bluuebunny/crossref_metadata_2025 huggingface dataset:
The TodS–TodT two-component regulatory system recognizes a wide range of effectors and works with DNA-bending proteins
Authors: Lacal Jesús , Busch Andreas , Guazzaroni María-Eugenia , Krell Tino , Ramos Juan L.
Published: May 2006

The TodS and TodT proteins form a previously unrecognized and highly specific two-component regulatory system in which the TodS sensor protein contains two input domains, each of which are coupled to a histidine kinase domain. This system regulates the expression of the genes involved in the degradation of toluene, benzene, and ethylbenzene through the toluene dioxygenase pathway. In contrast to the narrow substrate range of this catabolic pathway, the TodS effector profile is broad. TodS has basal autophosphorylation activity
in vitro
, which is enhanced by the presence of effectors. Toluene binds to TodS with high affinity (
K
d
= 684 ± 13 nM) and 1:1 stoichiometry. The analysis of the truncated variants of TodS reveals that toluene binds to the N-terminal input domain (
K
d
= 2.3 ± 0.1 μM) but not to the C-terminal half. TodS transphosphorylates TodT, which binds to two highly similar DNA binding sites at base pairs −107 and −85 of the promoter. Integration host factor (IHF) plays a crucial role in the activation process and binds between the upstream TodT boxes and the −10 hexamer region. In an IHF-deficient background, expression from the
tod
promoter drops 8-fold.
In vitro
transcription assays confirmed the role determined
in vivo
for TodS, TodT, and IHF. A functional model is presented in which IHF favors the contact between the TodT activator, bound further upstream, and the α-subunit of RNA polymerase bound to the downstream promoter element. Once these contacts are established, the
tod
operon is efficiently transcribed.
Optimization of WAVE2 complex–induced actin polymerization by membrane-bound IRSp53, PIP3, and Rac
Authors: Suetsugu Shiro , Kurisu Shusaku , Oikawa Tsukasa , Yamazaki Daisuke , Oda Atsushi , Takenawa Tadaomi
Published: May 2006

WAVE2 activates the actin-related protein (Arp) 2/3 complex for Rac-induced actin polymerization during lamellipodium formation and exists as a large WAVE2 protein complex with Sra1/PIR121, Nap1, Abi1, and HSPC300. IRSp53 binds to both Rac and Cdc42 and is proposed to link Rac to WAVE2. We found that the knockdown of IRSp53 by RNA interference decreased lamellipodium formation without a decrease in the amount of WAVE2 complex. Localization of WAVE2 at the cell periphery was retained in IRSp53 knockdown cells. Moreover, activated Cdc42 but not Rac weakened the association between WAVE2 and IRSp53. When we measured Arp2/3 activation in vitro, the WAVE2 complex isolated from the membrane fraction of cells was fully active in an IRSp53-dependent manner but WAVE2 isolated from the cytosol was not. Purified WAVE2 and purified WAVE2 complex were activated by IRSp53 in a Rac-dependent manner with PIP3-containing liposomes. Therefore, IRSp53 optimizes the activity of the WAVE2 complex in the presence of activated Rac and PIP3.
NDC1: a crucial membrane-integral nucleoporin of metazoan nuclear pore complexes
Authors: Stavru Fabrizia , Hülsmann Bastian B. , Spang Anne , Hartmann Enno , Cordes Volker C. , Görlich Dirk
Published: May 2006

POM121 and gp210 were, until this point, the only known membrane-integral nucleoporins (Nups) of vertebrates and, thus, the only candidate anchors for nuclear pore complexes (NPCs) within the nuclear membrane. In an accompanying study (see Stavru et al. on p. 477 of this issue), we provided evidence that NPCs can exist independently of POM121 and gp210, and we predicted that vertebrate NPCs contain additional membrane-integral constituents. We identify such an additional membrane protein in the NPCs of mammals, frogs, insects, and nematodes as the orthologue to yeast Ndc1p/Cut11p. Human NDC1 (hNDC1) likely possesses six transmembrane segments, and it is located at the nuclear pore wall. Depletion of hNDC1 from human HeLa cells interferes with the assembly of phenylalanine-glycine repeat Nups into NPCs. The loss of NDC1 function in Caenorhabditis elegans also causes severe NPC defects and very high larval and embryonic mortality. However, it is not ultimately lethal. Instead, homozygous NDC1-deficient worms can be propagated. This indicates that none of the membrane-integral Nups is universally essential for NPC assembly, and suggests that NPC biogenesis is an extremely fault-tolerant process.
Riding the DUBway: regulation of protein trafficking by deubiquitylating enzymes
Authors: Millard Susan M. , Wood Stephen A.
Published: May 2006

Ubiquitylation is a key regulator of protein trafficking, and much about the functions of ubiquitin ligases, which add ubiquitin to substrates in this regulation, has recently come to light. However, a clear understanding of ubiquitin-dependent protein localization cannot be achieved without knowledge of the role of deubiquitylating enzymes (DUBs). DUBs, by definition, function downstream in ubiquitin pathways and, as such, have the potential to be the final editors of protein ubiquitylation status, thus determining substrate fate. This paper assimilates the current evidence concerning the substrates and activities of DUBs that regulate protein trafficking.
Mechanisms Underlying Heterogeneous Ca2+ Sparklet Activity in Arterial Smooth Muscle
Authors: Navedo Manuel F. , Amberg Gregory C. , Nieves Madeline , Molkentin Jeffery D. , Santana Luis F.
Published: May 2006

In arterial smooth muscle, single or small clusters of Ca2+ channels operate in a high probability mode, creating sites of nearly continual Ca2+ influx (called “persistent Ca2+ sparklet” sites). Persistent Ca2+ sparklet activity varies regionally within any given cell. At present, the molecular identity of the Ca2+ channels underlying Ca2+ sparklets and the mechanisms that give rise to their spatial heterogeneity remain unclear. Here, we used total internal reflection fluorescence (TIRF) microscopy to directly investigate these issues. We found that tsA-201 cells expressing L-type Cavα1.2 channels recapitulated the general features of Ca2+ sparklets in cerebral arterial myocytes, including amplitude of quantal event, voltage dependencies, gating modalities, and pharmacology. Furthermore, PKCα activity was required for basal persistent Ca2+ sparklet activity in arterial myocytes and tsA-201 cells. In arterial myocytes, inhibition of protein phosphatase 2A (PP2A) and 2B (PP2B; calcineurin) increased Ca2+ influx by evoking new persistent Ca2+ sparklet sites and by increasing the activity of previously active sites. The actions of PP2A and PP2B inhibition on Ca2+ sparklets required PKC activity, indicating that these phosphatases opposed PKC-mediated phosphorylation. Together, these data unequivocally demonstrate that persistent Ca2+ sparklet activity is a fundamental property of L-type Ca2+ channels when associated with PKC. Our findings support a novel model in which the gating modality of L-type Ca2+ channels vary regionally within a cell depending on the relative activities of nearby PKCα, PP2A, and PP2B.
High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis
Authors: West Marilyn A.L. , van Leeuwen Hans , Kozik Alexander , Kliebenstein Daniel J. , Doerge R.W. , St. Clair Dina A. , Michelmore Richard W.
Published: May 2006

Expression microarrays hybridized with RNA can simultaneously provide both phenotypic (gene expression) and genotypic (marker) data. We developed two types of genetic markers from Affymetrix GeneChip expression data to generate detailed haplotypes for 148 recombinant inbred lines (RILs) derived from Arabidopsis thaliana accessions Bayreuth and Shahdara. Gene expression markers (GEMs) are based on differences in transcript levels that exhibit bimodal distributions in segregating progeny, while single feature polymorphism (SFP) markers rely on differences in hybridization to individual oligonucleotide probes. Unlike SFPs, GEMs can be derived from any type of DNA-based expression microarray. Our method identifies SFPs independent of a gene’s expression level. Alleles for each GEM and SFP marker were ascertained with GeneChip data from parental accessions as well as RILs; a novel algorithm for allele determination using RIL distributions capitalized on the high level of genetic replication per locus. GEMs and SFP markers provided robust markers in 187 and 968 genes, respectively, which allowed estimation of gene order consistent with that predicted from the Col-0 genomic sequence. Using microarrays on a population to simultaneously measure gene expression variation and obtain genotypic data for a linkage map will facilitate expression QTL analyses without the need for separate genotyping. We have demonstrated that gene expression measurements from microarrays can be leveraged to identify polymorphisms across the genome and can be efficiently developed into genetic markers that are verifiable in a large segregating RIL population. Both marker types also offer opportunities for massively parallel mapping in unsequenced and less studied species.
A Social-Neuroscience Perspective on Empathy
Authors: Decety Jean , Jackson Philip L.
Published: May 2006

In recent years, abundant evidence from behavioral and cognitive studies and functional-imaging experiments has indicated that individuals come to understand the emotional and affective states expressed by others with the help of the neural architecture that produces such states in themselves. Such a mechanism gives rise to shared representations, which constitutes one important aspect of empathy, although not the sole one. We suggest that other components, including people's ability to monitor and regulate cognitive and emotional processes to prevent confusion between self and other, are equally necessary parts of a functional model of empathy. We discuss data from recent functional-imaging studies in support of such a model and highlight the role of specific brain regions, notably the insula, the anterior cingulate cortex, and the right temporo-parietal region. Because this model assumes that empathy relies on dissociable information-processing mechanisms, it predicts a variety of structural or functional dysfunctions, depending on which mechanism is disrupted.
Polymorphisms of the porcine dopamineβ‐hydroxylase gene and their relation to reproduction and piglet survivability in an Iberian × Meishan F2 intercross
Authors: Tomás A. , Casellas J. , Ramírez O. , Pérez‐Enciso M. , Rodríguez C. , Noguera J. L. , Sánchez A.
Published: May 2006

The goals of this study were to sequence and physically map the porcine dopamineβ‐hydroxylase (DBH) gene, as well as to perform an association study between polymorphisms of this gene and the reproductive performance and piglet survivability of F2 pigs from an Iberian × Meishan cross. The porcine DBH gene was positioned by RH mapping near the telomere of chromosome 1q2.13, close to markers SSC10D08 and SW1301. Sequencing of DBH cDNAs from 10 pigs revealed the existence of six nucleotide polymorphisms, two of which led to non‐synonymous amino acid substitutions within exon 3 at positions 463A>G and 616A>G that corresponded to Thr155Ala and Lys206Glu respectively. Three haplotypes segregated in an Iberian × Meishan population: DBHX (A436–A616), DBHY (A436–G616) and DBHZ (G436–G616). The DBH haplotypes significantly affected rectal temperatures 1 h after birth (P = 0.002) and have a suggestive effect on the time to first colostrum intake (P = 0.019) and on birth weight (P = 0.019).
The turnover of carbon pools contributing to soil CO2 and soil respiration in a temperate forest exposed to elevated CO2 concentration
Authors: TANEVA LINA , PIPPEN JEFFREY S. , SCHLESINGER WILLIAM H. , GONZALEZ‐MELER MIQUEL A.
Published: May 2006

Soil carbon is returned to the atmosphere through the process of soil respiration, which represents one of the largest fluxes in the terrestrial C cycle. The effects of climate change on the components of soil respiration can affect the sink or source capacity of ecosystems for atmospheric carbon, but no current techniques can unambiguously separate soil respiration into its components. Long‐term free air CO2 enrichment (FACE) experiments provide a unique opportunity to study soil C dynamics because the CO2 used for fumigation has a distinct isotopic signature and serves as a continuous label at the ecosystem level. We used the 13C tracer at the Duke Forest FACE site to follow the disappearance of C fixed before fumigation began in 1996 (pretreatment C) from soil CO2 and soil‐respired CO2, as an index of belowground C dynamics during the first 8 years of the experiment. The decay of pretreatment C as detected in the isotopic composition of soil‐respired CO2 and soil CO2 at 15, 30, 70, and 200 cm soil depth was best described by a model having one to three exponential pools within the soil system. The majority of soil‐respired CO2 (71%) originated in soil C pools with a turnover time of about 35 days. About 55%, 50%, and 68% of soil CO2 at 15, 30, and 70 cm, respectively, originated in soil pools with turnover times of less than 1 year. The rest of soil CO2 and soil‐respired CO2 originated in soil pools that turn over at decadal time scales. Our results suggest that a large fraction of the C returned to the atmosphere through soil respiration results from dynamic soil C pools that cannot be easily detected in traditionally defined soil organic matter standing stocks. Fast oxidation of labile C substrates may prevent increases in soil C accumulation in forests exposed to elevated [CO2] and may consequently result in shorter ecosystem C residence times.
Antioxidant activities of different Teucrium montanum L. Extracts
Authors: Čanadanović‐Brunet Jasna M. , Djilas Sonja M. , Ćetković Gordana S. , Tumbas Vesna T. , Mandić Anamarija I. , Čanadanović Vladimir M.
Published: May 2006

The sequential extraction of Teucrium montanum L. was realised with five solvents of different polarities (70% methanol, petroleum ether, chloroform, ethyl acetate, and n‐butanol) and HPLC method was used for identification of phenolic compounds. The total phenolic content of the extracts was determined spectrophotometrically according to the Folin–Ciocalteau procedure and range from 0 to 296 mg g−1. The antioxidant activity of extracts was tested by measuring their ability to scavenge reactive hydroxyl radical during the Fenton reaction, using electron spin resonance (ESR) spectroscopy. Moreover, the influence of these extracts on lipid peroxyl radicals obtained during lipid peroxidation of: (1) sunflower oil (37 °C, 3 h) induced by 4,4′‐azobis(4‐cyanovaleric acid) (ACVA) and (2) liposomes induced by 2,2′‐azobis(2‐amidino‐propane)dihydrochloride (AAPH) was studied. n‐Butanol extract, because of the highest content of total phenolic compounds (296 mg g−1) had the best antioxidant activity (100% at 0.16 mg mL−1 in Fenton reaction system; 90.57% at 5 mg mL−1 in system I; 100% at 5 mg mL−1 in system II).
Phylogeography of the lacertid lizard, Psammodromus algirus, in Iberia and across the Strait of Gibraltar
Authors: Carranza S. , Harris D. J. , Arnold E. N. , Batista V. , Gonzalez de la Vega J. P.
Published: May 2006

Aim  To determine genetic substructuring within the lacertid lizard Psammodromus algirus. To compare levels of variation across a geological barrier, the Strait of Gibraltar, and to compare this against the known age of the barrier using a molecular clock hypothesis. To compare the effect of the barrier within this species with previously published data from other organisms.

Location  The Iberian Peninsula and North Africa.

Methods  Partial sequences from the mitochondrial cytochrome b, 12S rRNA and 16S rRNA genes were obtained from 101 specimens belonging to the subfamily Gallotiinae and used in this study. The data set was aligned using ClustalX and phylogenetic trees produced using both maximum‐parsimony and maximum‐likelihood methods. Maximum likelihood estimates of divergence times for the combined data set (12S + 16S + cytochrome b) were obtained after discovery of lineage rate constancy across the tree using a likelihood ratio test.

Results  Psammodromus algirus contains divergent eastern and western mtDNA clades within the Iberian Peninsula. The western clade has northern and southern lineages in Iberia and one in North Africa. This phylogeographical pattern indicates that the lizard invaded North Africa after the opening of the Strait, presumably by natural rafting.

Main conclusions  As in several other species, current patterns of genetic diversity within P. algirus are not directly related to the opening of the Strait of Gibraltar. Widespread sampling on both sides of the barrier is necessary to determine its effect on species in this area accurately.
Diurnal Variation in the Responsiveness of the Hypothalamic‐Pituitary‐Adrenal Axis of the Male Rat to Noise Stress
Authors: Atkinson H. C. , Wood S. A. , Kershaw Y. M. , Bate E. , Lightman S. L.
Published: May 2006

Basal activity of the rat hypothalamic‐pituitary‐adrenal (HPA) axis is highly dynamic and displays both circadian and ultradian rhythmicity in corticosterone secretion. This study investigated the relationship between basal corticosterone pulsatility and the corticosterone response to noise during the early light phase when there are no endogenous corticosterone pulses and during the early dark phase when there are hourly pulses of corticosterone. An automated blood sampling system was used to collect blood in conscious male rats at 5‐min intervals before, during and after exposure to 10‐min periods of white noise (104 dB). Behavioural responses to noise were also monitored during these periods. During the early light phase (morning), there was a consistent corticosteroid response to noise with corticosterone concentrations rising rapidly and reaching peak values 10–15 min after the noise had ceased, following which circulating concentrations declined at a rate comparable to the hormones half‐life. A second noise stress, 80 min later, resulted in adaptation of the corticosterone response. During the early dark phase (evening), the corticosterone response to the noise was similar to that seen in the morning, although there was no adaptation to a second stimulus. During the evening, the inhibition of endogenous HPA activity after the sound was limited to 40 min following stress.
Use of the oculocardiac reflex to assess vagal reactivity during quiet sleep in neonates
Authors: DUCROCQ JACQUES , CARDOT VIRGINIE , TOURNEUX PIERRE , CHARDON KAREN , TELLIEZ FRÉDÉRIC , LIBERT JEAN‐PIERRE , DE BROCA ALAIN , BACH VÉRONIQUE
Published: May 2006

Arousal from sleep can be a protective response to life‐threatening stimuli. Hence, faults within state‐switching processes may lead to fatal events. To investigate the role of the nervous system during cardiac failure triggered by phasic, vagally mediated stimulation, we analysed autonomic and behavioural reactions in 50 premature neonates during quiet sleep (QS) – a sleep state characterized by a preponderance of tonic, parasympathetic activity. Bradycardia was induced with a standardized ocular compression test. Neither awakening nor behavioural escape reactions were observed during or after an episode of bradycardia. Eighty‐six per cent of the provoked bradycardic episodes induced central apnoea. During QS, the neonates’ respiratory response and arousability were found to be time‐dependent: when the test was performed early in the QS episode, apnoea was more frequent (94%), and no sleep state change occurred. When ocular compression was performed in the later part of the QS episode, a transition towards active sleep was observed, together with significantly fewer episodes of apnoea (64%). These results indicate that a progressive decrease in the respiratory system's responsiveness to phasic, parasympathetic stimulation occurs during QS, whereas arousability increases. Our study suggests that newborns could be more vulnerable to potentially fatal events during the initial portion of a QS episode.
The cardiorespiratory activation response at an arousal from sleep is independent of the level of CO2
Authors: TRINDER JOHN , IVENS CLARE , KLEIMAN JAN , KLEVERLAAN DARCI , WHITE DAVID P.
Published: May 2006

Arousal from sleep is associated with transient cardiorespiratory activation. Traditionally, this response has been understood to be a consequence of state‐dependent changes in the homeostatic control of ventilation. The hypothesis predicts that the magnitude of ventilatory and cardiac responses at an arousal will be a function of the intensity of concurrent respiratory stimuli (primarily PCO2). Alternatively, it has been proposed that increased cardiorespiratory activity is due to reflex activation. This hypothesis predicts that the magnitude of the cardiorespiratory response will be independent of respiratory stimuli. To compare these hypotheses we measured minute ventilation (Vi), heart rate (HR) and blood pressure (BP) during wakefulness and stage 2 sleep, while manipulating PetCO2. Further, we assessed the magnitude of the response of these variables to an arousal from sleep at the various levels of PetCO2. The subjects were male aged 18–25 years. PetCO2 was manipulated by clamping it at four levels during wakefulness [wake eucapnic, sleep eucapnic (Low), and sleep eucapnic +3 mmHg (Medium) and +6 mmHg (High)] and three levels during sleep (Low, Medium and High). The average number of determinations for each subject at each level was 14 during wakefulness and 25 during sleep. Arousals were required to meet American Sleep Disorders Association criteria and were without body movement. The results indicated that average increases in Vi, HR and BP at arousal from sleep did not significantly differ as a function of the level of PetCO2 present at the time of the arousal (all P > 0.05). Further, the magnitude of the ventilatory response to an arousal was significantly less than the values predicted by the homeostatic hypothesis (P < 0.05). We conclude that, in normal subjects, the cardiorespiratory response to an arousal from sleep is not because of a homeostatic response, but of a reflex activation.
Circadian and homeostatic sleep regulation in morningness–eveningness
Authors: MONGRAIN V. , CARRIER J. , DUMONT M.
Published: May 2006

Morningness–eveningness has been associated with the entrained circadian phase. However, we recently identified morning and evening types having similar circadian phases. In this paper, we compared parameters of slow‐wave activity (SWA) decay in non‐rapid‐eye‐movement (NREM) sleep between these two subgroups to test the hypothesis that differences in the dynamics of nocturnal homeostatic sleep pressure could explain differences in sleep timing preference. Twelve morning‐type subjects and 12 evening‐type subjects with evening types (aged 19–34 years) selected using the Morningness–Eveningness Questionnaire were further classified according to the phase of their dim light melatonin onset (DLMO). The six morning types with the earliest DLMO were compared to the six evening types with the latest DLMO (‘extreme’ phases), and the six morning types with the latest DLMO were compared to the six evening types with the earliest DLMO (‘intermediate’ phases). Subjects slept according to their preferred sleep schedule. Spectral activity in four midline derivations (Fz, Cz, Pz, Oz) was calculated in NREM sleep and an exponential decay function was applied on SWA data averaged per sleep cycle. In the subjects with intermediate circadian phases, both initial level and decay rate of SWA in Fz were significantly higher in morning than in evening types. No difference appeared between chronotypes of extreme circadian phases. There was no correlation between individual estimates of SWA decay and DLMO. These results support the hypothesis that chronotype can originate from differences in the dissipation of sleep pressure and that homeostatic and circadian processes influence the sleep schedule preference independently.
Oxygen dynamics during submergence in the halophytic stem succulentHalosarcia pergranulata
Authors: PEDERSEN O. , VOS H. , COLMER T. D.
Published: May 2006

This study elucidated O2dynamics in shoots and roots of submergedHalosarcia pergranulata(Salicornioideae), a perennial halophytic stem succulent that grows on flood‐prone mudflats of salt lakes. Oxygen within shoots and roots was measured using microelectrodes, for plants when waterlogged or completely submerged, with shoots in light or in darkness, in a controlled environment. Net photosynthesis (PN) when underwater, at a range of dissolved CO2concentrations, was measured by monitoring O2production rates by excised stems. The bulky nature and apparently low volume of gas‐filled spaces of the succulent stems resulted in relatively high radial resistance to gas diffusion. At ambient CO2, quasi‐steady state rates ofPNby excised succulent stems were estimated to be close to zero; nevertheless, in intact plants, underwater photosynthesis provided O2to tissues and led to radial O2loss (ROL) from the roots, at least during the first several hours (the time period measured) after submergence or when light periods followed darkness. The influence of light on tissue O2dynamics was confirmed in an experiment on a submerged plant in a salt lake in south‐western Australia. In the late afternoon, partial pressure of O2(pO2) in the succulent stem was 23.2 kPa (i.e. ∼10% above that in the air), while in the roots, it was 6.2–9.8 kPa. Upon sunset, the pO2in the succulent stems declined within 1 h to below detection, but then showed some fluctuations with the pO2increasing to at most 2.5 kPa during the night. At night, pO2in the roots remained higher than in the succulent stems, especially for a root with the basal portion in the floodwater. At sunrise, the pO2increased in the succulent stems within minutes. In the roots, changes in the pO2lagged behind those in the succulent stems. In summary, photosynthesis in stems of submerged plants increased the pO2in the shoots and roots so that tissues experience diurnal changes in the pO2, but O2from the H2O column also entered submerged plants.
Canine Spinal Cord Neuron and Axon Myelin Sheath Morphometry
Authors: De Francischini Carvalho A. C. , Pacheco M. R. , Baraldi Artoni S. M. , Mateus O.
Published: May 2006

This inedited morphometric study has been developed from healthy canine spinal cord neuron cytoplasm and nucleus, and white matter axonal myelin sheath, from cervical, thoracic and lumbar regions. For the morphometric study, the parameters were area, perimeter, maximum and minimum diameters and roundness for neurons and myelin thickness for axon. For each parameter, 300 neurons were analysed. The results revealed that lumbar neurons had the highest mean values for the analysed parameters, indicating the presence of large neurons in this region, with large axons as a result of myelin thickness, which is proportional to axon calibre. We conclude that these morphometric results can contribute for the establishment of normal patterns, for canine spinal cord cervical, thoracic and lumbar segments.
Quantification by Image Analysis of the Gallus gallus Lung Elastic Fibres from Embryonic to Adult Birds
Authors: De Lurdes Pinto M. , Gonçalves C. , Rodrigues P. , Bairos V. A.
Published: May 2006

The organization of the lung's elastic fibres is amazingly uniform in all vertebrates, with the possible exception of birds, whose pulmonary architecture and air movement are unique. The overall goal of this work was to study and quantify elastic fibre distribution patterns and relative amounts in the parabronchi, during the incubation period until the 42nd day after hatching. Chick embryo lungs were examined on the 14th, 16th, 18th and 20th days of incubation and chick lungs on the 1st, 2nd, 7th, 14th, 35th and 42nd days after hatching. Four animals were used daily, and the observations were randomly performed on both lungs. A morphometric study was carried out focusing on the computerized image analysis of histological sections stained according to a modified Gomori technique. The values obtained for each day result from the observation and processing of 20 images. Complementary studies were performed using transmission electron microscopy, as on the 14th embryonic day the fibres were not visible on light microscopy. The results show that the area occupied by the elastic fibres increases gradually from the 16th day of incubation up till the 7th day after hatching and decreases slowly in the following days of the study. A prominent increase takes place before hatching, which points out to the adequate and essential structural roles played by the elastic fibres in the pulmonary maturation process.
Can low densities of carnivores result in genetic depletion? An investigation within French polecat populations
Authors: Lodé T.
Published: May 2006

Carnivores as top predators are commonly found in relatively low densities even in optimal habitats. Despite a lack of empirical studies, it could be suspected that long‐term low density could result in genetic depletion. The genetic structure of European polecatMustela putoriusnatural populations was investigated by allozyme electrophoresis in five distinct areas. Density estimates significantly differed among sites from 0.17 to 0.83 individuals/km2with an average of 0.56 individuals per km2, resulting in a scattered distribution. Genetic structure varied among distinct populations both in number of polymorphic loci and heterozygosity. Polecats from Brittany revealed a very low observed heterozygosity (HO = 0.028) whereas mean heterozygosity reachedHO = 0.072 in Brière. That the lowest heterozygosity levels and highest inbreeding coefficientFISwere significantly associated with the lowest densities suggests that low densities may affect populations of carnivores. Both the loss of polymorphic loci and the reduction in heterozygosity rates suggest a density‐dependent effect and population density can be arguably regarded as a factor affecting genetic diversity in top carnivores.
Molecular Characterization of the Rice Pathogenesis‐related Protein, OsPR‐4b, and Its Antifungal Activity Against Rhizoctonia solani
Authors: Zhu T. , Song F. , Zheng Z.
Published: May 2006

We cloned and identified a new rice pathogenesis‐related (PR)‐4 gene, OsPR‐4b. OsPR‐4b encodes a 151 amino acid protein with a predicted molecular mass of 16.47 kDa and pI of 4.42. The putative OsPR‐4b shows high similarity to PR‐4 type proteins from various plant species and belongs to the Barwin family. Like other PR‐4s from monocot plants, OsPR‐4b contains a conserved Barwin domain and has a signal peptide at its N‐terminus. Recombinant OsPR‐4b protein expressed in Escherichia coli showed antifungal activity in vitro against the sheath blight fungus, Rhizoctonia solani. The results suggest that the OsPR‐4b may play a role in the disease resistance responses of rice against pathogen attacks through its antifungal activity.
Spontaneous regression of intraoral mucosa‐associated lymphoid tissue lymphoma: Molecular study of a case
Authors: Sakuma Hidenori , Okabe Mitsukuni , Yokoi Motoo , Eimoto Tadaaki , Inagaki Hiroshi
Published: May 2006

Mucosa‐associated lymphoid tissue (MALT) lymphoma presentation in the oral cavity is very rare. Reported herein is a case of intraoral MALT lymphoma of the minor salivary gland in a 70‐year‐old woman with Sjogren’s syndrome. Unexpectedly, a spontaneous clinically and histologically confirmed regression occurred 1 month after the tumor biopsy for diagnosis. Considering that salivary MALT lymphoma is associated with Sjogren’s syndrome and that the chronic inflammation caused by Sjogren’s syndrome persisted, it is hypothesized that the tumor clone might be present in the regressed lesion. Minimal residual tumor clone identical with the primary lesion was detected using the polymerase chain reaction (PCR) clonality assay for immunoglobulin heavy chain gene (IgH) rearrangement. No recurrence was clinically evident 38 months after the diagnosis. Spontaneous regression of MALT lymphoma should be examined at the molecular level in addition to clinical and histological evaluations. When minimal residual disease is detected, close follow up is necessary for early detection of the tumor relapse.
Fellow eye of patients with retinal detachment associated with macular hole and bilateral high myopia
Authors: Tsujikawa Akitaka , Kikuchi Masashi , Ishida Kazuhiro , Nonaka Atsushi , Yamashiro Kenji , Kurimoto Yasuo
Published: May 2006

Abstract

Purpose:  To estimate the risk of retinal detachment in the fellow eye of patients with bilateral high myopia who had retinal detachment associated with macular hole (MH‐RD) in one eye.

Methods:  The present study examined retrospectively 56 patients with bilateral high myopia who had MH‐RD. To determine the incidence of involvement of the fellow eye, patients who completed a follow up of 12 months or longer were eligible for the current study.

Results:  Of 56 patients with MH‐RD due to high myopia, 54 had unilateral detachment at presentation and two had bilateral detachment. Of the 54 highly myopic fellow eyes without retinal detachment at presentation, 37 eyes underwent 12 or more months of documented follow up. Mean follow up after initial surgery to the primary eye was 6.5 ± 4.9 years. During follow up, a macular hole without retinal detachment was noted in one (2.7%) of these 37 eyes. Three other eyes (8.1%) had MH‐RD at 1, 2 and 7 years, respectively, after the initial surgery to the primary eye. At the final visit, 12 eyes (32%) had visual acuity of ≥6/9, whereas 12 eyes (32%) had visual acuity of ≤6/60.

Conclusions:  When patients with bilateral high myopia have MH‐RD in one eye, they would be expected to be at increased risk of retinal detachment in the fellow eye.
Notch controls proliferation and differentiation of stem cells in a dose‐dependent manner
Authors: Guentchev Marin , McKay Ronald D. G.
Published: May 2006

Self‐renewal and differentiation of CNS stem cells are regulated by still poorly understood cell–cell interactions. Notch is a well‐known cell surface protein that can promote both cell cycle progression and mitotic arrest but the molecular mechanism controlling these opposite effects is unknown. Here we demonstrate that, in CNS stem cells, the level of active Notch1 determines the cellular response. Specifically, low levels of the active form of Notch1 promote proliferation whereas high levels lead to growth arrest. Here we provide the first evidence that Notch effects on proliferation and differentiation are a function of dose, and propose a hypothesis on how oncogenes may also act as tumor suppressors.
Oxidative modulation of the transient potassium current IA by intracellular arachidonic acid in rat CA1 pyramidal neurons
Authors: Angelova Plamena , Müller Wolfgang
Published: May 2006

Oxidative stress affects cellular membrane lipids and proteins. Using whole‐cell patch‐clamp recording we demonstrate differential oxidative inhibition of voltage‐gated transient (IA) and delayed rectifier [IK(V)] K+ currents by arachidonic acid (AA) and H2O2 in CA1 neurons in hippocampal slice. We show that intracellular application of 1 pm AA or its non‐metabolizable analog eicosatetraynoic acid (100 pm) reduced IA by ∼42% but did not affect IK(V). AA shifted the voltage dependence of steady‐state inactivation of IA by 12 mV to more negative potentials whereas the rate of inactivation was unchanged. Surprisingly, intracellular glutathione (GSH, 20 mm) enhanced the effect of AA on maximal IA (−62%) and with AA slowed inactivation of IA. The combination of GSH and extracellular ascorbate (0.4 mm) prevented reduction of IA by AA. Intracellular Trolox (a vitamin E analog, 10 µm) reduced IA by 61%and IK(V) by 39%. Like AA, intracellular Trolox caused a 10‐mV left shift of IA steady‐state inactivation but Trolox and AA did not cause a shift when coapplied. Extracellular Trolox (100 µm) had no effects on IA. H2O2 (80 µm) reduced both IA and IK(V) in a GSH‐ and ascorbate‐sensitive manner and slowed the rate of inactivation of IA by a factor of 2. Coapplication of H2O2 with GSH and extracellular ascorbate caused ∼22 mV negative shifts of both steady‐state inactivation and activation. We conclude that AA is extremely potent in affecting IA by oxidative modifications. Antioxidants can augment these effects, probably by catalysis of the underlying reactions between oxidants and IA channel proteins.
The light‐activated signaling pathway in SCN‐projecting rat retinal ganglion cells
Authors: Warren Erin J. , Allen Charles N. , Brown R. Lane , Robinson David W.
Published: May 2006

In mammals, the master circadian clock resides in the suprachiasmatic nuclei (SCN) of the hypothalamus. The period and phase of the circadian pacemaker are calibrated by direct photic input from retinal ganglion cells (RGCs). SCN‐projecting RGCs respond to light in the absence of rod‐ and cone‐driven synaptic input, a property for which they are termed intrinsically photosensitive. In SCN‐projecting RGCs, light activates a nonselective cationic current that displays inward and outward rectification. The goal of the present study was to investigate the identity of the light‐activated ion channel and the intracellular signaling pathway leading to its activation. We considered two candidate channels, cyclic nucleotide‐gated (CNG) channels and transient receptor potential (TRP) channels, which mediate vertebrate and invertebrate phototransduction, respectively. We report that the intrinsic light response relies upon a G‐protein‐dependent process. Although our data indicate that cyclic nucleotides modulate the signaling pathway, CNG channels do not appear to conduct the light‐activated current because (i) cyclic nucleotides in the pipette solution do not activate a conductance or completely block the light response, (ii) CNG channel blockers fail to inhibit the light response, (iii) the effects of internal and external divalent cations are inconsistent with their effects on CNG channels, and (iv) immunohistochemistry reveals no CNG channels in SCN‐projecting RGCs. Finally, we show that the pharmacology of the light‐activated channel resembles that of some TRPC channel family members; the response is blocked by lanthanides and ruthenium red and SK&F 96365, and is enhanced by flufenamic acid and 1‐oleoyl‐2‐acetyl‐sn‐glycerol. Furthermore, immunohistochemical experiments reveal that TRPC6 is expressed in many RGCs, including those that express melanopsin.
NMDA receptors and the differential ischemic vulnerability of hippocampal neurons
Authors: Gee Christine E. , Benquet Pascal , Raineteau Olivier , Rietschin Lotty , Kirbach Sebastian W. , Gerber Urs
Published: May 2006

Transient cerebral ischemia causes an inhomogeneous pattern of cell death in the brain. We investigated mechanisms, which may underlie the greater susceptibility of hippocampal CA1 vs. CA3 pyramidal cells to ischemic insult. Using anin vitrooxygen–glucose deprivation (OGD) model of ischemia, we found thatN‐methyl‐d‐aspartate (NMDA) responses were enhanced in the more susceptible CA1 pyramidal cells and transiently depressed in the resistant CA3 pyramidal cells. The long‐lasting potentiation of NMDA responses in CA1 cells was associated with delayed cell death and was prevented by blocking tyrosine kinase‐dependent up‐regulation of NMDA receptor function. In CA3 cells, the energy deprivation‐induced transient depression of NMDA responses was converted to potentiation by blocking protein phosphatase signalling. These results suggest that energy deprivation differentially shifts the intracellular equilibrium between the tyrosine kinase and phosphatase activities that modulate NMDA responses in CA1 and CA3 pyramidal cells. Therapeutic modulation of tyrosine phosphorylation may thus prove beneficial in mitigating ischemia‐induced neuronal death in vulnerable brain areas.
Microbial diversity in alpine tundra wet meadow soil: novel Chloroflexi from a cold, water‐saturated environment
Authors: Costello Elizabeth K. , Schmidt Steven K.
Published: May 2006

Cold, water‐saturated soils play important biogeochemical roles, yet almost nothing is known about the identity and habitat of microbes active under such conditions. We investigated the year‐round microenvironment of an alpine tundra wet meadow soil in the Colorado Rocky Mountains, focusing on the biogeochemistry and microbial diversity of spring snowmelt – a dynamic time for alpine ecosystems.In situmeasurements revealed spring and autumn periods of long‐term temperature stability near 0°C, and that deeper soil (30 cm) was more stable than surface soil, with more moderate summers and winters, and longer isothermal phases. The soil was saturated and water availability was limited by freezing rather than drying. Analyses of bioavailable redox species showed a shift from Mn reduction to net Fe reduction at 2–3 cm depth, elevated SO42–and decreased soluble Zn at spring snowmelt. Terminal restriction fragment length polymorphism profiles detected a correlated shift in bacterial community composition at the surface to subsurface transition. Bacterial and archaeal small‐subunit rRNA genes were amplified from saturated spring soil DNA pooled along a depth profile. The most remarkable feature of these subsurface‐biased libraries was the high relative abundance of novel, uncultivated Chloroflexi‐related sequences comprising the third largest bacterial division sampled, and representing seven new Chloroflexi subdivisions, thereby dramatically expanding the known diversity of this bacterial division. We suggest that these novel Chloroflexi are active at near −0°C temperatures, under likely anoxic conditions, and utilize geochemical inputs such as sulfide from upslope weathering.
A comparison of stable‐isotope probing of DNA and phospholipid fatty acids to study prokaryotic functional diversity in sulfate‐reducing marine sediment enrichment slurries
Authors: Webster Gordon , Watt Lynsey C. , Rinna Joachim , Fry John C. , Evershed Richard P. , Parkes R. John , Weightman Andrew J.
Published: May 2006

Marine sediment slurries enriched for anaerobic, sulfate‐reducing prokaryotic communities utilizing glucose and acetate were used to provide the first comparison between stable‐isotope probing (SIP) of phospholipid fatty acids (PLFA) and DNA (16S rRNA and dsrA genes) biomarkers. Different 13C‐labelled substrates (glucose, acetate and pyruvate) at low concentrations (100 µM) were used over a 7‐day incubation to follow and identify carbon flow into different members of the community. Limited changes in total PLFA and bacterial 16S rRNA gene DGGE profiles over 7 days suggested the presence of a stable bacterial community. A broad range of PLFA were rapidly labelled (within 12 h) in the 13C‐glucose slurry but this changed with time, suggesting the presence of an active glucose‐utilizing population and later development of another population able to utilize glucose metabolites. The identity of the major glucose‐utilizers was unclear as 13C‐enriched PLFA were common (16:0, 16:1, 18:1ω7, highest incorporation) and there was little difference between 12C‐ and 13C‐DNA 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) profiles. Seemingly glucose, a readily utilizable substrate, resulted in widespread incorporation consistent with the higher extent of 13C‐incorporation (∼10 times) into PLFA compared with 13C‐acetate or 13C‐pyruvate. 13C‐PLFA in the 13C‐acetate and 13C‐pyruvate slurries were similar to each other and to those that developed in the 13C‐glucose slurry after 4 days. These were more diagnostic, with branched odd‐chain fatty acids (i15:0, a15:0 and 15:1ω6) possibly indicating the presence of Desulfococcus or Desulfosarcina sulfate‐reducing bacteria (SRB) and sequences related to these SRB were in the 13C‐acetate‐DNA dsrA gene library. The 13C‐acetate‐DNA 16S rRNA gene library also contained sequences closely related to SRB, but these were the acetate‐utilizing Desulfobacter sp., as well as a broad range of uncultured Bacteria. In contrast, analysis of DGGE bands from 13C‐DNA demonstrated that the candidate division JS1 and Firmicutes were actively assimilating 13C‐acetate. Denaturing gradient gel electrophoresis also confirmed the presence of JS1 in the 13C‐DNA from the 13C‐glucose slurry. These results demonstrate that JS1, originally found in deep subsurface sediments, is more widely distributed in marine sediments and provides the first indication of its metabolism; incorporation of acetate and glucose (or glucose metabolites) under anaerobic, sulfate‐reducing conditions. Here we demonstrate that PLFA‐ and DNA‐SIP can be used together in a sedimentary system, with low concentrations of 13C‐substrate and overlapping incubation times (up to 7 days) to provide complementary, although not identical, information on carbon flow and the identity of active members of an anaerobic prokaryotic community.
The philosophical basis of character coding for the inference of phylogenetic hypotheses
Authors: Fitzhugh Kirk
Published: May 2006

The coding of observations of organisms into a data matrix for the inference of phylogenetic hypotheses has suffered from a variety of problems that have precluded development of a uniform approach to the issue. Probably the most notable consequence is that the philosophical basis for coding has been prominently ignored in lieu of emphasis placed on specific coding strategies. From an epistemic standpoint, part of the problem lies with the distinction of ‘characters’ and ‘character states’, which does not accurately convey perceptual beliefs or observation statements. The ability to perceive objects is by the nature of the properties of those objects. One's sense perceptions are of characters, not states; or more appropriately, one observes objects by way of the properties perceived of those objects. The proper distinction is therefore not one of character/state, but one of object/character, as communicated by subject–predicate relations. With observation statements referring to shared similarities among organisms distributed among two or more species, and phylogenetic hypotheses in the form of cladograms serving as at least tentative explanations for those effects, then what dictates the coding of observations is not adherence to a particular coding strategy, but the need to accurately convey the causal questions that address those observations. A phylogenetic data matrix is therefore not composed of columns as ‘characters’ and cells as ‘states’. Rather, column headings indicate the observed subjects that instantiate various characters; columns represent specifiable causal questions based on observations, and cells present the subject–predicate relations of observation statements. Since data matrices must represent one's causal questions, the inclusion of outgroup taxa is justified as components of those questions. With these criteria, the coding strategies summarized by Pleijel (1995) are critiqued. It is shown that advocacy of any one of those approaches is not possible, and that strategies that incorrectly apply the notion of ‘absence’ are especially prone to misrepresent observations.
Risk Preference and Employment Contract Type
Authors: Brown Sarah , Farrell Lisa , Harris Mark N. , Sessions John G.
Published: May 2006

We explore the possibility that a systematic relationship exists between employment within a particular type of contract and risk preference. We exploit a set of proxies for risk preference, whereby some of the proxies capture risk loving behaviour (expenditure on gambling, smoking and alcohol) whereas others capture risk averse behaviour (expenditure on life and contents insurance, and unearned income). The empirical analysis, based on pooled cross-section data from the UK Family Expenditure Survey, 1997–2000, provides evidence of a systematic relationship between employment contract type and risk preference, with, for example, self-employed workers being more or less likely to engage in the consumption of ‘risky’ or financial security products respectively. The results are based on the ordered generalized extreme value model, a relatively infrequently used discrete choice model, which allows for ordering and correlation in the alternatives observed.