bluuebunny/crossref_metadata_2025 huggingface dataset:
Somatic mutations of mitochondrial DNA in digestive tract cancers
Authors: KOSE KAZUHIRO , HIYAMA TORU , TANAKA SHINJI , YOSHIHARA MASAHARU , YASUI WATARU , CHAYAMA KAZUAKI
Published: September 2005

Background:  Somatic mutations of mitochondrial DNA (mtDNA) have been reported to play an important role in the carcinogenesis of several human cancers. However, there are few reports on mtDNA mutations in digestive tract cancers, including esophageal, gastric and colorectal cancers. The present study examined somatic mtDNA mutations in these cancers.

Methods:  Samples of 82 esophageal cancers, 96 gastric cancers and 138 colorectal cancers were collected. Mutations in the D310 mononucleotide repeat of mtDNA were examined by microsatellite assay.

Results:  Frequencies of mtDNA mutations were similar in each digestive tract cancer: 14% (7/51) in esophageal cancers, 15% (14/94) in gastric cancers and 8% (11/133) in colorectal cancers. There were no significant relationships between mtDNA mutations and clinicopathological features, such as patient age or sex, tumor location, depth of tumor invasion and lymph node metastasis in each digestive tract cancer.

Conclusions:  The results suggest that mtDNA mutations play a role in the development but not progression in each digestive tract cancer, and that the role of mtDNA mutations might be similar among the digestive tract cancers.
Phase I study of biweekly gemcitabine followed by oxaliplatin and simplified 48‐h infusion of fluorouracil/leucovorin for advanced pancreatic cancer
Authors: CH’ANG HUI‐JU , WANG CHUAN‐CHENG , CHENG ANN‐LII , HSU CHIUN , LU YEN‐SHEN , CHANG MING‐CHU , LIN JAW‐TOWN , WANG HSIU‐PO , SHIAH HER‐SHYONG , LIU TSANG‐WU , CHANG JANG‐YANG , WHANG‐PENG JACQUELINE , CHEN LI‐TZONG
Published: September 2005

Objectives:  To evaluate the feasibility and maximal tolerated dose (MTD) of oxaliplatin of a triplet regimen consisting of gemcitabine, oxaliplatin and infusional fluorouracil (5‐FU)/leucovorin (LV) (GOFL) for advanced pancreatic cancer.

Patients and Methods:  Patients with histologically proven metastatic or unresectable, locally advanced pancreatic adenocarcinoma were eligible to take part in the study. The treatment consisted of fixed‐rate infusion (10 mg/m2/minute) of 800 mg/m2 gemcitabine followed by 2‐h infusion of oxaliplatin and then 48‐h infusion of 5‐FU/LV day 1 and day 15 every 4 weeks. The oxaliplatin would be evaluated at three dose levels, 65, 75 and 85 mg/m2.

Results:  A total of 15 patients were enrolled at three dose levels. Dose‐limiting toxicity of neutropenic fever and grade 4 thrombocytopenia occurred in one of each six patients at oxaliplatin dose level of 65 mg/m2 and 85 mg/m2, respectively. The MTD of oxaliplatin for this combination was 85 mg/m2. After a median four cycles of treatment, grade 3/4 neutropenia occurred in 46.7% of patients and thrombocytopenia in 13.3%. Non‐hematological toxicities were generally of grade 1/2. Objective tumor response was observed in five patients (33.3%, 95% confidence interval, 6.3–60.4%).

Conclusion:  Biweekly GOFL is a feasible regimen for advanced pancreatic cancer. For further phase II studies, the recommended dose of oxaliplatin is 85 mg/m2.
Hepatic arterial infusion alternating with systemic chemotherapy in patients with non‐resectable hepatic metastases from colorectal cancer
Authors: KIM JIN C , KIM HEE C , LEE KANG H , YU CHANG S , KIM TAE W , CHANG HEUNG M , RYU MIN H , KIM JONG H , HA HYUN K , LEE MOON G
Published: September 2005

Background and Aim:  Hepatic arterial infusion (HAI) chemotherapy has a number of limitations, including a low rate of complete response and frequent extrahepatic recurrence, in colorectal cancer patients with non‐resectable hepatic metastases.

Methods:  Twenty‐nine colorectal cancer patients with non‐resectable hepatic metastases were consecutively enrolled for HAI alternating with systemic chemotherapy (HA + SC group). The protocol comprised six cycles of alternating HAI (5‐FU + leucovorin for 14 days, and mitomycin C on the first day) and systemic chemotherapy (5‐FU + leucovorin). Colorectal cancer patients with two or more hepatic metastases treated using hepatic resection and systemic chemotherapy (HR + SC group) were selected as a comparative group.

Results:  Within the HA + SC group, complete response was achieved in eight patients (28%), whereas 13 patients (45%) showed progressive disease. Six of the eight patients with complete response lived for more than 38 months. Extrahepatic recurrences were more frequent in the HR + SC group than the HA + SC group (47 vs 21%, P = 0.024). The two groups did not differ with respect to overall and hepatic progression‐free survival (P = 0.947 and 0.444, respectively), displaying median ± SE values of 38 ± 7 and 20 ± 3 months in the HA + SC group, and 39 ± 9 and 33 ± 14 months in the HR + SC group, respectively. One patient in each group experienced toxic hepatitis, and sclerosing cholangitis occurred in one patient of the HA + SC group. Other complications were mostly grade 1 or 2.

Conclusions:  HAI alternating with systemic chemotherapy led to a promising response and hepatic progression‐free survival, possibly reducing extrahepatic recurrence in colorectal cancer patients with non‐resectable liver metastases.
Autoantibody profiles in microscopic colitis
Authors: HOLSTEIN ANDREAS , BURMEISTER JOERG , PLASCHKE ARMIN , ROSEMEIER DIRK , WIDJAJA ADJI , EGBERTS EICK‐HARTWIG
Published: September 2005

Objective:  The etiology of microscopic colitis is unclear; an autoimmune response and pharmacological induction have been proposed as possible mechanisms. We conducted a multicentre cross‐sectional study to compare the antibody profiles of patients with collagenous and lymphocytic colitis with those of a control group.

Methods:  The medical histories and antibody profiles of 26 patients with collagenous and 16 patients with lymphocytic colitis were compared with the corresponding data of 43 controls without gastroenterological disease. Antibodies to the following structures were determined: intestinal goblet cells, antinuclear antibodies (ANA), antineutrophil cytoplasmic antibodies, anti‐Saccharomyces cerevisiae antibody (ASCA), tissue transglutaminase, gliadin, pancreatic acini, glutamate decarboxylase, tyrosine phosphatase IA‐2 and thyroid (microsomal anitbodies, MAB).

Results:  Patients with collagenous and lymphocytic colitis had been treated significantly more often with H2‐receptor antagonists and non‐steroidal anti‐inflammatory drugs (P = 0.026 and 0.014, respectively). Additional diseases of presumed autoimmune etiology were present in 43% (18/42) of patients. Comparison with the controls showed significantly more positive findings for ANA immunoglobulin G (IgG), gliadin immunoglobulin A (IgA) and ASCA (IgA and IgG) in patients with collagenous colitis but not in those with lymphocytic colitis. Collagenous colitis was associated with positive ASCA in 15% of patients and lymphocytic colitis in 13%.

Conclusions:  The autoantibodies investigated are of no diagnostic relevance to microscopic colitis. Positive ANA and strong associations with other autoimmune diseases point to an autoimmune etiology. H2‐receptor antagonists and non‐steroidal anti‐inflammatory drugs might also be of pathogenetic significance.
Highways block gene flow and cause a rapid decline in genetic diversity of desert bighorn sheep
Authors: Epps Clinton W. , Palsbøll Per J. , Wehausen John D. , Roderick George K. , Ramey Rob R. , McCullough Dale R.
Published: September 2005

The rapid expansion of road networks has reduced connectivity among populations of flora and fauna. The resulting isolation is assumed to increase population extinction rates, in part because of the loss of genetic diversity. However, there are few cases where loss of genetic diversity has been linked directly to roads or other barriers. We analysed the effects of such barriers on connectivity and genetic diversity of 27 populations ofOvis canadensis nelsoni(desert bighorn sheep). We used partial Mantel tests, multiple linear regression and coalescent simulations to infer changes in gene flow and diversity of nuclear and mitochondrial DNA markers. Our findings link a rapid reduction in genetic diversity (up to 15%) to as few as 40 years of anthropogenic isolation. Interstate highways, canals and developed areas, where present, have apparently eliminated gene flow. These results suggest that anthropogenic barriers constitute a severe threat to the persistence of naturally fragmented populations.
New techniques and findings in the study of a candidate allelochemical implicated in invasion success
Authors: Blair Amy C. , Hanson Bradley D. , Brunk Galen R. , Marrs Robin A. , Westra Philip , Nissen Scott J. , Hufbauer Ruth A.
Published: September 2005

Allelopathy has been hypothesized to promote the success of invasive plants. Support for the role of allelopathy in invasions has emerged from research on the candidate allelochemical (−)‐catechin, which is secreted by spotted knapweed. Here we describe new methods to quantify catechin in liquid and soil. With a new technique, we assayed catechin production by individual plants in liquid media and found levels up to two orders of magnitude less than previously reported. An acetone/water solution provided consistent recovery of catechin from soil, with percent recovery depending upon soil type. We evaluated soils from two spotted knapweed sites in Montana, USA, but found no measurable catechin. Idaho fescue, a native species reportedly sensitive to catechin, only exhibited slightly reduced growth at concentrations 10 times higher than previously reported to cause 100% mortality. Our results emphasize that more research is required to clarify the role of catechin in the invasion of spotted knapweed.
Direct and indirect fishery effects on small coastal elasmobranchs in the northern Gulf of Mexico
Authors: Shepherd Travis D. , Myers Ransom A.
Published: September 2005

Globally, bycatch in tropical/subtropical shrimp trawl and longline fisheries is threatening many marine species. Here we examine the joint effects of increased mortality caused by shrimp trawling bycatch, and reduced predation caused by losses of large sharks because of longline fishing. Research surveys in the Gulf of Mexico (1972–2002) demonstrated precipitous declines in shallow water coastal elasmobranchs where shrimping effort was highest (bonnethead 96%, Bancroft's numbfish (lesser electric ray) 98%, smooth butterfly ray > 99%) and consistent increases in deeper water elasmobranchs (Atlantic angel shark, smooth dogfish). These increases are the first empirical support for predation release caused by the loss of large sharks, which have been theorized to structure tropical/subtropical marine ecosystems. Bycatch of elasmobranchs in shrimp trawls is a critical conservation concern which is not solved by present mitigation measures; similar loss of elasmobranchs is expected to be occurring in tropical/subtropical regions worldwide where ever intensive shrimp trawling occurs.
Life‐history correlates of plant invasiveness at regional and continental scales
Authors: Hamilton Mark A. , Murray Brad R. , Cadotte Marc W. , Hose Grant C. , Baker Andrew C. , Harris Carla J. , Licari Damian
Published: September 2005

We implemented cross‐species and independent‐contrasts multiple regression models to compare life‐history correlates of invasion success between regional and continental spatial scales among non‐native plants of eastern Australia. We focussed on three life‐history traits that represent major axes of variation in plant life history: specific leaf area (SLA), plant height and seed mass. After controlling for residence time and cross‐correlation with other life‐history traits, small seed mass was significantly and uniquely correlated with invasion success at continental and regional scales. High SLA was significantly and uniquely correlated with invasion success at the continental scale only. Plant height could not explain unique variation in invasion success at either spatial scale. Variation among spatial scales in the significance and strength of life‐history relationships with invasion success suggests that the search for predictive tools of invasion need not be fruitless, as long as predictive investigations are targeted at appropriate spatial scales.
Interaction frequency as a surrogate for the total effect of animal mutualists on plants
Authors: Vázquez Diego P. , Morris William F. , Jordano Pedro
Published: September 2005

We evaluate whether species interaction frequency can be used as a surrogate for the total effect of a species on another. Because interaction frequency is easier to estimate than per‐interaction effect, using interaction frequency as a surrogate of total effect could facilitate the large‐scale analysis of quantitative patterns of species‐rich interaction networks. We show mathematically that the correlation between interaction frequency (I) and total effect (T) becomes more strongly positive the greater the variation of I relative to the variation of per‐interaction effect (P) and the greater the correlation between I and P. A meta‐analysis using data on I, P and T for animal pollinators and seed dispersers visiting plants shows a generally strong, positive relationship between T and I, in spite of no general relationship between P and I. Thus, frequent animal mutualists usually contribute the most to plant reproduction, regardless of their effectiveness on a per‐interaction basis.
Patch area, population density and the scaling of migration rates: the resource concentration hypothesis revisited
Authors: Hambäck Peter A. , Englund Göran
Published: September 2005

Empirical research has for a long time observed that animal densities may both increase and decrease with patch size, and these variable responses have been difficult to explain using the current theoretical framework. The most influential hypothesis, the resource concentration hypothesis, predicts only positive density–area relations, as a consequence of different emigration and immigration rates in small and large patches, and empirical deviations have inspired a flurry of alternative explanations. In this paper, we use realistic rules for the relationship between patch size and migration rates and show a wider predictive range for density–area relations than previously believed. Comparisons with published data suggest that observed density–area relations may easily fit in a framework based on a minimum set of behavioural and population processes. This does not imply that other mechanisms are unimportant, but merely that their quantitative importance can only be evaluated relative to patch geometry and local growth.
Size and functional diversity of microbe populations control plant persistence and long‐term soil carbon accumulation
Authors: Fontaine Sébastien , Barot Sébastien
Published: September 2005

Soil organic matter (SOM) models are based on the equation dC/dt = −kC which states that the decomposition rate of a particular carbon (C) pool is proportional to the size of the pool and the decomposition constant k. However, this equation does not adequately describe the decomposition of recalcitrant SOM compounds. We present an alternative theory of SOM dynamics in which SOM decay rate is controlled by the size and the diversity of microbe populations and by the supply of energy‐rich litter compounds. We show that the SOM pool does not necessarily reach equilibrium and may increase continuously, which explains how SOM can accumulate over thousands of years. However, the simulated SOM accumulation involves the sequestration of available nutrients. How can plants persist? This question is explored with two models that couple the C cycle with a limiting nutrient. The first model considers a single type of microbe whereas the second includes two functional types in competition for energy and nutrient acquisition. The condition for plant persistence is the presence of these two competing microbial types.
Why are birds’ eggs speckled?
Authors: Gosler Andrew G. , Higham James P. , James Reynolds S.
Published: September 2005

Birds are unique in laying eggs with pigmented shells, but for most species (e.g. most passerines, which lay white eggs speckled with reddish spots of protoporphyrin) the pigments’ function is unknown. We studied a bird population at a geologically variable site, and considered a hitherto untested hypothesis: that protoporphyrin pigments might compensate for reduced eggshell‐thickness (caused partly by calcium deficiency), which is known to reduce eggshell‐strength and increase eggshell‐permeability. We found that pigment spots specifically demarcated thinner areas of shell, with darker spots marking yet thinner shell than paler spots. Variation in pigmentation was thus associated with variation in shell thickness both within and between clutches, so accounting for the eggshell's characteristic spot patterns. Geological variability at this site has resulted in a great range of calcium availability and, as predicted by the hypothesis, variation in calcium availability was found to affect between‐clutch variation in both eggshell‐mass (+) and pigmentation characteristics (−). We suggest a physiological mechanism and some important implications of these findings.
Potential photosynthesis gene recombination between Prochlorococcus and Synechococcus via viral intermediates
Authors: Zeidner Gil , Bielawski Joseph P. , Shmoish Michael , Scanlan David J. , Sabehi Gazalah , Béjà Oded
Published: September 2005

Genes (psbA and psbD) encoding for photosynthetically important proteins were recently found in a number of cultured cyanophage genomes. This phenomenon may be a beneficial trait to the viruses or their photosynthetic cyanobacterial hosts, or may represent an untapped pool of genes involved in the formation of the photosynthetic apparatus that are prone to lateral gene transfer. Here we show analyses of psbA genes from uncultured environmental viruses and prophage populations. We observe a statistically significant separation between viral genes and their potential Synechococcus hosts’ genes, and statistical analyses under models of codon evolution indicate that the psbA genes of viruses are evolving under levels of purifying selection that are virtually indistinguishable from their hosts. Furthermore, our data also indicate the possible exchange and reshuffling of psbA genes between Synechococcus and Prochlorococcus via phage intermediates. Overall, these observations raise the possibility that marine viruses serve as a potential genetic pool in shaping the evolution of cyanobacterial photosynthesis.
Incidence of novel and potentially archaeal nitrogenase genes in the deep Northeast Pacific Ocean
Authors: Mehta Mausmi P. , Huber Julie A. , Baross John A.
Published: September 2005

Archaea have been detected throughout the oceanic water column and are quantitatively important members of picoplankton in the deep ocean. Two common groups, group I Crenarchaeota and group II Euryarchaeota, are consistently detected in warm hydrothermal fluid and are assumed to have been drawn into the subseafloor, mixed with hydrothermal fluid and then expelled. However, because they remain resistant to cultivation, very little is known about their physiology. Here we show that cold deep‐seawater from the axial valley of Endeavour Segment on the Juan de Fuca Ridge contains not only groups I and II archaea as expected, but also unique potentially archaeal nitrogenase (nifH) genes, which are required for nitrogen fixation. These nifH genes are phylogenetically distinct and have dissimilar G+C content compared with those of hydrothermal vent archaea, suggesting that they belong to non‐thermophilic deep‐sea archaea. Furthermore, this sample did not contain mcrA genes, which are present in methanogens, the only known archaeal nitrogen fixers. These nifH genes were not detected in upper water column samples, or in a deep‐seawater sample 100 km away from the spreading axis of the Juan de Fuca Ridge. We propose that these unique nifH genes may be localized to archaea that circulate through the nitrogen‐poor subseafloor at the mid‐ocean ridge as part of their life cycle.
Species recognition in the truffle genus Tuber– the synonyms Tuber aestivum and Tuber uncinatum
Authors: Wedén Christina , Danell Eric , Tibell Leif
Published: September 2005

The two morphologically similar truffles Tuber aestivum and T. uncinatum have caused confusion because T. uncinatum is regarded by different authors, as either a distinct species, variety, subspecies, or synonym of T. aestivum. A clarification of the relationship between the two truffles would help both conservation biology and cultivation. We aimed both to test the reliability of the only quantitative morphological character used to distinguish the two taxa, i.e. the height of the spore reticulum, and to compare sequences of the ribosomal DNA (rDNA) internal transcribed spacer (ITS) region. Our study included 117 fruit bodies of T. aestivum and T. uncinatum, originating from eight European countries. The results showed that the spore reticulum height is not diagnostic. The phylogenetic analysis of ITS sequences from 81 fruit bodies and an additional 32 sequences from GenBank showed that T. aestivum and T. uncinatum were intermingled in one highly supported (100% bootstrap) monophyletic clade, separate from its sister species Tuber mesentericum. We conclude that T. aestivum and T. uncinatum are synonyms and the species should be named T. aestivum, as the oldest name has priority. For traders, T. aestivum syn. T. uncinatum should be used until conformity has been reached.
Methanogen communities and Bacteria along an ecohydrological gradient in a northern raised bog complex
Authors: Juottonen Heli , Galand Pierre E. , Tuittila Eeva‐Stiina , Laine Jukka , Fritze Hannu , Yrjälä Kim
Published: September 2005

Mires forming an ecohydrological gradient from nutrient‐rich, groundwater‐fed mesotrophic and oligotrophic fens to a nutrient‐poor ombrotrophic bog were studied by comparing potential methane (CH4) production and methanogenic microbial communities. Methane production was measured from different depths of anoxic peat and methanogen communities were detected by detailed restriction fragment length polymorphism (RFLP) analysis of clone libraries, sequencing and phylogenetic analysis. Potential CH4 production changed along the ecohydrological gradient with the fens displaying much higher production than the ombrotrophic bog. Methanogen diversity also decreased along the gradient. The two fens had very similar diversity of methanogenic methyl‐coenzyme M reductase gene (mcrA), but in the upper layer of the bog the methanogen diversity was strikingly lower, and only one type of mcrA sequence was retrieved. It was related to the Fen cluster, a group of novel methanogenic sequences found earlier in Finnish mires. Bacterial 16S rDNA sequences from the fens fell into at least nine phyla, but only four phyla were retrieved from the bog. The most common bacterial groups were Deltaproteobacteria, Verrucomicrobia and Acidobacteria.
Global physiological analysis of carbon‐ and energy‐limited growing Escherichia coli confirms a high degree of catabolic flexibility and preparedness for mixed substrate utilization
Authors: Ihssen Julian , Egli Thomas
Published: September 2005

Growth conditions for heterotrophic bacteria in the environment are characterized by low concentrations of carbon and energy sources and complex substrate mixtures. While mechanisms of starvation‐survival in the absence of carbon substrates have been studied in considerable detail, information on the physiology of slow growth under oligotrophic conditions is limited. We intended to elucidate general strategies by which Escherichia coli adapts to low concentrations of a mixed carbon and energy source pool. A new screening method based on BIOLOG AN MicroPlatesTM, which allowed us to distinguish repressed and induced catabolic functions in E. coli, was combined with the analysis of periplasmic high‐affinity binding proteins. Extending previous findings for E. coli and other microbial species, we found that numerous alternative catabolic functions and high‐affinity binding proteins are derepressed under either glucose‐ or arabinose‐limited growth conditions, in spite of the absence of the respective inducers. Escherichia coli cells growing in carbon‐limited complex medium chemostat cultures exhibited an even higher degree of catabolic flexibility and were able to oxidize 43 substrates. The BIOLOG respiration pattern indicated simultaneous dissimilation of diverse sugars, amino acids and dipeptides (mixed substrate growth). The observed physiological adaptations of E. coli to low concentrations of carbon and energy substrates presumably are advantageous in many natural growth situations and also offer an explanation why many heterotrophic bacteria have and maintain such a broad carbon substrate range.
Methane fluxes in permafrost habitats of the Lena Delta: effects of microbial community structure and organic matter quality
Authors: Wagner Dirk , Lipski André , Embacher Arndt , Gattinger Andreas
Published: September 2005

For the understanding and assessment of recent and future carbon dynamics of arctic permafrost soils the processes of CH4 production and oxidation, the community structure and the quality of dissolved organic matter (DOM) were studied in two soils of a polygonal tundra. Activities of methanogens and methanotrophs differed significantly in their rates and distribution patterns among the two investigated profiles. Community structure analysis showed similarities between both soils for ester‐linked phospholipid fatty acids (PLFAs) and differences in the fraction of unsaponifiable PLFAs and phospholipid ether lipids. Furthermore, a shift of the overall composition of the microbiota with depth at both sites was indicated by an increasing portion of iso‐ and anteiso‐branched fatty acids related to the amount of straight‐chain fatty acids. Although permafrost soils represent a large carbon pool, it was shown that the reduced quality of organic matter leads to a substrate limitation of the microbial metabolism. It can be concluded from our and previous findings first that microbial communities in the active layer of an Arctic polygon tundra are composed by members of all three domains of life, with a total biomass comparable to temperate soil ecosystems, and second that these microorganisms are well adapted to the extreme temperature gradient of their environment.
Grazing resistance of Pseudomonas aeruginosa biofilms depends on type of protective mechanism, developmental stage and protozoan feeding mode
Authors: Weitere Markus , Bergfeld Tanja , Rice Scott A. , Matz Carsten , Kjelleberg Staffan
Published: September 2005

In a previous study we identified microcolony formation and inhibitor production as the major protective mechanisms of Pseudomonas aeruginosa biofilms against flagellate grazing [Matz, C., Bergfeld, T., Rice, S.A., and Kjelleberg, S. (2004) Microcolonies, quorum sensing and cytotoxicity determine the survival of Pseudomonas aeruginosa biofilms exposed the protozoan grazing. Environ Microbiol 6: 218–226]. Here we compared the efficacy of these two key protective mechanisms by exposing biofilms of the non‐toxic alginate overproducing strain PDO300 and the wild‐type toxic strain PAO1 to a range of feeding types commonly found in the succession of protozoans associated with natural biofilms. Alginate‐mediated microcolony formation conferred effective protection for strain PDO300 against the suspension feeding flagellate Bodo saltans and, as reported earlier, the surface feeding flagellate Rhynchomonas nasuta, both of which are considered as early biofilm colonizers. However, microcolonies of mature PDO300 biofilms were highly susceptible to late biofilm colonizers, the surface‐feeding amoeba Acanthamoeba polyphaga and the planktonic ciliate Tetrahymena sp., resulting in a significant reduction of biofilm biomass. Mature biofilms of strain PAO1 inhibited growth of flagellates and A. polyphaga while the grazing activity of Tetrahymena sp. remained unaffected. Our findings suggest that inhibitor production of mature P. aeruginosa biofilms is effective against a wider range of biofilm‐feeding predators while microcolony‐mediated protection is only beneficial in the early stages of biofilm formation.
A green light‐absorbing phycoerythrin is present in the high‐light‐adapted marine cyanobacterium Prochlorococcus sp. MED4
Authors: Steglich Claudia , Frankenberg‐Dinkel Nicole , Penno Sigrid , Hess Wolfgang R.
Published: September 2005

In the high‐light‐adapted unicellular marine cyanobacterium Prochlorococcus sp. MED4 the cpeB gene is the only gene coding for a structural phycobiliprotein. The absence of any other phycoerythrin gene in the fully sequenced genome of this organism, the previous inability to detect a gene product, and the mutation of two out of four cysteine residues, normally involved in binding chromophores, suggested that MED4‐cpeB might not code for a functional protein. Here, transcription of MED4‐cpeB at a low level was detected and the transcriptional start site was mapped. Enrichment of the protein identified phycoerythrobilin as its sole chromophore in vivo, which was confirmed by chromophorylation assays in vitro using the recombinant protein. Phycourobilin is the major chromophore in low‐light‐adapted Prochlorococcus ecotypes such as strain SS120. Therefore, spectrally tuned phycoerythrins are a characteristic feature of distinct Prochlorococcus ecotypes. Further in vitro mutagenesis experiments replacing one or both cysteines C61R/C82S by arginine or serine, respectively, revealed that only Cys82 is required for chromophore binding. Thus, an unusual green light‐absorbing phycoerythrin evolved in the high‐light‐adapted ecotypes of Prochlorococcus, which potentially serves as a photoreceptor.
Bacterial communities associated with benthic organic matter in headwater stream microhabitats
Authors: Fazi Stefano , Amalfitano Stefano , Pernthaler Jakob , Puddu Alberto
Published: September 2005

Bacterial communities associated with a variety of benthic detritus types were studied in three streams in the context of the chemical characteristics of the sediment material and the stream water. A cell purification assay was developed for a quantitative microscopic evaluation of bacterial community structure in detritus samples by fluorescence in situ hybridization (FISH). The efficiency of FISH with fluorescently monolabelled probes was compared with FISH with signal amplification by catalysed reporter deposition (CARD‐FISH). In detritus types poor in organic carbon and nitrogen, the numbers of prokaryotes were related to the chemical characteristics of the stream water column, whereas no such relationship was found for detritus types rich in organic carbon and nitrogen. These results might help to provide criteria for the selection of detritus types for river ecosystem assessment and monitoring. The percentage of bacteria detected by FISH with monolabelled probes was correlated with the detritus total organic matter (OM). This is likely attributed to a higher ribosome content of microbial cells on substrates rich in OM. Cell detection by CARD‐FISH did not show any correlation with OM content, indicating that this technique renders the results more independent from the activity state of cells. Fluorescence in situ hybridization with four group‐specific probes suggested a relationship between substrate quality and the composition of the microbial assemblages on the various types of detritus. The improved protocol for cell purification and CARD‐FISH may facilitate future investigations on the relationship between the riverine benthic detritus quality and microbial community composition.
Contrasting microcystin production and cyanobacterial population dynamics in two Planktothrix‐dominated freshwater lakes
Authors: Janse Ingmar , Kardinaal W. Edwin A. , Agterveld Miranda Kamst‐van , Meima Marion , Visser Petra M. , Zwart Gabriel
Published: September 2005

Microcystin concentrations in two Dutch lakes with an important Planktothrix component were related to the dynamics of cyanobacterial genotypes and biovolumes. Genotype composition was analysed by using denaturing gradient gel electrophoresis (DGGE) profiling of the intergenic transcribed spacer region of the rrn operon (rRNA‐ITS), and biovolumes were measured by using microscopy. In Lake Tjeukemeer, microcystins were present throughout summer (maximum concentration 30 µg l−1) while cyanobacterial diversity was low and very constant. The dominant phototroph was Planktothrix agardhii. In contrast, Lake Klinckenberg showed a high microcystin peak (up to 140 µg l−1) of short duration. In this lake, cyanobacterial diversity was higher and very dynamic with apparent genotype successions. Several genotypes derived from DGGE field profiles matched with genotypes from cultures isolated from field samples. The microcystin peak measured in Lake Klinckenberg could be confidently linked to a bloom of Planktothrix rubescens, as microscopic and genotypic analysis showed identity of bloom samples and a toxin‐producing P. rubescens culture. Toxin‐producing genotypes were detected in the microbial community before they reached densities at which they were detected by using microscopy. Cyanobacterial biovolumes provided additional insights in bloom dynamics. In both lakes, the microcystin content per cell was highest at the onset of the blooms. Our results suggest that while genotypic characterization of a lake can be valuable for detection of toxic organisms, for some lakes a monitoring of algal biomass has sufficient predictive value for an assessment of toxin production.
Phylogenetic resolution and habitat specificity of members of the Photobacterium phosphoreum species group
Authors: Ast Jennifer C. , Dunlap Paul V.
Published: September 2005

Substantial ambiguity exists regarding the phylogenetic status of facultatively psychrophilic luminous bacteria identified as Photobacterium phosphoreum, a species thought to be widely distributed in the world's oceans and believed to be the specific bioluminescent light‐organ symbiont of several deep‐sea fishes. Members of the P. phosphoreum species group include luminous and non‐luminous strains identified phenotypically from a variety of different habitats as well as phylogenetically defined lineages that appear to be evolutionarily distinct. To resolve this ambiguity and to begin developing a meaningful knowledge of the geographic distributions, habitats and symbiotic relationships of bacteria in the P. phosphoreum species group, we carried out a multilocus, fine‐scale phylogenetic analysis based on sequences  of  the  16S  rRNA,  gyrB and  luxABFE  genes of many newly isolated luminous strains from symbiotic and saprophytic habitats, together with previously isolated luminous and non‐luminous strains identified as P. phosphoreum from these and other habitats. Parsimony analysis unambiguously resolved three evolutionarily distinct clades, phosphoreum, iliopiscarium and kishitanii. The tight phylogenetic clustering within these clades and the distinct separation between them indicates they are different species, P. phosphoreum, Photobacterium iliopiscarium and the newly recognized ‘Photobacterium kishitanii’. Previously reported non‐luminous strains, which had been identified phenotypically as P. phosphoreum, resolved unambiguously as P. iliopiscarium, and all examined deep‐sea fishes (specimens of families Chlorophthalmidae, Macrouridae, Moridae, Trachichthyidae and Acropomatidae) were found to harbour ‘P. kishitanii’, not P. phosphoreum, in their light organs. This resolution revealed also that ‘P. kishitanii’ is cosmopolitan in its geographic distribution. Furthermore, the lack of phylogenetic variation within ‘P. kishitanii’ indicates that this facultatively symbiotic bacterium is not cospeciating with its phylogenetically divergent host fishes. The results of this fine‐scale phylogenetic analysis support the emerging view that bacterial species names should designate singular historical entities, i.e. discrete lineages diagnosed by a significant divergence of shared derived nucleotide characters.
Regulation of Arabidopsis thaliana 4‐coumarate:coenzyme‐A ligase‐1 expression by artificial zinc finger chimeras
Authors: Sánchez Juan Pablo , Ullman Christopher , Moore Michael , Choo Yen , Chua Nam‐Hai
Published: September 2005

The use of artificial zinc finger chimeras to manipulate the expression of a gene of interest is a promising approach because zinc finger proteins can be engineered to bind any given DNA sequence in the genome. We have previously shown that a zinc finger chimera with a VP16 activation domain can activate a reporter gene in transgenic Arabidopsis thaliana (Sánchez, J.P., Ullman, C., Moore, M., Choo, Y. and Chua, N.H. (2002) Regulation of gene expression in Arabidopsis thaliana by artificial zinc finger chimeras. Plant Cell Physiol. 43, 1465–1472). Here, we report the use of artificial zinc finger chimeras to specifically regulate the 4‐coumarate:coenzyme‐A ligase‐1 (At4CL1) gene in A. thaliana. At4CL1 is a key enzyme in lignin biosynthesis and the down‐regulation of At4CL1 can lead to a decrease in lignin content, which has a significant commercial value for the paper industry. To this end, we designed zinc finger chimeras containing either an activation or a repression domain, which bind specifically to the At4CL1 promoter region. Transgenic lines expressing a zinc finger chimera with the VP16 activation domain showed an increase in At4CL1 expression and enzyme activity. In contrast, transgenic lines expressing a chimera with the KOX (KRAB) repression domain displayed repression of At4CL1 expression and enzyme activity. The activation of At4CL1 expression produced an increase in lignin content, and transgenic plant stems showed ectopic lignin distribution. Repression of the At4CL1 gene resulted in reduced lignin content, and lignin distribution in transgenic stems was severely diminished. Our results confirm and extend previous studies of gene regulation using various artificial zinc finger chimeras in animal and plant systems, and show that this system can be used to up‐ and down‐regulate the expression of an endogenous plant gene such as At4CL1.
INSIDE/INTERIORS: CHARDIN'S IMAGES OF THE FAMILY
Authors: Démoris René
Published: September 2005

This article examines afresh well‐known paintings by Jean‐Siméon Chardin that represent the domestic interior, and questions the extent to which they circumscribe a moral realm and invoke an ideal of ‘happy families’. Chardin's families are rarely nuclear; rather they constitute complex and potentially dynamic households that include servants as well as parents and children. Through a close analysis of individual works, including still‐life and figure subjects, this essay draws attention to the ambiguity of the domestic domain as a space of the presocial, of wild, untamed drives, and one in which social aspirations are occasionally played out. It reflects on the passions and desires of the domestic world, intimated by an artist usually associated with Enlightenment.
PATTERNS OF ATTENTION: FROM SHOP WINDOWS TO GALLERY ROOMS IN EARLY TWENTIETH‐CENTURY BERLIN
Authors: Klonk Charlotte
Published: September 2005

In the aesthetic programmes promoted by the various German cultural reform movements that flourished in the years before the 1914–18 war patterns took on unprecedented significance. This article investigates the importance of abstract pattern‐making in the display strategies adopted in the museum and in the market place. Philosophical and experimental psychology was a common background in both cases. Among the questions that the article addresses are the following: Why were abstract colours and forms and their rhythmic arrangement assigned such a prominent place in Germany in the first decades of the twentieth century? Why were they favoured above the more traditional illusionistic designs? Did gendered assumptions about consumption determine design choices? The article ends with an account of a new kind of display strategy that emerged in the late 1920s in antithesis to pre‐war efforts to engage patterns of attention. This abandoned the attempt to make a psycho‐physical impact on the perceiving subject in favour of a discursive strategy that posits subjects as part of rational collectives.
ART HISTORY AND CULTURAL DIFFERENCE: ALFRED GELL'S ANTHROPOLOGY OF ART
Authors: Rampley Matthew
Published: September 2005

The problems presented by recognition of cultural difference and alterity have long been recognized as presenting substantial challenges to traditional assumptions about the scope and limits of art history. This article examines some of the arguments that have emerged in relation to this issue, focusing in particular on ways in which anthropology and, specifically, the work of Alfred Gell, might contribute to debates. It argues that Gell's theory of the art nexus offers new possibilities for the cross‐cultural study of art, which can be applied not only to the art of small‐scale oral societies but also to Western art history. In so doing, it suggests that the art‐historical engagement with anthropology should imply more than the promotion of difference as a value; rather, it suggests alternative methods of analysis that examine the role of art within social transactions.
Can Instructional and Emotional Support in the First‐Grade Classroom Make a Difference for Children at Risk of School Failure?
Authors: Hamre Bridget K. , Pianta Robert C.
Published: September 2005

This study examined ways in which children's risk of school failure may be moderated by support from teachers. Participants were 910 children in a national prospective study. Children were identified as at risk at ages 5–6 years on the basis of demographic characteristics and the display of multiple functional (behavioral, attention, academic, social) problems reported by their kindergarten teachers. By the end of first grade, at‐risk students placed in first‐grade classrooms offering strong instructional and emotional support had achievement scores and student–teacher relationships commensurate with their low‐risk peers; at‐risk students placed in less supportive classrooms had lower achievement and more conflict with teachers. These findings have implications for understanding the role that classroom experience may play in pathways to positive adaptation.
Physically Abused Children's Regulation of Attention in Response to Hostility
Authors: Pollak Seth D. , Vardi Shira , Putzer Bechner Anna M. , Curtin John J.
Published: September 2005

The present study examines the effects of early emotional experiences on children's regulation or strategic control of attention in the presence of interpersonal hostility. Abused children's reactions to the unfolding of a realistic interpersonal emotional situation were measured through multiple methods including autonomic nervous system changes and overt behavioral performance. Although physically abused and non‐physically abused 4‐year‐old children did not differ in terms of their baseline levels of arousal, marked differences in physically abused children's regulatory responses to background anger emerged. These data suggest that the emergence of anger leads to increases in anticipatory monitoring of the environment among children with histories of abuse. Results are discussed in terms of risk factors in the development of psychopathology.
Preschool Children's Mapping of Number Words to Nonsymbolic Numerosities
Authors: Lipton Jennifer S. , Spelke Elizabeth S.
Published: September 2005

Five‐year‐old children categorized as skilled versus unskilled counters were given verbal estimation and number word comprehension tasks with numerosities 20–120. Skilled counters showed a linear relation between number words and nonsymbolic numerosities. Unskilled counters showed the same linear relation for smaller numbers to which they could count, but not for larger number words. Further tasks indicated that unskilled counters failed even to correctly order large number words differing by a 2 : 1 ratio, whereas they performed well on this task with smaller numbers, and performed well on a nonsymbolic ordering task with the same numerosities. These findings provide evidence that large, approximate numerosity representations become linked to number words around the time that children learn to count to those words reliably.
The Joint Contribution of Early Parental Warmth, Communication and Tracking, and Early Child Conduct Problems on Monitoring in Late Childhood
Authors: Patrick M. Renee , Snyder James , Schrepferman Lynn M. , Snyder John
Published: September 2005

The relationship of parental warmth, communication, and tracking (WCT), and child conduct problems in early elementary school (age 5.5 years) to monitoring in late elementary school (age 9.5 years) was longitudinally examined in a sample of 267 boys and girls. WCT in kindergarten was associated with lower kindergarten levels and less growth of conduct problems into the first grade, and was prospectively associated with effective monitoring in the third and fourth grades. Overt and covert conduct problems in kindergarten and growth in covert problems during kindergarten and first grade were associated with less effective later monitoring. Early conduct problems mediated the prospective association of WCT on later monitoring. The results are described in a transactional model of parent–child relationships and child problem behavior.
Attachment in Institutionalized and Community Children in Romania
Authors: Zeanah Charles H. , Smyke Anna T. , Koga Sebastian F. , Carlson Elizabeth ,   The Bucharest Early Intervention Project Core Group
Published: September 2005

This study examined attachment in institutionalized and community children 12–31 months of age in Bucharest, Romania. Attachment was assessed using ratings of attachment behaviors and ratings of caregiver descriptions in a structured interview. As predicted, children raised in institutions exhibited serious disturbances of attachment as assessed by all methods. Observed quality of caregiving was related to formation and organization of attachment in children living in institutions. These results held even when other variables, such as cognitive level, perceived competence, and quantitative interaction ratings, were controlled for. Ratings of attachment behavior in the Strange Situation and caregiver reports of signs of Reactive Attachment Disorder converged moderately. The implications of these findings for different perspectives on attachment are discussed.
The Mother–Infant Relationship and Infant Attachment in a South African Peri‐Urban Settlement
Authors: Tomlinson Mark , Cooper Peter , Murray Lynne
Published: September 2005

A sample of 147 mother–infant dyads was recruited from a peri‐urban settlement outside Cape Town and seen at 2‐ and 18‐months postpartum. At 18 months, 61.9% of the infants were rated as securely attached (B); 4.1% as avoidant (A); 8.2% as resistant (C); and 25.8% disorganized (D). Postpartum depression at 2 months, and indices of poor parenting at both 2 and 18 months, were associated with insecure infant attachment. The critical 2‐month predictor variables for insecure infant attachment were maternal intrusiveness and maternal remoteness, and early maternal depression. When concurrent maternal sensitivity was considered, the quality of the early mother–infant relationship remained important, but maternal depression was no longer predictive. Cross‐cultural differences and consistencies in the development of attachment are discussed.