bluuebunny/crossref_metadata_2025 huggingface dataset:
Nuclear myosin I acts in concert with polymeric actin to drive RNA polymerase I transcription
Authors: Ye Jing , Zhao Jian , Hoffmann-Rohrer Urs , Grummt Ingrid
Published: January 2008

Actin is associated with all three nuclear RNA polymerases and acts in concert with nuclear myosin I (NM1) to drive transcription. Practically nothing is known regarding the state of actin and the functional interplay of actin and NM1 in transcription. Here we show that actin and NM1 act in concert to promote RNA polymerase I (Pol I) transcription. Drugs that prevent actin polymerization or inhibit myosin function inhibit Pol I transcription in vivo and in vitro. Mutants that stabilize the polymeric state actin are tightly associated with Pol I and activate transcription, whereas a polymerization-deficient mutant does not bind to Pol I and does not promote rDNA transcription. Consistent with nuclear actin and myosin synergizing in transcription activation, NM1 mutants that lack specific functions, such as binding to ATP, actin, or calmodulin, are incapable of associating with Pol I and rDNA. The results show that actin polymerization and the motor function of NM1 are required for association with the Pol I transcription machinery and transcription activation. These observations provide insights into the cooperative action of actin and myosin in the nucleus and reveal an actomyosin-based mechanism in transcription.
MicroRNA–target pairs in the rat kidney identified by microRNA microarray, proteomic, and bioinformatic analysis
Authors: Tian Zhongmin , Greene Andrew S. , Pietrusz Jennifer L. , Matus Isaac R. , Liang Mingyu
Published: January 2008

Mammalian genomes contain several hundred highly conserved genes encoding microRNAs. In silico analysis has predicted that a typical microRNA may regulate the expression of hundreds of target genes, suggesting miRNAs might have broad biological significance. A major challenge is to obtain experimental evidence for predicted microRNA–target pairs. We reasoned that reciprocal expression of a microRNA and a predicted target within a physiological context would support the presence and relevance of a microRNA–target pair. We used microRNA microarray and proteomic techniques to analyze the cortex and the medulla of rat kidneys. Of the 377 microRNAs analyzed, we identified 6 as enriched in the renal cortex and 11 in the renal medulla. From ∼2100 detectable protein spots in two-dimensional gels, we identified 58 proteins as more abundant in the renal cortex and 72 in the renal medulla. The differential expression of several microRNAs and proteins was verified by real-time PCR and Western blot analyses, respectively. Several pairs of reciprocally expressed microRNAs and proteins were predicted to be microRNA–target pairs by TargetScan, PicTar, or miRanda. Seven pairs were predicted by two algorithms and two pairs by all three algorithms. The identification of reciprocal expression of microRNAs and their computationally predicted targets in the rat kidney provides a unique molecular basis for further exploring the biological role of microRNA. In addition, this study establishes a differential profile of microRNA expression between the renal cortex and the renal medulla and greatly expands the known differential proteome profiles between the two kidney regions.
Coevolution of gene families in prokaryotes
Authors: Cordero Otto X. , Snel Berend , Hogeweg Paulien
Published: January 2008

We study gene family coevolution on a tree of life based on a large-scale ancestral gene content reconstruction, which includes gene duplication and deletion events. The insights obtained from this study are threefold: (1) Global properties, such as the distribution of coevolution partners and the formation of disconnected clusters of coevolving families, can be an inevitable consequence of evolution along a tree. (2) Concerted family expansion (gene duplication) and contraction (gene deletion) reflect functional constraints and therefore lead to better function prediction. (3) “Long-range” coevolutionary relationships, caused mostly by large family expansions or contractions, reveal high-level evolutionary organization of cellular processes in prokaryotes.
Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders
Authors: Rada-Iglesias Alvaro , Ameur Adam , Kapranov Philipp , Enroth Stefan , Komorowski Jan , Gingeras Thomas R. , Wadelius Claes
Published: January 2008

Transcription factors and histone modifications are crucial regulators of gene expression that mutually influence each other. We present the DNA binding profiles of upstream stimulatory factors 1 and 2 (USF1, USF2) and acetylated histone H3 (H3ac) in a liver cell line for the whole human genome using ChIP-chip at a resolution of 35 base pairs. We determined that these three proteins bind mostly in proximity of protein coding genes transcription start sites (TSSs), and their bindings are positively correlated with gene expression levels. Based on the spatial and functional relationship between USFs and H3ac at protein coding gene promoters, we found similar promoter architecture for known genes and the novel and less-characterized transcripts human mRNAs and spliced ESTs. Furthermore, our analysis revealed a previously underestimated abundance of genes in a bidirectional conformation, where USFs are bound in between TSSs. After taking into account this promoter conformation, the results indicate that H3ac is mainly located downstream of TSS, and it is at this genomic location where it positively correlates with gene expression. Finally, USF1, which is associated to familial combined hyperlipidemia, was found to bind and potentially regulate nuclear mitochondrial genes as well as genes for lipid and cholesterol metabolism, frequently in collaboration with GA binding protein transcription factor alpha (GABPA, nuclear respiratory factor 2 [NRF-2]). This expands our understanding about the transcriptional control of metabolic processes and its alteration in metabolic disorders.
Constitutive activation of the G-protein subunit Gαs within forebrain neurons causes PKA-dependent alterations in fear conditioning and corticalArcmRNA expression
Authors: Kelly Michele P. , Cheung York-Fong , Favilla Christopher , Siegel Steven J. , Kanes Stephen J. , Houslay Miles D. , Abel Ted
Published: January 2008

Memory formation requires cAMP signaling; thus, this cascade has been of great interest in the search for cognitive enhancers. Given that medications are administered long-term, we determined the effects of chronically increasing cAMP synthesis in the brain by expressing a constitutively active isoform of the G-protein subunit Gαs (Gαs*) in postnatal forebrain neurons of mice. Previously, we showed that Gαs* mice exhibit increased adenylyl cyclase activity but decreased cAMP levels in cortex and hippocampus due to a PKA-dependent increase in total cAMP phosphodiesterase (PDE) activity. Here, we extend previous findings by determining if Gαs* mice show increased activity of specific PDE families that are regulated by PKA, if Gαs* mice show PKA-dependent deficits in fear memory, and if these memory deficits are associated with PKA-dependent alterations in neuronal activity as mapped byArcmRNA expression. Consistent with previous findings, we show here that Gαs* mice exhibit a significant compensatory increase in cAMP PDE1 activity and a trend toward increased cAMP PDE4 activity. Further, inhibiting the presumably elevated PKA activity in Gαs* mice fully rescues short- and long-term memory deficits in a fear-conditioning task, while extending the training session from one to four CS–US pairings partially rescues these deficits. Mapping ofArcmRNA levels suggests these PKA-dependent memory deficits may be related to decreased neuronal activity specifically within the cortex. Gαs* mice show decreasedArcmRNA expression in CA1, orbital cortex, and cortical regions surrounding the hippocampus; however, only the deficits in cortical regions surrounding the hippocampus are PKA dependent. Our results imply that chronically stimulating targets upstream of cAMP may detrimentally affect cognition.
Impaired discrimination learning in mice lacking the NMDA receptor NR2A subunit
Authors: Brigman Jonathan L. , Feyder Michael , Saksida Lisa M. , Bussey Timothy J. , Mishina Masayoshi , Holmes Andrew
Published: January 2008

N-Methyl-D-aspartate receptors (NMDARs) mediate certain forms of synaptic plasticity and learning. We used a touchscreen system to assess NR2A subunit knockout mice (KO) for (1) pairwise visual discrimination and reversal learning and (2) acquisition and extinction of an instrumental response requiring no pairwise discrimination. NR2A KO mice exhibited significantly retarded discrimination learning. Performance on reversal was impaired in NR2A KO mice during the learning phase of the task; with no evidence of heightened perseverative responses. Acquisition and extinction of an instrumental behavior requiring no pairwise discrimination was normal in NR2A KO mice. The present findings demonstrate a significant and selective deficit in discrimination learning following loss of NR2A.
Amygdala infusions of an NR2B-selective or an NR2A-preferring NMDA receptor antagonist differentially influence fear conditioning and expression in the fear-potentiated startle test
Authors: Walker David L. , Davis Michael
Published: January 2008

Within the amygdala, most N-methyl-D-aspartic acid (NMDA) receptors consist of NR1 subunits in combination with either NR2A or NR2B subunits. Because the particular subunit composition greatly influences the receptors’ properties, we investigated the contribution of both subtypes to fear conditioning and expression. To do so, we infused the NR1/NR2B receptor antagonist CP101,606 (0.5, 1.5, or 4.5 μg/amygdala) or the NR1/NR2A-preferring antagonist NVP-AAM077 (0.075, 0.25, 0.75, or 2.5 μg/amygdala) into the amygdala prior to either fear conditioning (i.e., light-shock pairings) or fear-potentiated startle testing. CP101,606 nonmonotonically disrupted fear conditioning but did not disrupt fear expression. NVP-AAM077 dose-dependently disrupted fear conditioning as well as fear expression. The results suggest that amygdala NR1/NR2B receptors play a special role in fear memory formation, whereas NR1/NR2A receptors participate more generally in synaptic transmission.
AX+/BX− discrimination learning in the fear-potentiated startle paradigm in monkeys
Authors: Winslow James T. , Noble Pamela L. , Davis Michael
Published: January 2008

Individuals with anxiety disorders often do not respond to safety signals and hence continue to be afraid and anxious. Consequently, it is important to develop paradigms in animals that can directly study brain systems involved in learning about, and responding to, safety signals. We previously developed a discrimination procedure in rats of the form AX+/BX−, where cues A and X presented together are paired with an aversive stimulus and cues B and X presented together predict the absence of an aversive stimulus. The present experiment adapted this procedure to the fear-potentiated startle paradigm in rhesus monkeys.
Clinical uses of interferons
Authors: Friedman Robert M.
Published: January 2008

Interferons were first described by Isaacs & Lindenmann working at the National Institute for Medical Research, Mill Hill in 1957 [1]. Thus, the fiftieth year of their discovery is being celebrated this year at Oxford in a meeting of the International Society for Interferon and Cytokine Research. This then is an appropriate time to review the clinical applications of the interferons. To accomplish this coherently it is necessary also to review briefly what led to the discovery of interferons, why their clinical applications were so slow in coming, and the impact of interferon research on the biomedical sciences.
Buffer capacity and Cu affinity of soil particulate organic matter (POM) size fractions
Authors: Sebastia J. , VanOort F. , Lamy I.
Published: January 2008

Particulate organic matter fractions (POM), defined as sand‐sized organic separates in soils, are known to be labile organic components with a rapid turnover. Recently, POM fractions were identified to be metal‐enriched in both metal‐contaminated and uncontaminated soils. However, mechanisms for such metal‐enrichment are poorly understood, because of the paucity of information on the chemical properties of POM. The aim of this study was to quantify the reactivity of POM towards Cu and to show a POM‐size effect on this reactivity. POM was isolated from soils with different organic amendment managements: straw (S), conifer compost (CC), and non‐amended (NA). Two POM size fractions were isolated by density‐fractionation in water: 50–200 μm and 200–2000 μm. These fractions were studied for their metal contents, acid‐base properties and affinity toward Cu. The buffer capacity and Cu affinity were modeled by FITEQL 4.0 software and compared between the two POM size fractions. Each POM size fraction provided a buffer capacity due to the presence of reactive sites, the greatest being for the 50–200 μm POM fractions. A signature of organic inputs as seen by the buffer capacities was observed for the 50–200 μm but not for the 200–2000 μm POM fractions. But Cu affinity was comparable between the coarse and fine POM fractions and no significant differences were found between NA, S and CC samples. We checked the hypothesis that decreasing POM size due to degradation processes generates more reactive surface sites. Results confirmed that soil POM plays a key role as a metal sink, due to its chemical properties.
Effect of organic matter applications on 13C‐NMR spectra of humic acids of soil
Authors: Dou S. , Zhang J. J. , Li K.
Published: January 2008

Much attention has been paid to improving soil fertility with organic matter (OM) application, which not only deals with organic wastes and protects the environment, but also maintains soil fertility and increases crop yields. Much research has also been on the effects of OM applications on the soil’s physical, chemical and biological properties, but relatively less attention has been spent on humic substance (HS). In order to clarify the mechanism of improving soil fertility by applying OM, we analysed the changes of structural characteristics of humic acid (HA) from OM applications to soils by 13C‐NMR, chemical analysis, thermal analysis, optical properties, IR and fluorescence spectroscopy. Samples of a brown soil (Paleudalf) and a paddy soil (an anthropogenic soil originating from Udifluvents) were collected from the plough layer of the long‐term field experiment at Shenyang Agricultural University and Liaoning Provincial Alkali‐Saline Soil Institute, respectively. Both field experiments included three treatments each: (i) brown soil, zero‐treatment (CKbr) and two pig manure (PM) applications (O1 and O2) at annual rates of 0.9 t ha−1 and 1.8 t ha−1 of organic carbon, respectively; and (ii) paddy soil, zero‐treatment (CKpad), pig manure (Op) and rice straw (Or) at annual rates of 2.62 t ha−1 and 1.43 t ha−1 of organic carbon, respectively. An incubation experiment was also carried out to test the field experiment on the brown soil, namely four treatments: zero‐treatment (CKc), and three pig manure applications at rates of 30 g kg−1 (C1), 50 g kg−1 (C2) and 70 g kg−1 (C3), respectively. The total incubation was 180 days. The results indicated that number‐average molecular weights (Mn), total acidity, aromaticity, excitation maximum wavelength (λExmax), and the heat ratio of the high to moderate temperature exothermic regions (H3/H2) of the HA all decreased after OM application. The degree of activation (AD), the absorption intensity ratio of 2920 cm−1 to 1720 cm−1 in infrared spectra (IR2920/1720), alkyl C and O‐alkyl C of the HA increased. The HA structure tended to become simpler and more aliphatic.
Population density and age structure of the freshwater pearl mussel,Margaritifera margaritifera, in two Iberian rivers
Authors: OUTEIRO ADOLFO , ONDINA PAZ , FERNÁNDEZ CARLOS , AMARO RAFAELA , MIGUEL EDUARDO SAN
Published: January 2008

1. The European freshwater pearl mussel,Margaritifera margaritifera(Bivalvia: Unionoida), is one of the most threatened mussels. The Iberian populations of this species are considered peripheral because their distinct characters such as growth rate and longevity, and require development of effective conservation strategies.

2. We assessed population density and age structure of pearl mussels in two Galician rivers (Eo and Masma in north‐west Spain). Four sampling sites were selected in each river to cover stretches of 100 m. The mean density of mussels in each of these sampling transects was estimated using the adaptive sampling technique, given that mussels occur at low densities and are highly aggregated in these rivers.

3. Age structure was inferred for each population using length–age keys. The empty shells encountered during sampling were used to determine the length of the specimens at different ages (years), together with length‐at‐age data from shells previously analysed for computing growth rates from the same rivers. Water samples from both rivers were analysed for typical physicochemical parameters.

4. Mean densities were very variable, even within the same river (from 0.27 to 6.55 m−2in the River Eo and from 0.98 to 2.38 m−2in the River Masma). Individuals in the 0‐ to 5‐year age class were scarce in both rivers.

5.Margaritifera margaritiferashowed a preference for the strip of river bed within 1.5 m from the river bank and avoided sites at greater distances. The species also showed a preference for sites with more than 80% tree cover and avoided sites with <50% cover.

6. Iberian populations exhibit the highest growth rate, together with the lowest maximum age and maximum length known forM. margaritifera. Detailed knowledge about these peripheral Iberian populations will contribute to developing strategies for conservation and management of this endangered species.
Does the Redfield ratio infer nutrient limitation in the macroalga Spirogyra fluviatilis?
Authors: TOWNSEND S. A. , SCHULT J. H. , DOUGLAS M. M. , SKINNER S.
Published: January 2008

1. The cellular nutrient contents of microalgae, when growing at or approaching maximum rates, approximate the Redfield C : N : P (molar) ratio of 106 : 16 : 1. Deviations from this optimal ratio can be used to infer nutrient limitation of microalgal growth. However, this ratio may not be applicable to macroalgae, which are distinguished from microalgae by forming a thallus that is a discrete structure visible to the naked eye. The utility of the Redfield ratio to infer nutrient limitation of the growth of macroalgae was tested for Spirogyra fluviatilis in a field experiment conducted in tropical Australia.

2. The optimal cellular C : N : P ratio for S. fluvialitis was estimated by means of in situ nutrient addition. This was compared with S. fluvialitis cellular ratios determined from eight sites with a wide range of soluble N concentrations (<1–90 μg L−1), a smaller range of soluble P concentrations (5–12 μg L−1), and soluble molar N : P ratios of 0.11– 27.

3. Spirogyra fluviatilis had an optimal molar C : N : P ratio of 1800 : 87 : 1 which differs substantially from the Redfield ratio, and suggests that the latter ratio is not applicable to this macroalga. Concentrations of N and P in the river deviated from the optimal N : P ratio of 87 : 1, inferring nutrient limitation of growth.

4. C : P and C : N ratios of S. fluviatilis varied in accordance with general stoichiometric relationships for autotrophs under nutrient limitation of growth. Ratios of C : P and C : N increased, respectively, with increased severity of P‐ and N‐limitation. Additionally, C : P ratios increased with increased N : P ratios, whilst the C : N ratio increased with decreased N : P ratios. The C : N molar ratio however was an insensitive indicator of nutrient depletion compared with the C : P ratio. Under N‐limitation of growth, luxury amounts of P were stored by S. fluviatilis.

5. In aquatic environments where macroalgae are sufficiently abundant to be sampled, their cellular carbon, nitrogen and phosphorus stoichiometry can be used to infer nutrient limitation of growth when their optimal C : N : P ratio is known.
Variability in factors causing light attenuation in Lake Victoria
Authors: LOISELLE STEVEN A. , AZZA NICHOLAS , CÓZAR ANDRES , BRACCHINI LUCA , TOGNAZZI ANTONIO , DATTILO ARDUINO , ROSSI CLAUDIO
Published: January 2008

1. The major optical components controlling the attenuation of photosynthetic available radiation in nearshore areas of Lake Victoria (Uganda and Kenya) were examined and their impact compared. It was found that chromophoric dissolved organic matter and tripton play a dominating role in many nearshore areas, indicating that the coastal areas of Lake Victoria cannot be considered as Case I waters.

2. Concentrations of chromophoric dissolved organic matter declined with distance from the coast in an exponential manner indicating dilution and degradation of terrestrial sources of organic matter rather than in situ production. The importance of tripton was found to follow a similar pattern, while the relative importance of phytoplankton biomass in overall attenuation of photosynthetic available radiation was found to increase with distance from the coast. A specific attenuation coefficient for phytoplankton biomass was determined (0.019 m2 mg Chl a−1).

3. Using a light limitation approach based on carrying capacity, it was possible to map areas that are closer to being light limited. Light limitation appears to occur throughout most bays and some coastal areas receiving catchment waters. This spatial information, geographically referenced to bathymetric and catchment conditions, was utilized to understand the importance of environmental conditions in limiting phytoplankton biomass.
Invertebrate traits for the biomonitoring of large European rivers: an assessment of specific types of human impact
Authors: DOLÉDEC SYLVAIN , STATZNER BERNHARD
Published: January 2008

1. The power of selected biological invertebrate traits for discriminating different types of human impact (heavy metal pollution and cargo‐ship traffic) were tested using ecological reasoning and linear Discriminant Function Analysis (DFA).

2. Frequency distributions of individual traits and categories of traits from 68 least impacted river reaches (LIRRs) and 304 impacted river reaches were used to define simple assessment rules based on ecological reasoning for specific impairments in large European rivers. In calibration, a maximum of three variables with a priori predictions and two different impairment threshold levels were used. Similarly, DFA was performed on the same variables included in the ecological reasoning approach, but also on all available traits or trait categories.

3. Validation with an independent data set (40 LIRRs, 291 variously impacted river reaches) and using the ecological reasoning approach showed that 75–78% of the reaches were correctly assign with rules on all impact types, 35–57% with rules on heavy metal pollution and 78–93% with rules on cargo‐ship traffic. By comparison, validation showed that DFA performed globally poorer than the ecological reasoning approach. In addition, the performance of the rules based on ecological reasoning remained stable, whereas DFA performance changed between calibration and validation.

4. Although not defined for this purpose, our study provided alarming evidence regarding the impact of cargo‐ship traffic on invertebrate communities in river reaches. Reaches with cargo‐ship traffic were found to have more genera with long life cycles that reproduce repeatedly by ovoviviparity and have a sessile life.

5. The performance of our trait‐based approach to correctly assign reaches to either least impacted or impacted conditions should promote further research on the topic across larger geographic areas (without regionalization) and across smaller stream types to provide a powerful biomonitoring tool that fulfils current European Union directives.
To sink or float: the fate of dormant offspring is determined by maternal behaviour in Daphnia
Authors: ŚLUSARCZYK MIROSŁAW , PIETRZAK BARBARA
Published: January 2008

As the ephippia (chitinous shells enclosing diapausing eggs) of pelagic crustaceans of the genus Daphnia have been occasionally reported to float at the water surface, we considered that this might be an adaptation promoting their passive dispersal. We investigated the mechanisms by which ephippia appear at the water surface.

While field surveys revealed that floating Daphnia ephippia are often numerous in various freshwater habitats, laboratory tests showed that newly formed ephippia are not buoyant initially. Once transferred to the surface by whatever means, however, they may remain there due either to surface tension or gas absorption.

Video recordings showed that all ephippia at the water surface in laboratory vessels were shed there by ephippial females when moulting (despite the attendant risk of exposure to UV radiation). This implies that the moulting behaviour of female Daphnia may determine the fate of their dormant offspring, predetermining whether they remain in the natal environment (when the ephippium is released into the water column) or disperse (when it is deposited at the water surface).

Our findings reveal a potential mechanism underlying the high dispersal capacity of freshwater cladocerans inhabiting island‐like aquatic habitats.
Functional analysis of Src homology 3‐encoding exon (exon 2) of p130Cas in primary fibroblasts derived from exon 2‐specific knockout mice
Authors: Tazaki Tatsuya , Miyazaki Kazuko , Hiyama Eiso , Nakamoto Tetsuya , Sakai Ryuichi , Yamasaki Norimasa , Honda Zen‐ichiro , Noda Masaki , Miyasaka Nobuyuki , Sueda Taijiro , Honda Hiroaki
Published: January 2008

p130Cas (Cas, Crk‐associated substrate) is an adaptor molecule composed of a Src homology 3 (SH3) domain, a substrate domain (SD) and a Src binding domain (SBD). The SH3 domain of Cas associates with focal adhesion kinase (FAK), but its role in cellular function has not fully been understood. To address this issue, we established and analyzed primary fibroblasts derived from mice expressing a truncated Cas lacking exon 2, which encodes the SH3 domain (Cas Δexon 2). In comparison to wild‐type cells, Cas exon 2Δ/Δ cells showed reduced motility, which could be due to impaired tyrosine‐phosphorylation of FAK and Cas, reduced FAK/Cas/Src/CrkII binding, and also impaired localization of Cas Δexon 2 to focal adhesions on fibronectin. In addition, to analyze downstream signaling pathways regulated by Cas exon 2, we performed microarray analyses. Interestingly, we found that a deficiency of Cas exon 2 up‐regulated expression of CXC Chemokine Receptor‐4 and CC Chemokine Receptor‐5, which may be regulated by IκBα phosphorylation. These results indicate that the SH3‐encoding exon of Cas participates in cell motility, tyrosine‐phosphorylation of FAK and Cas, FAK/Cas/Src/CrkII complex formation, recruitment of Cas to focal adhesions and regulation of cell motility‐associated gene expression in primary fibroblasts.
Dynamic events of sister chromosomes in the cell cycle of Escherichia coli
Authors: Adachi Shun , Fukushima Toru , Hiraga Sota
Published: January 2008

Various events involving partitioning of sister chromosomes were precisely analyzed in asynchronously growing Escherichia coli cells in various conditions. To examine the cohesion between sister chromosomes, we analyzed living cells growing under various conditions for the number of the replication origin (oriC) copies by flow cytometry and the foci of oriC by fluorescence microscopy. The average number of the oriC foci per cell was significantly smaller than the number of oriC copies per cell with few exceptions, suggesting cohesion of oriC sister copies. Cohesion phenomenon of oriC sister copies was also observed in a mukB null mutant cells under some growth conditions. Sister copies of the terminal region (ter) were also found to be cohesive. Immunofluorescence microscopy for nascent DNA pulse‐labeled with 5‐bromo‐2′‐deoxyuridine (BrdU) indicated that paired replication forks acting on bidirectional replication were able to migrate toward opposite directions during ongoing replication in poor medium; however, some of them were closely associated in rich media. Analysis of the foci of MukB–GFP indicates that the number of MukB foci was always larger than the number of replication forks. The number of MukB–GFP foci increased together with cell length. The sequence of these chromosomal events in the growing cells has been depicted.
Meteorite impact structures: the good and the bad
Authors: Osinski Gordon R.
Published: January 2008

Meteorite impact structures are found on all planetary bodies in the Solar System with a solid surface. On many planets, impact craters are the dominant landform. Earth's active geology, however, tends to rapidly erase impact structures from the geological record, although we know currently of 174 confirmed impact sites. Impact events are destructive and have been linked to at least one of the ‘big five’ mass extinctions over the past 540 Ma. But they also provide certain economic benefits, including the formation of metalliferous ore deposits and hydrocarbon reservoirs. Impact structures can also form new biological niches, which can provide favourable conditions for the survival and evolution of life. Despite this, it was only in the past 40 years that the importance of impact cratering as a geological process was recognized and only during the past 15–20 years that the study of meteorite impact structures has moved into the geological mainstream. There is, therefore, still considerable potential for new and exciting advancements.
Identifying and quantifying uncertainty and spatial disagreement in the comparison of Global Land Cover for different applications
Authors: FRITZ STEFFEN , SEE LINDA
Published: January 2008

This paper provides a methodology for comparing global land cover maps that allows for differences in legend definitions between products to be taken into account. The legends of the two maps are first reconciled by creating a legend lookup table that shows how the legends map onto one another. Where there is overlap, the specific definitions for each legend class are used to calculate the degree of overlap between legend classes. In this way, one‐to‐many mappings are accounted for unlike in most methods where the legend definitions are often forced into place. Another advantage over previous map comparison methods is that application‐specific requirements are captured using expert input, whereby the user rates the importance of disagreement between different legend classes based on the needs of the application. This user‐defined matrix in conjunction with the degree of overlap between legend classes is applied on a pixel‐by‐pixel basis to create maps of spatial disagreement and uncertainty. The user can then highlight the areas of highest thematic uncertainty and disagreement between the different land cover maps allowing for areas that require further detailed examination to be readily identified. It would also be possible for several users to input their knowledge into the process, leading to a potentially more robust comparison of land cover products. The methodology of map comparison is illustrated using different land cover products including Global Land Cover 2000 (GLC‐2000) and the MODIS land cover data set. Two diverse applications are provided including the estimation of global forest cover and monitoring of agricultural land. In the case of global forest cover, an example was provided for Columbia, which showed that the MODIS land cover map overestimates forest cover in comparison with the GLC‐2000. The agricultural example, on the other hand, served to illustrate that for Sudan, MODIS tends to underestimate crop areas while GLC‐2000 overestimates them.
Determination of the relative avidity of the specific IgG antibodies in human toxocariasis
Authors: DZIEMIAN E. , ŻARNOWSKA H. , KOŁODZIEJ‐SOBOCIŃSKA M. , MACHNICKA B.
Published: January 2008

Human toxocariasis is a zoonosis caused by infection with larvae of the ascarid nematode Toxocara canis and, less frequently, T. cati. Our study developed a method for distinguishing distant from recent human toxocariasis by assessing the avidity of the IgG antibodies. The avidity of specific antibodies increases with time after antigen challenge and assessment of the degree of avidity can be used to discriminate between recent and distant infections. The relative avidity was measured in 150 sera from children with visceral toxocariasis and in 46 sera from children with ocular toxocariasis. The probable time of infection was estimated on the basis of the medical history and clinical syndrome. Our study showed that 94·2% of positive sera collected from patients reporting infection > 6 months ago had high IgG avidity values, confirming distant toxocariasis, whereas 25·9% of positive sera taken < 6 months after infection showed low indices of IgG avidity.

Our results suggest that measurement of the specific IgG avidity may assist in discriminating between recent and distant toxocariasis. The method can be used effectively to rule out (because of high avidity) a recently acquired infection. Low avidity is less reliable in discriminating between recent and distant infections.
Evidence for Pleistocene wet aeolian dune and interdune accumulation, S. Pedro da Maceda, north‐west Portugal
Authors: GRANJA HELENA M. , DTE GROOT THOMAS A. M. , COSTA ANA L.
Published: January 2008

Outcrops and cored/counter‐flushed boreholes in the coastal area between Espinho and Aveiro (north‐west Portugal) were investigated to reconstruct the changing patterns of sedimentation during the Late Pleistocene–Holocene. To obtain a common comparison basis, the grain‐size data from outcrop and borehole samples were analysed. The outcrops and the cored parts of the boreholes were dated by radiocarbon and optically stimulated luminescence. The results show that, on top of pebble‐rich beds of fluvial origin, a wet aeolian dune and interdune environment was active during the later part of the Pleistocene, turning to dry aeolian at the transition to the Holocene. The data indicate also that aeolian accumulation was controlled by vegetation changes (climate) and groundwater table fluctuations. During the Holocene, a podzol formed on the Pleistocene dunes and extensive vegetation precluded major aeolian accumulations. Remobilization of sand started again because of human deforestation and – last but not least – the Little Ice Age.
Phytochrome‐mediated inhibition of shade avoidance involves degradation of growth‐promoting bHLH transcription factors
Authors: Lorrain Séverine , Allen Trudie , Duek Paula D. , Whitelam Garry C. , Fankhauser Christian
Published: January 2008

Plant growth and development are particularly sensitive to changes in the light environment and especially to vegetational shading. The shade‐avoidance response is mainly controlled by the phytochrome photoreceptors. In Arabidopsis, recent studies have identified several related bHLH class transcription factors (PIF, for phytochrome‐interacting factors) as important components in phytochrome signaling. In addition to a related bHLH domain, most of the PIFs contain an active phytochrome binding (APB) domain that mediates their interaction with light‐activated phytochrome B (phyB). Here we show that PIF4 and PIF5 act early in the phytochrome signaling pathways to promote the shade‐avoidance response. PIF4 and PIF5 accumulate to high levels in the dark, are selectively degraded in response to red light, and remain at high levels under shade‐mimicking conditions. Degradation of these transcription factors is preceded by phosphorylation, requires the APB domain and is sensitive to inhibitors of the proteasome, suggesting that PIF4 and PIF5 are degraded upon interaction with light‐activated phyB. Our data suggest that, in dense vegetation, which is rich in far‐red light, shade avoidance is triggered, at least partially, as a consequence of reduced phytochrome‐mediated degradation of transcription factors such as PIF4 and PIF5. Consistent with this idea, the constitutive shade‐avoidance phenotype of phyB mutants partially reverts in the absence of PIF4 and PIF5.
Cytomegalovirus‐associated chorioretinitis after liver transplantation: case report and review of the literature
Authors: Egli A. , Bergamin O. , Müllhaupt B. , Seebach J.D. , Mueller N.J. , Hirsch H.H.
Published: January 2008

Abstract:A cytomegalovirus (CMV) donor positive/recipient negative liver transplant recipient developed CMV syndrome with presumed colitis 2 weeks after discontinuing the standard 3 months of valganciclovir prophylaxis. Treatment with intravenous ganciclovir (GCV) reduced, but did not clear, CMV replication. A CMV UL97 mutation (M460V) conferring GCV resistance was identified. Reduction of immunosuppression was followed by rapidly rising lymphocyte counts as well as by clearance of CMV viremia and of clinical symptoms. However, bilateral chorioretinitis was diagnosed 2 weeks later and treated with foscarnet and cidofovir. Then, right eye vitritis occurred necessitating vitrectomy due to a partially rhegmatogeneous retinal detachment. Because chorioretinitis–vitritis after rising lymphocyte counts and clearance of CMV viremia was strongly suggestive of an immune reconstitution syndrome (IRS)‐like disease, we investigated CMV‐specific T‐cells in the peripheral blood available during follow‐up. We found strong CD8+but only low CD4+T‐cell responses (4.77% vs.<0.1%) to the CMV immediate early pp72, while responses to CMV‐lysate or CMV‐pp65 (CD4+<0.01%; CD8+<0.01%) were low. Over 16 weeks of follow‐up, pp72‐specific CD8+responses declined, while responses to pp65 gradually increased (CD4+0.16%; CD8+0.76%) indicating a slowly adapting CMV‐specific cellular T‐cell response. Review of 12,653 published liver transplant patients identified only 14 (0.1%) reported cases of CMV‐associated chorioretinitis at a median 41.7 weeks post transplant. CMV‐associated opthalmologic complications late post transplantation may possibly involve 2 different entities of cytopathic retinitis and IRS‐like chorioretinitis–vitritis.
Mycotic keratitis: an overview of diagnosis and therapy
Authors: Shukla P. K. , Kumar M. , Keshava G. B. S.
Published: January 2008

The increased incidence of fungal infections in the recent past has been attributed to the increase in the number of human immunodeficiency virus‐positive and AIDS patients. Early diagnosis of mycoses in patients is crucial for prompt antifungal therapy. The yield of clinical examination in the diagnosis of keratomycosis is 63–83% and KOH mount is 91%. This still highlights the limitation of routine clinical examination and smear examination, which is not performing 100% efficiently. It is for these 37%, 17% and 9% of cases, every day advanced technologies are called for. Those who deal with patient care are aware of certainties and uncertainties of results of clinical examination. The best reported figures at specialized centres might not translate into clinical practice. Another factor to be kept in mind is that many patients who come after secondary and tertiary referrals are already treated with antibiotics, antivirals, steroids and sometimes even antifungals that distort the clinical picture completely. Further, one has to consider as well the cases caused by yeast‐like fungi, which resemble bacterial keratitis. Confirmation of diagnosis, not only in case of mycotic keratitis but also for other diseases, to initiate prompt and accurate therapy would avoid unnecessary and indiscriminate use of steroids/antibacterials/antivirals and antifungals.
Expression of a fungal ferulic acid esterase increases cell wall digestibility of tall fescue (Festuca arundinacea)
Authors: Buanafina Marcia M. de O. , Langdon Tim , Hauck Barbara , Dalton Sue , Morris Phillip
Published: January 2008

In the cell walls of forage grasses, ferulic acid is esterified to arabinoxylans and participates with lignin monomers in oxidative coupling pathways to generate ferulate–polysaccharide–lignin complexes that cross‐link the cell wall. Such cross‐links hinder cell wall degradation by ruminant microbes, reducing plant digestibility. In this study, genetically modified Festuca arundinacea plants were produced expressing an Aspergillus niger ferulic acid esterase (FAEA) targeted to the vacuole. The rice actin promoter proved to be effective for FAEA expression, as did the cauliflower mosaic virus (CaMV) 35S and maize ubiquitin promoters. Higher levels of expression were, however, found with inducible heat‐shock and senescence promoters. Following cell death and subsequent incubation, vacuole‐targeted FAEA resulted in the release of both monomeric and dimeric ferulic acids from the cell walls, and this was enhanced several fold by the addition of exogenous endo‐1,4‐β‐xylanase. Most of the FAEA‐expressing plants showed increased digestibility and reduced levels of cell wall esterified phenolics relative to non‐transformed plants. It is concluded that targeted FAEA expression is an effective strategy for improving wall digestibility in Festuca and, potentially, other grass species used for fodder or cellulosic ethanol production.
Agricultural trade reform under the Doha Agenda: some key issues*
Authors: Martin Will , Anderson Kym
Published: January 2008

A successful agreement on agriculture is essential for an overall agreement under the WTO's Doha trade negotiations. Reaching agreement has been difficult, and as of August 2007, much still remains to be done if a successful agreement is to be reached. We consider three of the most controversial areas of the agricultural negotiations: the relative importance of domestic support, market access and export subsidies; three market access issues of sensitive‐product exceptions sought for all countries and, the additional special product exceptions sought for developing countries, the proposed special safeguard mechanism; and the domestic support issue. We show that decisions made on reform in these areas will have a critical influence on whether the negotiations achieve their objectives of promoting trade reform and reducing poverty.
Investment planning under uncertainty and flexibility: the case of a purchasable sales contract*
Authors: Musshoff Oliver , Hirschauer Norbert
Published: January 2008

Investment decisions are not only characterised by irreversibility and uncertainty but also by flexibility with regard to the timing of the investment. This paper describes how stochastic simulation can be successfully integrated into a backward recursive programming approach in the context of flexible investment planning. We apply this hybrid approach to a marketing question from primary production which can be viewed as an investment problem: should grain farmers purchase sales contracts which guarantee fixed product prices over the next 10 years? The model results support the conclusion from dynamic investment theory that it is essential to take simultaneously account of uncertainty and flexibility.
Singapore's policy responses to ageing, inequality and poverty: An assessment
Authors: Asher Mukul G. , Nandy Amarendu
Published: January 2008

Abstract  Singapore represents an instructive case study in responding to rapid ageing, growing inequalities, and significant relative poverty. Unlike other high‐income Asian countries, it has relied on single‐tier mandatory savings to finance retirement, housing, and to a lesser extent, healthcare. To address the low fertility rates, it has permitted the share of the non‐citizen population to triple between 1990 and 2005 to nearly 30 per cent. This is subtly altering Singapore's socio‐political dynamics, while assisting in sustaining growth and competitiveness. The paper argues that Singapore has the fiscal, institutional, and organizational capacities for a modern multi‐tier social security system. Singapore is, however, determined to continue with current inadequate and inequitable arrangements, requiring individuals and their families to bear disproportionate risks in financing retirement, healthcare, and short‐term income support. This reflects conscious policy choices arising from a Darwinist vision of society, and the need for socio‐political control.
Delayed combinatorial treatment with flavopiridol and minocycline provides longer term protection for neuronal soma but not dendrites following global ischemia
Authors: Iyirhiaro Grace O. , Brust Tyson B. , Rashidian Juliet , Galehdar Zohreh , Osman Aweis , Phillips Maryam , Slack Ruth S. , MacVicar Brian A. , Park David S.
Published: January 2008

We previously reported that delayed administration of the general cyclin‐dependent kinase inhibitor flavopiridol following global ischemia provided transient neuroprotection and improved behavioral performance. However, it failed to provide longer term protection. In the present study, we investigate the ability of delayed flavopiridol in combination with delayed minocycline, another neuroprotectant to provide sustained protection following global ischemia. We report that a delayed combinatorial treatment of flavopiridol and minocycline provides synergistic protection both 2 and 10 weeks following ischemia. However, protected neurons in the hippocampal CA1 are synaptically impaired as assessed by electrophysio logical field potential recordings. This is likely because of the presence of degenerated processes in the CA1 even with combinatorial therapy. This indicates that while we have addressed one important pre‐clinical parameter by dramatically improving long‐term neuronal survival with delayed combinatorial therapy, the issue of synaptic preservation of protected neurons still exists. These results also highlight the important observation that protection does not always lead to proper function.
Rapid, stimulation‐induced reduction of C12‐resorufin in motor nerve terminals: linkage to mitochondrial metabolism
Authors: Talbot Janet D. , Barrett John N. , Barrett Ellen F. , David Gavriel
Published: January 2008

The Alamar blue (resazurin) assay of cell viability monitors the irreversible reduction of non‐fluorescent resazurin to fluorescent resorufin. This study focused on the reversible reduction of C12‐resorufin to non‐fluorescent C12‐dihydroresorufin in motor nerve terminals innervating lizard intercostal muscles. Resting C12‐resorufin fluorescence decreased when the activity of the mitochondrial electron transport chain (ETC) was accelerated with carbonyl cyanide m‐chloro phenyl hydrazone, and increased when ETC activity was inhibited with cyanide. Trains of action potentials (50 Hz for 20–50 s), which reversibly decreased NADH fluorescence and partially depolarized the mitochondrial membrane potential, produced a reversible decrease in C12‐resorufin fluorescence which had a similar time course. The stimulation‐induced decrease in C12‐resorufin fluorescence was blocked by inhibitors of ETC complexes I, III, and IV and by carbonyl cyanide m‐chloro phenyl hydrazone, but not by inhibiting mitochondrial ATP synthesis with oligomycin. Mitochondrial depolarization and the decreases in C12‐resorufin and NADH fluorescence depended on Ca2+ influx into the terminal, but not on vesicular transmitter release. These results suggest that the reversible reduction of C12‐resorufin in stimulated motor nerve terminals is linked, directly or indirectly, to the reversible oxidation of NADH and to Ca2+ influx into mitochondria, and provides an assay for rapid changes in motor terminal metabolism.