the first 10 years of the study, were far less clear when the 20‐year sequence was analyzed. If the causative mechanism is tree stress – as assumed previously – then the biannual pattern may not be expected except in years of favorable conditions, when gall abundance is high enough to drain the tree of resources and cause a lower gall abundance the following year. The life cycle of galling aphids is very complex. A clone enclosed in a gall on a tree alternates with a subterranean population on the roots of herbaceous plants, with two migratory phases in between. Moreover, a sequence of parthenogenetic generations is interrupted by a single event of sexual reproduction. In B. pistaciae, this cycle takes two years to complete. Regulating mechanisms of gall abundance at the different stages may work in different directions, canceling each other out. I suggest that direct effects of weather on the aphids at any stage of their complex life cycle may be obscured when the net result (gall abundance) is studied. Weather effects may be detectable only when it is extremely favorable or unfavorable for the aphids (or the host plant).
The effect of osteogenic growth factors on bone growth into a ceramic filled defect around an implant
Authors: Clarke S. A. , Brooks R. A. , Lee P. T. H. , Rushton N.
Published: March 2004

Currently available synthetic bone substitutes perform poorly compared to autograft. It is hoped that by adding osteogenic growth factors to the materials, new bone formation could be increased and the clinical outcome improved. In this study, IGF‐1, bFGF and TGFβl, alone and in combination, were absorbed onto a carrier of β‐tricalcium phosphate (βTCP) and implanted into a defect around a hydroxyapatite‐coated, stainless steel implant in the proximal tibia of rat in a model of revision arthroplasty. Animals were sacrificed at 6 and 26 weeks for routine histology and histomorphometry and mechanical push out tests. The results show that only bFGF had a significant effect on ceramic resorption. The groups that received bFGF and bFGF in combination with TGFβl had smaller and fewer βTCP particles remaining in the defect at 6 and 26 weeks. No growth factor combination significantly enhanced new bone formation or the mechanical strength of the implant. These results indicate that, of the growth factors tested, only bFGF had any beneficial effect on the host response to the implant, perhaps by delaying osteoblast differentiation and thereby prolonging osteoclast access to the ceramic. © 2004 Orthopaedic Research Society. Published by Elsevier Ltd. All rights reserved.
Crystallographic analysis of AcrB
Authors: Pos Klaas M , Schiefner André , Seeger Markus A , Diederichs Kay
Published: March 2004

A His‐tagged derivative of the multidrug efflux pump AcrB could be crystallized in three different space groups (R3, R32 and P321). Experimental MAD‐phasing maps from R32 AcrBHis crystals were obtained to a resolution of 3.5 Å. Datasets of native and substrate soaked AcrBHis crystals were collected at the Swiss Light Source X06SA beamline up to a resolution of 2.7 Å and refinement of these data provided good quality electron density maps, which allowed us to complement the published AcrB structure (PDB code 1iwg). Introduction of amino acids 860–865 and 868 lacking in the 1iwg structure and deletion of a highly disordered region (amino acids 669–678) improved R
free and average B factors in the 2.7 Å model. We could not identify significant densities indicating specific antibiotic binding sites in the AcrB R32 space group datasets under the soaking conditions tested.
Mutation of the major 5′ splice site renders a CMV‐driven HIV‐1 proviral clone Tat‐dependent: connections between transcription and splicing
Authors: Bohne Jens , Kräusslich Hans-Georg
Published: March 2004

Efficient transcription from the human immunodeficiency virus type 1 long terminal repeat (HIV‐1 LTR) promoter is dependent on the viral transactivator Tat. To generate a Tat‐independent proviral plasmid, we replaced the promoter in the HIV‐1 LTR with the immediate early promoter of cytomegalovirus. Transfection of this plasmid yielded Tat‐independent production of infectious HIV‐1. Tat‐independent expression was lost, however, when the major 5′ splice site in the HIV‐1 genome was mutated and no HIV‐1‐specific RNA or protein was detected. This defect was restored when a Tat expression plasmid was cotransfected. Our results support recent reports indicating an influence of the recognition of splice sites on efficient transcriptional elongation.
Slow ADP‐dependent acceleration of microtubule translocation produced by an axonemal dynein
Authors: Kikushima Kenji , Yagi Toshiki , Kamiya Ritsu
Published: March 2004

Dynein has four nucleotide binding sites, of which the functional significance is unknown except for the single catalytic site. To obtain clues to the function of non‐catalytic nucleotide binding, we examined the effect of ADP on the in vitro motility of Chlamydomonas inner‐arm dynein species ‘a’. Upon continuous perfusion with ATP and ADP, microtubules glided on a dynein‐coated glass surface with a velocity that gradually increased over a few minutes. The velocity increased faster at higher ADP concentrations. These results suggest that this dynein is activated by nucleotide binding to regulatory site(s) through an extremely slow process.
Expression analysis of the entire MMP and TIMP gene families during mouse tissue development
Authors: Nuttall Robert K , Sampieri Clara L , Pennington Caroline J , Gill Sean E , Schultz Gilbert A , Edwards Dylan R
Published: March 2004

Matrix metalloproteinases (MMPs) and adamalysins (ADAMs) cleave many extracellular proteins, including matrix, growth factors, and receptors. We profiled the RNA levels of every MMP, several ADAMs, and inhibitors of metalloproteinases (TIMPs and RECK) in numerous mouse tissues during development and in the uterus during pregnancy. Observations include: most secreted MMPs are expressed at low to undetectable levels in tissues, whereas membrane‐bound MMPs, ADAMs and inhibitors are abundant; almost every proteinase and inhibitor is present in the uterus or placenta at some time during gestation; the mouse collagenases mColA and mColB are found exclusively in the uterus and testis; and each tissue has its unique signature of proteinase and inhibitor expression.
Resolving the evolutionary paradox of genetic instability: a cost–benefit analysis of DNA repair in changing environments
Authors: Breivik Jarle , Gaudernack Gustav
Published: March 2004

Loss of genetic stability is a critical phenomenon in cancer and antibiotic resistance, and the prevailing dogma is that unstable cells survive because instability provides adaptive mutations. Challenging this view, we have argued that genetic instability arises because DNA repair may be a counterproductive strategy in mutagenic environments. This paradoxical relationship has also been confirmed by explicit experiments, but the underlying evolutionary principles remain controversial. This paper aims to clarify the issue, and presents a model that explains genetic instability from the basic perspective of molecular evolution and information processing.
Polyamidoamine dendrimers inhibit binding of Tat peptide to TAR RNA
Authors: Zhao Hong , Li Jinru , Xi Fu , Jiang Long
Published: March 2004

The binding of polyamidoamine (PAMAM) dendrimer or Tat peptide to trans‐acting responsive element (TAR) RNA has been studied using microgravimetric quartz crystal microbalance (QCM). Experimental results showed that PAMAM dendrimer could form complexes with TAR RNA. Especially, PAMAM dendrimer could disrupt the interaction of Tat peptide with TAR RNA, which is essential for HIV‐1 virus replication, suggesting that QCM is a powerful tool for studying the binding processes of Tat peptide–TAR RNA and drug–TAR RNA and has great significance for the design of new drugs. An equation to measure the binding ability between TAR RNA and other species has been proposed.
Identification of Aniakchak (Alaska) tephra in Greenland ice core challenges the 1645 BC date for Minoan eruption of Santorini
Authors: Pearce Nicholas J. G. , Westgate John A. , Preece Shari J. , Eastwood Warren J. , Perkins William T.
Published: March 2004

Minute shards of volcanic glass recovered from the 1645 ± 4 BC layer in the Greenland GRIP ice core have recently been claimed to originate from the Minoan eruption of Santorini [Hammer et al., 2003]. This is a significant claim because a precise age for the Minoan eruption provides an important time constraint on the evolution of civilizations in the Eastern Mediterranean. There are however significant differences between the concentrations of SiO2, TiO2, MgO, Ba, Sr, Nb and LREE between the ice core glass and the Minoan eruption, such that they cannot be correlatives. New chemical analyses of tephra from the Late Holocene eruption of the Aniakchak Volcano in Alaska, however, show a remarkable similarity to the ice core glass for all elements, and this eruption is proposed as the most likely source of the glass in the GRIP ice core. This provides a precise date of 1645 BC for the eruption of Aniakchak and is the first firm identification of Alaskan tephra in the Greenland ice cores. The age of the Minoan eruption of Santorini, however, remains unresolved.
Observations of solar cyclical variations in geocoronal Hα column emission intensities
Authors: Nossal S. M. , Roesler F. L. , Mierkiewicz E. J. , Reynolds R. J.
Published: March 2004

Observations of thermospheric + exospheric Hα column emissions by the Wisconsin Hα Mapper (WHAM) Fabry‐Perot (Kitt Peak, Arizona) over the 1997–2001 rise in solar cycle 23 show a statistically significant solar cyclical variation. The higher signal‐to‐noise WHAM observations corroborate suggestions of a solar cycle trend in the Hα emissions seen in Wisconsin observations over solar cycle 22. Here we compare WHAM 1997 and 2000–2001 winter solstice geocoronal Hα observations toward regions of the sky with low galactic emission. The observed variation in geocoronal hydrogen column emission intensities over the solar cycle is small compared with variations in hydrogen exobase densities. Higher Hα emissions are seen during solar maximum periods of the solar cycle. At a mid range shadow altitude (3000 km), WHAM geocoronal Hα intensities are about 45% higher during solar maximum than during solar minimum.
Effects of aerosol and SST gradients on marine stratocumulus albedo
Authors: Hegg D. A. , Durkee P. A. , Jonsson H. H. , Nielsen K. , Covert D. S.
Published: March 2004

Airborne data are reported on the effect of sea surface temperature and aerosol gradients on the albedo of marine stratocumulus clouds off the coast of central California. Both types of gradients, at the magnitudes and spatial scales observed, produce significant and comparable trends in the cloud albedo (∼15% changes over 40 km).
Convective cooling of an initially stably stratified fluid with temperature‐dependent viscosity: Implications for the role of solid‐state convection in planetary evolution
Authors: Zaranek Sarah E. , Parmentier E. M.
Published: March 2004

The possible role of solid‐state convective cooling is important in understanding planetary thermal evolution. A stable compositional stratification in planetary mantles, which can arise from partial melting due to adiabatic decompression or from early magmatic differentiation, may suppress or delay convective instability, restrict the depth scale of convective motions, and reduce the convective heat flux out of the mantle. Two‐dimensional numerical experiments on convection in a stably stratified viscous fluid with a strongly temperature‐dependent viscosity cooled from above are carried out to understand how convecting, well‐mixed layers form and thicken in time because of cooling at the planetary surface. Simple scaling laws and parameterizations are developed that allow the results of our numerical experiments to be extrapolated to viscosity variations as large as would be expected for thermally activated creep in planetary mantles. Strongly temperature‐dependent viscosity reduces the available thermal buoyancy in the cold top boundary layer and therefore increases the impact of compositional stratification. Scaling laws for the mixed layer thickening rate indicate that thickening occurs mainly by buoyant, rather than viscous, entrainment of the underlying still stratified fluid. Compositional stratification may be important in the thermal evolution of the oceanic upper mantle, formation of cratonic continental lithosphere, and in planetary evolution, more generally. In several geologically realistic settings, a restricted depth of stratification or mantle viscosities on the order of 1018 Pa s or less are required for convective instability.
On the statistical stability of the M2 barotropic and baroclinic tidal characteristics from along‐track TOPEX/Poseidon satellite altimetry analysis
Authors: Carrère Loren , Le Provost Christian , Lyard Florent
Published: March 2004

An along‐track analysis of 7 years of TOPEX/Poseidon (T/P) data has been performed on the global ocean over the period 1993–1999. Such long time series allow us to determine the semidiurnal tidal component very accurately, while resolving the aliasing problems, at least for the main tidal wave M2. As already inferred by other authors, this along‐track analysis detects the surface signatures of the internal tides signal that maintains coherence with the M2 astronomical forcing. By analyzing the T/P data in different periods of 3 years or more, the stability of the M2 tidal characteristics is demonstrated for the barotropic component as well as for the baroclinic signal observed in the altimetric data. This stability varies with location. For the barotropic component the dispersion of the results as a function of the length and period of analysis is only significant over the areas of ocean mesoscale activity (noise impact) and of large barotropic tidal signal (separating the different components of the tidal signal proves difficult). The baroclinic tidal signal appears to be surprisingly stable over many areas located around strong topographic gradients like submarine ridges. A methodology has been developed to draw a map of these areas. This can be of help for ocean modelers to specify areas of higher vertical mixing associated with internal tidal wave activity and for those who assimilate altimetric data in their models by giving guidance on where to increase the uncertainty of the altimeter data over these areas.
Satellite observations of the water vapor greenhouse effect and column longwave cooling rates: Relative roles of the continuum and vibration‐rotation to pure rotation bands
Authors: Inamdar Anand K. , Ramanathan V. , Loeb Norman G.
Published: March 2004

The Clouds and the Earth's Radiant Energy System (CERES) instrument on board the Tropical Rainfall Measuring Mission (TRMM) satellite provides, for the first time, a large‐scale (40 S to 40 N) data set for the atmospheric greenhouse effect and the column‐averaged longwave (LW) radiative cooling rates in the broadband (5–100 microns) and the window (8–12 microns) regions. We demonstrate here that the separation into the window and the nonwindow (5–8 microns and 12–100 microns) fluxes provides the first global‐scale data set to exhibit the sensitivity of the atmospheric greenhouse effect to vertical water vapor distribution. The nonwindow greenhouse effect varies linearly with the logarithm of column water vapor amount weighted with the atmospheric pressure, while the window component varies quadratically with the water vapor partial pressure. The column cooling rates range from about −170 to −210 W m−2 for the nonwindow region. The window cooling rates are only about 10% to 20% of the above range and approach rapidly to near‐zero values for surface temperatures less than 288 K. The nonwindow component of the greenhouse effect and cooling rates are shown to be more sensitive to upper troposphere water vapor, while the window greenhouse effect and cooling rates are shown to be more sensitive to the lower troposphere water vapor amount. In addition, the data reveal that in tropical regions, with warm sea surface temperatures (greater than 297 K) and elevated upper tropospheric water vapor amounts, the continuum emission in the window region leads to enhanced cooling of the column, while the rotational bands in the nonwindow region lead to a net decrease in the longwave cooling of the atmospheric column.
CO as an important high‐altitude tracer of dynamics in the polar stratosphere and mesosphere
Authors: de Zafra R. L. , Muscari G.
Published: March 2004

We present new ground‐based measurements of polar stratospheric and mesospheric CO, made with a millimeter‐wave spectrometer at Thule, Greenland (76.5°N, 68.7°W). Almost daily measurements were made between 17 January and 4 March 2002 and again between 5 January and 22 February 2003. We stress here the retrieval and analysis of CO mixing ratios in the 50–80 km altitude range, though it can be monitored at lower altitudes as well. Since CO exhibits a strong positive latitude gradient from the summer to the winter pole, it is an excellent tracer for poleward transport from lower latitudes. Moreover, the mixing ratio of CO increases rapidly from ∼40 km to at least 100 km at midlatitudes, providing a good tracer for high‐altitude vertical transport as well. Our profiles indicate that in winter near the poles the CO mixing ratio decreases above ∼70 km because of subsidence of air and minimal high‐altitude photoproduction at high latitudes. Our data also show large variations in mixing ratio and vertical distribution, yielding a good picture of stratospheric and mesospheric dynamics‐induced changes on a scale of hours to days. These observations verify that CO serves as an excellent tracer of vortex‐related dynamics in the 30–80 km altitude range, where other information, particularly above ∼40 km, may be sparse, unreliable, or nonexistent. Our results are in general agreement with analyses of 1991–1992 Improved Stratospheric and Mesospheric Sounder (ISAMS) satellite data by Lopez‐Valverde et al. [1993, 1996] and by Allen et al. [1999, 2000]. We show the contrast between CO over the summer pole and CO over the winter pole with the aid of trial observations made at the South Pole during the austral summer of 1999–2000. Our Thule data indicate that large concentrations of CO generally exist in winter just outside the vortex boundary. The large rapid variations in vertical profile that are found in our data in 2002 appear to be well correlated with vortex position in the lower stratosphere. In 2003 this correlation appeared to be much weaker, but early 2003 was also a period of vortex splitting in the Arctic on three occasions during our observation period, accompanied by generally more complex vortex dynamics.
Plume‐induced topography and geoid anomalies and their implications for the Tharsis rise on Mars
Authors: Roberts James H. , Zhong Shijie
Published: March 2004

The topography and geoid anomalies produced from an upwelling plume are sensitive to the depth of plume buoyancy, Dp, and elastic lithospheric thickness, Te, both of which control the degree of compensation. We formulated spherically axisymmetric convection models of mantle plumes with temperature‐ and pressure‐dependent viscosity to dynamically determine Dp and Te and the resulting topography and geoid anomalies from the plume. From 10 cases with different Rayleigh number, activation energy, and activation volume, we determined Te ranging from 100 km to 180 km and Dp that is approximately twice Te. The ratio of geoid to topography, RG/T, from these plume models is either negative or slightly positive (<0.03) at wavelengths that are most relevant to the Tharsis rise (low harmonics from degrees 2 to 4). The modeled RG/T is significantly smaller than that observed for the Tharsis rise, suggesting that Tharsis is unlikely to be dynamically supported.
Definition and measurement of dust aeolian thresholds
Authors: Roney Jason A. , White Bruce R.
Published: March 2004

Dust suspension and particle “saltation threshold” speeds were measured in an environmental boundary layer wind tunnel located at the University of California, Davis. The results indicate that dust suspension threshold speeds occur at substantially lower friction speeds than “saltation threshold” speeds. Many of the dust suspension threshold values are half of the “saltation threshold” values. For example, surface soils from the most erodible areas of Owens (dry) Lake were tested in the wind tunnel, and we found that dust suspension thresholds varied from 50 to 75% of conventional “saltation threshold” values. Current regulatory models relying on “visual threshold” for estimating suspended dust may be incorrect and may lead to substantial underestimates of suspended material yield over large, expansive, erodible areas. Wind environments with average wind speeds at or around the “saltation threshold” speed values are especially susceptible to underestimation. Though this study focuses only on Owens (dry) Lake soils, we believe that the witnessed effect will occur in any soil with an abundance of dust particles interspersed among sand‐sized particles.
Fiber-optic sensor system for heat-flux measurement
Authors: Shen Yonghang , He Jinglei , Zhao Weizhong , Sun Tong , Grattan Kenneth T. V. , Pritchard William D. N.
Published: March 2004

Two different types of fiber-optic sensors were used in an experiment to measure the heat flux in a simulated refractory lining material. The results obtained with a sensor based on fluorescence lifetime detection and a sensor based on the peak wavelength shift of a fiber Bragg grating are presented and compared. Analysis of the results of the measurements taken indicates that these fiber-optic sensor systems are capable of performing multipoint temperature, and thus the heat flux, measurements. An approach is also presented for the measurement of the temperature dependence of the conductivity coefficient of the materials concerned, using the sensor systems detailed.
High brightness GaInAs/(Al)GaAs quantum-dot tapered lasers at 980 nm with high wavelength stability
Authors: Auzanneau Sophie-Charlotte , Calligaro Michel , Krakowski Michel , Klopf Frank , Deubert Stefan , Reithmaier Johann Peter , Forchel Alfred
Published: March 2004

High brightness (2 W with M2=3.4) is demonstrated at 980 nm using a gain-guided tapered GaInAs/(Al)GaAs quantum-dot laser. A remarkable low temperature shift (0.09 nm/K) of the emission wavelength is observed. Moreover, at 20 °C, the emission wavelength is quasiconstant as a function of the injected current.