bluuebunny/crossref_metadata_2025 huggingface dataset:
Proximate composition and fatty acid profile of three different fresh and dried commercial sea cucumbers from Turkey
Authors: Aydın Mehmet , Sevgili Hüseyin , Tufan Bekir , Emre Yilmaz , Köse Sevim
Published: February 2011

Proximate composition and fatty acid (FA) profile of three commercial sea cucumbers; Holothuria tubulosa, Holothuria polii and Holothuria mammata caught from Aegean Sea of Turkey were analysed. The effects of regional variation and drying process on FA composition were also investigated. Moisture, protein, fat and ash contents of the species ranged between 81.24% and 85.24%, 7.88% and 8.82%, 0.09% and 0.18%, and 5.13% and 7.85%, respectively, with a significant changes among species (P < 0.05) with some exceptions. Although FA values varied significantly (P < 0.05) among species and regions, the changes for most FA types representing the same region for different species were not significantly different. Total polyunsaturated fatty acids (PUFA) were found to be higher than total saturated (SFA) and monosaturated FAs (MUFA) accounting for 53.0–62.12% for ∑PUFA, 13.28–16.41% for ∑MUFA and 13.99–19.21% for ∑SFA. While some individual SFAs and PUFAs decreased after drying process, various individual FAs of MUFA increased in their amounts (P < 0.05). Among PUFAs, the highest mean value of eicosapentaenoic acid and docosahexaenoic acid for all regions were determined for H. polii as 7.25% and H. tubulosa as 12.37% in fresh samples, respectively. This study represents new information relating to FA contents and drying effect on FA profile for these species.
Classification of red and white wines by denomination of origin according to phenolic composition and colour characteristics and correlation with standard parameters
Authors: Soto Vázquez Elvira , Río Segade Susana , Cortés Diéguez Sandra
Published: February 2011

The two main phenolic compounds, namely anthocyanins and tannins, and some chromatic characteristics have been determined in 437 samples of red and white wines from northwest of Spain, which were commercialised in two consecutive years (2005 and 2006). The variation range for total polyphenol index (TPI) was 4.1–16.6 and 27.8–91.9 in white and red wines, respectively. Standard parameters were also investigated. The classification successful by Denominations of Origin was near 50% for both red and white wines. Statistical correlations among standard and colour parameters were established to find a simple methodology usually used in winery that permits to provide more complete information for the oenologist. So, a significant correlation was found for TPI or chromatic intensity and volume mass in red wines (0.547–0.583, P < 0.01), while tonality can be estimated from pH (0.601, P < 0.01). No lineal relationship was found in white wines.
Phenolic profile and antioxidant properties of Polish honeys
Authors: Socha Robert , Juszczak Lesław , Pietrzyk Sławomir , Gałkowska Dorota , Fortuna Teresa , Witczak Teresa
Published: February 2011

The phenolic components of honeys have great participation in their nutritional value and antioxidant activity. Moreover, phenolic components are promising markers for the determination of botanical and geographical origin of honey. The purpose of the present work was to study the antioxidant activity and profiles of phenolic acids and flavonoids of honeys of various origins. The total phenolic content of honeys varied from 4.46 to 15.04 mg of gallic acid equivalents per 100 g of product and the total phenolic acid content determined chromatographically varied from 201.05 to 2089.08 μg per 100 g of product. Buckwheat honey exhibited the highest antioxidant activity and contained the highest total phenolic amount, whereas rape honey exhibited the lowest values in this respect. Moreover, the buckwheat honey contained the highest amount of phenolic acids. There were significant linear correlations between total phenolic content and antioxidant activity of honey extracts in the reaction with DPPH•  (1,1‐diphenyl‐2‐picrylhydrazyl) and ABTS• + (2,2′‐azinobis‐(3‐ethylbenzothiazoline‐6‐sulfonic acid)) free radicals. In most samples, p‐coumaric acid was the dominant phenolic acid (39.1–677.2 μg per 100 g). The honeys also contained considerable amount of gallic acid (6.0–913.8 μg per 100 g). Among flavonoids naringenin was predominant in the most studied honey samples.
Antimicrobial activity of Zataria multiflora Boiss. essential oil incorporated with whey protein based films on pathogenic and probiotic bacteria
Authors: Shakeri Monir‐Sadat , Shahidi Fakhri , Beiraghi‐Toosi Shahram , Bahrami Ahmadreza
Published: February 2011

The antimicrobial potential of whey protein isolate (WPI) edible films containing 1–4% (v/v) Zataria multiflora Boiss. essential oil (EO) on food‐borne pathogenic bacteria (Escherichia coli, Salmonella enteritidis, Staphylococcus aureus and Bacillus cereus) and probiotic bacteria (Lactobacillus acidophilus, Lactobacillus rhamnosus, Lactobacillus plantarum and Lactobacillus casei subsp. casei) was evaluated. WPI films incorporated with 2% (v/v) of this EO inhibited the growth of all tested pathogenic bacteria and gram‐negative bacteria were more sensitive than gram‐positive bacteria. Incorporation of the EO at higher than 2% (v/v) showed significant antimicrobial effects (P < 0.05) for S. enteritidis and L. acidophilus. The growth of all probiotic lactic acid‐producing bacteria also inhibited when 2% of the EO was added. Comparison of an image processing‐based method with conventional method for measuring of inhibitory effects of edible films exhibited high correlations (R2 ≥ 0.876) between the two methods. These results revealed that Z. multiflora Boiss. EO is a good antimicrobial additive for some food applications when included into WPI edible films.
Comparison of the effect of microwave freeze drying and microwave vacuum drying upon the process and quality characteristics of potato/banana re‐structured chips
Authors: Jiang Hao , Zhang Min , Mujumdar Arun S. , Lim Rui‐Xin
Published: February 2011

This study investigated the drying characteristics of microwave freeze‐drying (MFD)/microwave vacuum drying (MVD) of banana/potato restructured chips of varying proportion and microwave power. The results showed the MFD drying time had a maximum one‐hour time difference between the samples treated with 2 W g−1 and 3 W g−1 microwave power; and the higher potato content samples have about 30 min predominance than low potato content samples in drying time and the total drying time of MVD samples was less than 60 min. For the rehydration ratio, MFD samples were far superior to the MVD samples. The MFD samples had more than 4.5 rehydration ratio. The data of the colour difference metre showed that 3 W g−1 microwave power would make samples slightly charred. The biggest differences between the MFD and MVD chips lie in their texture and shape; the hardness of MVD samples was 30.86 N, thrice higher than MFD samples.
Effect of insecticidal atmosphere and low dose X‐ray irradiation in combination with cold quarantine storage on bioactive compounds of clementine mandarins cv. ‘Clemenules’
Authors: Contreras‐Oliva Adriana , Pérez‐Gago María B. , Palou Lluís , Rojas‐Argudo Cristina
Published: February 2011

Citrus fruits are a rich source of vitamins and polyphenolic compounds with antioxidant capacity that need to be maintained during postharvest storage. The aim of this study was to determine the effect of two innovative quarantine treatments, such as insecticidal atmospheres (IA) (95% CO2 and balance air) applied at 20 or 25 °C for 20 h and low doses X‐ray irradiation (0, 30, 54 and 164 Gy), in combination with short periods of cold‐quarantine storage on the nutritional quality of ‘Clemenules’ mandarins. Mandarins were stored at 1.5 °C for 6, 9 or 12 days before the application of IA treatments or for 0, 6 or 12 days after the X‐ray radiation. Nutritional quality of mandarins was determined after the corresponding combination of quarantine treatment (IA or X‐ray) with cold quarantine followed by a shelf life period of 7 days at 20 °C to simulate shelf life conditions. Cold quarantine treatment combined with IA or with X‐ray radiation did not affect negatively total antioxidant capacity and total ascorbic acid content of ‘Clemenules’ mandarins. However, flavanone glycosides (FGs) and total phenolics content were slightly modified. Application of the IA at 20 °C induced a greater inhibition of the FGs than application at 25 °C. When X‐ray irradiation was applied without a previous quarantine period the synthesis of the FGs increased as irradiation dose increased.
Effect of food processing on the resistant starch content of cereals and cereal products – a review
Authors: Alsaffar Ayten Aylin
Published: February 2011

Depending on the conditions, processing of cereal grains may cause an increase or a decrease in the resistant starch (RS) content. This review discusses the impact of some of the processing techniques (cooking, tempering and extrusion) on the RS contents of cereals and cereal products. In addition to processing, the review briefly summarises the effects of lipids, dietary fibre and sugars, which may be present within the food matrix, on starch digestibility. The review also provides definitions for the four types of RS (RS type 1, 2, 3 and 4) and brief information about the beneficial effects of RS on human health.
Effect of rapeseed protein–gelatin film containing grapefruit seed extract on ‘Maehyang’ strawberry quality
Authors: Jang Sung‐Ae , Shin Yoon‐Ji , Song Kyung Bin
Published: February 2011

To develop a packaging film for ‘Maehyang’ strawberries, an edible film containing antimicrobial grapefruit seed extract (GSE) was manufactured. Addition of GSE to the rapeseed protein–gelatin (RG) film inhibited the growth of pathogenic bacteria such as Escherichia coli O157:H7 and Listeria monocytogenes. Packaging of ‘Maehyang’ strawberries with the RG film containing 1.0% GSE decreased the populations of total aerobic bacteria and of yeast and moulds in the strawberries by 1.03 and 1.34 log CFU g−1, respectively, after 14 days of storage, compared to that of the control. Sensory evaluation of the GSE‐RG film‐packaged strawberries produced better sensory scores than did the control. These results suggest that RG film containing GSE can be used to package strawberries and to extend shelf life.
Physicochemical characteristics and functional properties of grape (Vitis vinifera L.) seeds protein
Authors: Zhou Ting , Zhang Tuo , Liu Wenying , Zhao Guanghua
Published: February 2011

The amino acid composition, physicochemical and functional properties of grape (Vitis vinifera L.) seeds protein (GSP) were evaluated and compared with those of soybean protein isolate (SPI). Amino acid analyses of GSP revealed high levels of glutamic/glutamine, glycine and aspartic/asparagines. SDS‐PAGE analysis demonstrated that globulin was the major protein component in GSP, whose subunit molecular weights were mainly varied from 25.5 to 40.0 kDa. The isoelectric pH of GSP was found to be at the acidic pH of around 3.8. At all the pHs tested except pH 2.0, no significant changes of GSP secondary structure were observed. GSP exhibited beneficial functional properties such as preferable solubility and emulsifying activity, while the foaming properties and water holding capacity were relatively poor compared to SPI. It could then be employed to soup, sauce, beverage or meat product for improving nutritional and sensory quality of these foods at appropriate pHs.
Increased ethylene biosynthesis elevates incidence of chilling injury in cold‐stored ‘Amber Jewel’ Japanese plum (Prunus salicina Lindl.) during fruit ripening
Authors: Khan Ahmad S. , Ahmed Muhammad J. , Singh Zora
Published: February 2011

Mature ‘Amber Jewel’ Japanese plum fruit were stored at 0 or 5 °C for 3 and 6 weeks to investigate their effects on ethylene (C2H4) biosynthesis during ripening at ambient temperature in the development of chilling injury (CI) and fruit quality. CI (internal breakdown and browning) and fruit softening were higher during ripening, in the fruit stored at 5 °C than 0 °C, irrespective of storage period (SP). C2H4 production and activities of 1‐aminocyclopropane‐1‐carboxylic acid synthase (ACS) and 1‐aminocyclopropane‐1‐carboxylic acid oxidase (ACO) enzymes, and 1‐aminocyclopropane‐1‐carboxylic acid (ACC) content were higher during ripening in fruit stored at 5 °C than 0 °C. The fruit stored at 5 °C also exhibited higher respiration rate and higher soluble solids concentration/titratable acidity ratio. In conclusion, increase in storage temperature and SP elevates the activities of ACS and ACO enzymes and consequently C2H4 production which leads to the development of CI in plum fruit with advancement of ripening.
Effects of cooking methods on the proximate, mineral and fatty acid composition of European eel (Anguilla anguilla)
Authors: Ersoy Beyza
Published: February 2011

The influence of microwave cooking and traditional cooking methods such as baking, grilling and frying on the nutritional composition of eels (Anguilla anguilla) was studied. All methods reduced moisture and increased the protein and fat content. Although the potassium and sodium content of fish cooked by different methods decreased significantly (P = 0.000), the calcium and magnesium content increased. The zinc content of the fish was not affected by cooking. The manganese and iron content significantly increased only in fried fish. The copper content was increased by grilling and microwave cooking. The proportion of saturated fatty acids and monounsaturated fatty acids in cooked fish decreased. Omega‐3 polyunsaturated fatty acids were increased by all cooking methods. The grilling and microwave‐cooking methods were the most suitable considering the n3/n6 ratio and eicosapentaenoic acid levels. The increase in the docosahexaenoic acid level of fried fish enhanced its nutritional value.
Do mycorrhizal symbioses cause rarity in orchids?
Authors: Phillips Ryan D. , Barrett Matthew D. , Dixon Kingsley W. , Hopper Stephen D.
Published: February 2011

1. While rarely tested, the rarity of a species may be linked to the rarity of symbiotic partners. The requirement of many terrestrial plants to form a symbiosis with mycorrhizal fungi may limit the distribution and abundance of plant species. Here, in just the second test of the role of mycorrhiza in host species rarity, we investigate the influence of mycorrhizal specificity, distribution and ecological requirements in the genus Drakaea (Orchidaceae).

2. In situ seed baiting was used to resolve the distribution of mycorrhizal fungi for three common and two co‐occurring rare species of Drakaea. Mycorrhizal fungi were isolated from wild adult orchids and protocorms and the ITS nrDNA regions sequenced. An in vitro study tested the range of Drakaea species of which each fungus can support germination.

3. All Drakaea species studied used a narrow monophyletic clade of Tulasnella endophyte for protocorm, seedling and adult plant stages. In situ seed baiting revealed that germination of Drakaea is largely restricted to the same microhabitat as that of the orchid. However, within this habitat Drakaea exhibit comparable germination to other Western Australian orchid genera. Rare and common Drakaea exhibited no difference in germination rates and both germinated in suitable habitat not currently occupied.

4. Synthesis. In contrast to the previous study of the role of mycorrhiza in plant rarity, there was no evidence that mycorrhizal specificity contributed to rarity in Drakaea. However, the formation of mycorrhiza being mostly restricted to a specific microhabitat may limit the abundance of Drakaea in some landscapes. In Drakaea, the highly specific pollination system of sexual deception may contribute to rarity. A trend towards high specificity in orchid mycorrhizal associations in southern Australia is hypothesized to result from the predominance of old landscapes affording the opportunity for specialization on a single or few mycorrhiza(s) best adapted to the landscape conditions.
Niche overlap reveals the effects of competition, disturbance and contrasting assembly processes in experimental grassland communities
Authors: Mason Norman W.H. , de Bello Francesco , Doležal Jiři , Lepš Jan
Published: February 2011

1. Understanding the processes by which species sort themselves into communities remains a central puzzle for attempts to maintain biodiversity. It remains unclear whether any single assembly process is generally dominant or whether the influence of contrasting processes varies in a predictable way relative to biotic and abiotic gradients. Abundance‐weighted niche overlap between species provides a powerful means of contrasting two major assembly processes – niche complementarity and environmental filtering.

2. We examined mean overlap for four vegetative functional traits, relative to that expected when abundances were randomly allocated to species co‐occurring in experimental plots in a wet meadow. This provided a test of whether any single assembly process prevailed for the meadow as a whole and across all traits. The effects of mowing, fertilization and dominant species removal, and associated gradients of Simpson’s dominance and biomass on the niche overlap of plots, were also examined.

3. Niche overlap was higher than expected at random for three of the four traits studied (height, leaf and stem dry matter content, leaf C:N ratio). However, niche overlap was lower than expected for specific leaf area.

4. Mowing was the treatment with the greatest effect on both niche overlap and biomass, with overlap significantly lower in the absence of mowing for three of the traits, while biomass was lower in mown plots. For three of the traits there was evidence of a significant decrease in overlap with increasing biomass, but not increasing dominance. None of the significant mowing effects on overlap remained when the effect of biomass had been removed.

5. Synthesis: These results suggest that the importance of niche differences between species in structuring grassland communities should increase with increasing biomass and decrease with disturbance in grassland communities. They also emphasize that contrasting community assembly processes may occur for different niche axes, even within a single community.
Interactions among plants and evolution
Authors: Thorpe Andrea S. , Aschehoug Erik T. , Atwater Daniel Z. , Callaway Ragan M.
Published: February 2011

1. Interactions among plants and their consumers, pollinators and dispersers are central to evolutionary theory, but interactions among plants themselves have received much less attention. Thus focusing more attention on the evolutionary role of plant–plant interactions may provide greater insight into the processes that organize communities.

2. Here, we integrate divergent themes in the literature in an effort to provide a synthesis of empirical evidence and ideas about how plant interactions may affect evolution and how evolution may affect plant interactions.

3. First, we discuss the idea of niche partitioning evolving through competitive interactions among plants, the idea of niche construction evolving through facilitative interactions, and the connections between these ideas and more recent research on diversity and ecosystem function and trait‐based community organization.

4. We then review how a history of coexistence within a region might affect competitive outcomes and explore the mechanisms by which plants exert selective forces on each other. Next, we consider recent research on invasions suggesting that plant interactions can reflect regional evolutionary trajectories. Finally, we place these lines of research into the context of extended phenotypes and the geographic mosaic of co‐evolution.

5. Synthesis. Our synthesis of separate lines of inquiry is a step towards understanding the evolutionary importance of interactions among plants, and suggests that the evolutionary consequences of interactions contribute to communities that are more than assemblages of independent populations.
Allocation of foliar phosphorus fractions and leaf traits of tropical tree species in response to decreased soil phosphorus availability on Mount Kinabalu, Borneo
Authors: Hidaka Amane , Kitayama Kanehiro
Published: February 2011

1. Foliar phosphorus (P) concentration is the sum of the concentrations of P fractions in cells, such as inorganic P and various P‐containing biochemical compounds (e.g. nucleic acids, lipids and sugar phosphates). Plants generally reduce foliar P concentration and enhance P‐use efficiency in response to low soil P availability. However, how plants allocate P among foliar P fractions to reduce foliar P concentration remains unclear.

2. We investigated foliar P fractions and leaf traits of 21 tropical tree species along a soil P availability gradient across three tropical montane rain forests on Mount Kinabalu, Borneo. We chemically and sequentially fractionated foliar P into the following four fractions: structural P (i.e. phospholipids), metabolic P (collectively including Pi, ATP and sugar phosphates), nucleic acid P and residual P (phosphoproteins and unidentified residue).

3. With decreasing soil P availability, foliar P concentration decreased and leaf mass per area (LMA) increased. The reduction in foliar P concentration strongly correlated with the reduction in the concentrations of both metabolic P and nucleic acid P. Although increased LMA implies an increased allocation to structural tissues, there was no trade‐off in P allocation between metabolic P and structural P with increasing LMA. This suggests that tropical tree species on P‐poor soils increase the toughness of leaves (i.e. prolonged leaf life span) and also maintain high photosynthetic P‐use efficiency (PPUE) without increasing the cost of P for structural tissues.

4. Phosphorus resorption efficiency increased with decreasing soil P availability. The amount of P resorbed before leaf abscission on P‐poor soils exceeded that of metabolic P. This suggests that tropical tree species achieve the high P resorption efficiency by withdrawing immobile fractions (i.e. nucleic acid P and structural P) in addition to metabolic P.

5. Synthesis. We conclude that tree species on P‐poor soils reduce the demand for foliar P by reducing concentrations of both metabolic P and nucleic acid P, which may potentially limit growth and productivity. However, these tree species can maintain high whole‐plant P‐use efficiency, because such responses in foliar P fractions do not decrease PPUE, leaf life span and P resorption efficiency.
Microsatellite DNA analyses of a highly disjunct New Zealand tree reveal strong differentiation and imply a formerly more continuous distribution
Authors: SHEPHERD LARA D. , PERRIE LEON R.
Published: February 2011

Although New Zealand is a biodiversity hotspot, there has been little genetic investigation of why so many of its threatened and uncommon plants have naturally disjunct distributions. We investigated the small tree Pseudopanax ferox (Araliaceae), which has a widespread but highly disjunct lowland distribution within New Zealand. Genotyping of nuclear microsatellites and a chloroplast locus revealed pronounced genetic differentiation and four principal genetic clusters. Our results indicate that the disjunct distribution is a product of vicariance rather than long‐distance dispersal. This highlights the need to preserve multiple populations when disjunct distributions are the result of vicariance, rather than focusing conservation efforts on a core area, in order to retain as much as possible of a species’ evolutionary legacy and potential. Additionally, based on our genetic findings and the ecology of P. ferox, we hypothesize that it was more continuously distributed during the drier (but not maximally colder) interstadials of glacial periods and/or on the fertile soils available immediately postglacial. We further hypothesize that P. ferox belongs to a suite of species of drought‐prone and/or fertile habitats whose distributions are actually restricted during warmer and wetter interglacial periods, despite being principally of the lowlands. Our genetic data for P. ferox are also the first consistent with the survival during the Last Glacial Maxima of a lowland tree at high latitudes in the south‐eastern South Island.
Genetic signature of population fragmentation varies with mobility in seven bird species of a fragmented Kenyan cloud forest
Authors: CALLENS TOM , GALBUSERA PETER , MATTHYSEN ERIK , DURAND ERIC Y. , GITHIRU MWANGI , HUYGHE JEROEN R. , LENS LUC
Published: February 2011

Habitat fragmentation can restrict geneflow, reduce neighbourhood effective population size, and increase genetic drift and inbreeding in small, isolated habitat remnants. The extent to which habitat fragmentation leads to population fragmentation, however, differs among landscapes and taxa. Commonly, researchers use information on the current status of a species to predict population effects of habitat fragmentation. Such methods, however, do not convey information on species‐specific responses to fragmentation. Here, we compare levels of past population differentiation, estimated from microsatellite genotypes, with contemporary dispersal rates, estimated from multi‐strata capture–recapture models, to infer changes in mobility over time in seven sympatric, forest‐dependent bird species of a Kenyan cloud forest archipelago. Overall, populations of sedentary species were more strongly differentiated and clustered compared to those of vagile ones, while geographical patterning suggested an important role of landscape structure in shaping genetic variation. However, five of seven species with broadly similar levels of genetic differentiation nevertheless differed substantially in their current dispersal rates. We conclude that post‐fragmentation levels of vagility, without reference to past population connectivity, may not be the best predictor of how forest fragmentation affects the life history of forest‐dependent species. As effective conservation strategies often hinge on accurate prediction of shifts in ecological and genetic relationships among populations, conservation practices based solely upon current population abundances or movements may, in the long term, prove to be inadequate.
aprABC: a Mycobacterium tuberculosis complex‐specific locus that modulates pH‐driven adaptation to the macrophage phagosome
Authors: Abramovitch Robert B. , Rohde Kyle H. , Hsu Fong‐Fu , Russell David G.
Published: February 2011

Following phagocytosis by macrophages, Mycobacterium tuberculosis (Mtb) senses the intracellular environment and remodels its gene expression for growth in the phagosome. We have identified an acid and phagosome regulated (aprABC) locus that is unique to the Mtb complex and whose gene expression is induced during growth in acidic environments in vitro and in macrophages. Using the aprA promoter, we generated a strain that exhibits high levels of inducible fluorescence in response to growth in acidic medium in vitro and in macrophages. aprABC expression is dependent on the two‐component regulator phoPR, linking phoPR signalling to pH sensing. Deletion of the aprABC locus causes defects in gene expression that impact aggregation, intracellular growth, and the relative levels of storage and cell wall lipids. We propose a model where phoPR senses the acidic pH of the phagosome and induces aprABC expression to fine‐tune processes unique for intracellular adaptation of Mtb complex bacteria.
Mechanism of adhesion maintenance by methionine sulphoxide reductase in Streptococcus gordonii
Authors: Lei Y. , Zhang Y. , Guenther B. D. , Kreth J. , Herzberg M. C.
Published: February 2011

Methionine sulphoxide reductase maintains adhesin function during oxidative stress. Using Streptococcus gordonii as a model, we now show the mechanistic basis of adhesin maintenance provided by MsrA. In biofilms, S. gordonii selectively expresses the msrA gene. When the wild‐type strain was grown with exogenous hydrogen peroxide (H2O2), msrA‐specific mRNA expression significantly increased, while acid production was unaffected. In the presence of H2O2, a msrA‐deletion mutant (ΔMsrA) showed a 6 h delay in lag phase growth, a 30% lower yield of H2O2, significantly greater inhibition by H2O2 on agar plates (reversed by complementation), 30% less adhesion to saliva‐coated hydroxyapatite, 87% less biofilm formation and an altered electrophoretic pattern of SspAB protein adhesins. Using mass spectrometry, methionine residues in the Met‐rich central region of SspB were shown to be oxidized by H2O2 and reduced by MsrA. In intact wild‐type cells, MsrA colocalized with a cell wall‐staining dye, and MsrA was detected in both cell wall and cytosolic fractions. To maintain normal adhesion and biofilm function of S. gordonii in response to exogenous oxidants therefore msrA is upregulated, methionine oxidation of adhesins and perhaps other proteins is reversed, and adhesion and biofilm formation is maintained.
Fission yeast Ubr1 ubiquitin ligase influences the oxidative stress response via degradation of active Pap1 bZIP transcription factor in the nucleus
Authors: Kitamura Kenji , Taki Masumi , Tanaka Nobukazu , Yamashita Ichiro
Published: February 2011

Cells adapt to oxidative stress by transcriptional activation of genes encoding antioxidants and proteins of other protective roles. A bZIP transcription factor, Pap1, plays a critical role in this process and overexpression of Pap1 confers resistance to various oxidants and drugs in fission yeast. Pap1 temporarily enters the nucleus upon oxidative stress but returns to the cytoplasm once cells adapt to the stress, suggesting that cellular localization regulates Pap1 function. We report here an additional regulatory mechanism that Ubr1 ubiquitin ligase‐dependent degradation lowered the Pap1 protein levels. ubr1 cells were causally resistant to hydrogen peroxide because of the increment of Pap1 levels. Pap1 was preferentially degraded in the nucleus where Ubr1 was consistently enriched. Proteolysis was critical to downregulate Pap1 especially when its activation persisted, as constitutively nuclear Pap1 severely inhibited growth in ubr1 mutants. Inactive mutations in the bZIP DNA binding domain stabilized Pap1 but rescued the lethality caused by constitutively active Pap1 in ubr1 mutants. These findings indicate that either nuclear export or Ubr1‐mediated proteolysis must be operative to prevent uncontrolled Pap1 function. Coincidental dysfunction in both inhibitory pathways causes lethality because of prolonged activation of Pap1. Ubr1 is a critical regulator for the homeostasis of oxidative stress response.
Escherichia coli YaeJ protein mediates a novel ribosome‐rescue pathway distinct from SsrA‐ and ArfA‐mediated pathways
Authors: Chadani Yuhei , Ono Katsuhiko , Kutsukake Kazuhiro , Abo Tatsuhiko
Published: February 2011

Accumulation of stalled ribosomes at the 3′ end of mRNA without a stop codon (non‐stop mRNA) is supposed to be toxic to bacterial cells. Escherichia coli has at least two distinct systems to rescue such stalled ribosomes: SsrA‐dependent trans‐translation and ArfA‐dependent ribosome rescue. Combination of the ssrA and arfA mutations is synthetically lethal, suggesting the significance of ribosome rescue. In this study, we identified the E. coli yaeJ gene, encoding a peptide‐release factor homologue with GGQ motif, as a multicopy suppressor of the lethal phenotype of ssrA arfA double mutant. The YaeJ protein was shown to bind to ribosomes. Both in vivo and in vitro, YaeJ showed the ribosome‐rescue activity and promoted the hydrolysis of peptidyl‐tRNA residing in the stalled ribosome. Missense mutation in the GGQ motif or deletion of the C‐terminal unstructured tail abolished both the suppressor activity for ssrA arfA synthetic lethality and the ribosome‐rescue activity, suggesting the importance of these structural features. On the basis of these observations, we propose that YaeJ acts as a stop codon‐independent peptidyl‐tRNA hydrolysing factor through binding to ribosomes stalled at the 3′ end of non‐stop mRNAs. It was also suggested that ArfA and YaeJ rescue the stalled ribosomes by distinct mechanisms.
Short pulse gastric electrical stimulation for cisplatin‐induced emesis in dogs
Authors: Song J. , Zhong D.‐X. , Qian W. , Hou X.‐H. , Chen J. D. Z.
Published: February 2011

Background In a previous study, we investigated the ameliorating effect of gastric electrical stimulation (GES) with a single set of parameters on emesis and behaviors suggestive of nausea induced by cisplatin in dogs. The aim of this study was to investigate the effects of GES with different parameters on cisplatin‐induced emesis in dogs.

Methods Seven dogs implanted with gastric serosal electrodes were studied in six randomized sessions: one control session with cisplatin (2 mg kg−1) and five sessions with cisplatin plus GES of different parameters: GES‐A: 14 Hz, 5 mA, 0.3 ms, 0.1 s on and 5 s off; GES‐B: increased frequency and on‐time; GES‐C: increased frequency; GES‐D: increased frequency and pulse width; and GES‐E: increased frequency and amplitude. Gastric slow waves and emetic responses were recorded in each session.

Key Results (i) Cisplatin induced emetic responses and gastric dysrhythmia. The peak time of the emetic response was during the fourth hour after cisplatin. (ii) GES with appropriate parameters reduced cisplatin‐induced emesis. The number of vomiting times during the 6 h after cisplatin was 7.0 ± 1.4 in the control, 4.7 ± 1.2 with GES‐A (P = 0.179), 4.2 ± 1.2 with GES‐B (P = 0.109), 7.0 ± 0.8 with GES‐C (P = 0.928), 2.1 ± 0.3 with GES‐D (P = 0.005) and 4.7 ± 1.5 with GES‐E (P = 0.129). However, none of the GES parameters could improve gastric dysrhythmia.

Conclusions & Inferences Gastric electrical stimulation with appropriate parameters reduces cisplatin‐induced emetic responses and behaviors suggestive of nausea in dogs. Among the tested parameters, GES with increased pulse width seems to produce better relief of cisplatin‐induced emesis.
Development and application of new molecular markers for analysis of genetic diversity in Verticillium dahliae populations
Authors: Berbegal M. , Garzón C. D. , Ortega A. , Armengol J. , Jiménez‐Díaz R. M. , Jiménez‐Gasco M. M.
Published: February 2011

The aim of this study was to develop new polymorphic markers for analysis of genetic diversity in the fungal soilborne plant pathogen Verticillium dahliae. Twelve polymorphic markers (five microsatellites and seven polymorphic sequences) were developed from a genomic library enriched for microsatellites. Screening of polymorphic loci was done using a collection of 25 V. dahliae isolates of diverse geographic origins, host sources and vegetative compatibility groups (VCGs). Three methods were used to score alleles: polyacrylamide gel electrophoresis (PAGE), sequencing of PCR‐amplified loci, and capillary electrophoresis. The new markers were used to assess genetic differentiation between isolates associated with different host plants. Two collections of isolates were analysed, obtained from artichoke (30 isolates) and potato (20 isolates) from crops grown in rotation located in the same area in eastern‐central Spain. The resolution of genetic differentiation between these two collections using the new markers was compared to that provided by other often‐used markers (SCARs and VCGs). Sequence analysis of the alleles proved to be the most unambiguous technique for scoring microsatellite data. The relatively high genetic differentiation observed between isolates from different crops (genetic differentiation coefficient, GST = 0·24) and their high genotypic diversity suggest a divergence between V. dahliae from artichoke and potato. It is hypothesized that evolution of V. dahliae from the local resident population in association with the two host crops has occurred. The new markers are useful for resolving population structure within V. dahliae and may contribute to a better understanding of the population biology of this fungus.
Colorectal Cancer–Derived Foxp3+IL‐17+ T Cells Suppress Tumour‐Specific CD8+ T Cells
Authors: Ma C. , Dong X.
Published: February 2011

The pathogenesis of cancer is remained to be further understood. This study aims to investigate the role of tumour‐derived Foxhead box P3 (Foxp3)+interleukin (IL)‐17+ T cells on suppressing tumour‐specific CD8+ T cells. Colorectal cancer (CRC) tissue was collected from surgically removed cancer tissue of 22 patients with CRC. Foxp3+IL‐17+ T cells in cancer tissue were examined by flow cytometry. A set of cell markers and cytokines expressed by Foxp3+IL‐17+ T cells were determined by immune staining. By coculture with isolated peripheral CD8+ T cells, the immune regulatory capacity of Foxp3+IL‐17+ T cells was examined. The results showed that a number of Foxp3+IL‐17+ T cells were found in CRC tissue (22.8 ± 2.6 cells/mm2 tissue) that was significantly more than in non‐cancer colonic mucosa (5.6 ± 1.04 cells/mm2 tissue). The Foxp3+IL‐17+ cells also CD4+, CCR6+, transforming growth factor (TGF)‐beta+ and IL‐6+. The CD8+ T cells proliferated markedly after exposure to tumour protein in culture that was suppressed in the presence of CRC–derived Foxp3+IL‐17+ T cells; the suppression was attenuated by pretreatment with anti‐IL‐17 antibody. We conclude that CRC–derived Foxp3+IL‐17+ T cells have the ability to suppress tumour‐specific CD8+ T cells. This subset of T cells may be a novel therapeutic target in the treatment of CRC.
Interleukin‐6 −174 G/C Promoter Polymorphism is Associated with Persistence of Chlamydia pneumoniae Antibodies in Young Men
Authors: Rantala A. , Lajunen T. , Juvonen R. , Paldanius M. , Silvennoinen‐Kassinen S. , Peitso A. , Vainio O. , Leinonen M. , Saikku P.
Published: February 2011

A promoter polymorphism −174 G/C in the inflammatory cytokine interleukin‐6 (IL‐6) gene has been associated with differences in serum IL‐6 levels and a risk for inflammatory conditions, such as cardiovascular diseases. We investigated whether this polymorphism is associated with Chlamydia pneumoniae, a common causative agent of respiratory infection with tendency for persistent infections, in 867 Finnish military recruits. IgG seropositivity in arrival and departure serum samples during 6–12 months of military service was considered as persistence of antibodies and a possible prolonged or chronic infection. The −174C allele was significantly associated with IgG seropositivity (P = 0.0002) and the persistence of IgG antibodies (P = 0.0002) as well as with slightly elevated C‐reactive protein (CRP) levels (P = 0.003). In addition, the association was stronger when persistent C. pneumoniae antibodies were present together with elevated CRP than when either of them was positive alone (OR; 95% CI: 3.45; 2.00–5.98 and 1.41; 1.00–1.99, respectively). Our data suggest that IL‐6 −174 G/C polymorphism is associated with persistence of C. pneumoniae antibodies and may be linked to the chronic or prolonged infection with systemic low‐grade inflammation.
Defective Central Tolerance in Aire‐Deficient Mice is not Sufficient to Induce Symptomatic Autoimmunity During Lymphopenia‐Induced T cell Proliferation
Authors: Kekäläinen E. , Lehto M.‐K. , Smeds E. , Miettinen A. , Meri S. , Jarva H. , Petteri Arstila T.
Published: February 2011

Transcriptional regulator autoimmune regulator (AIRE) controls thymic negative selection but it is also expressed in secondary lymphoid organs. The relative contribution of AIRE’s central and peripheral function to the maintenance of tolerance is unclear. We transferred mature lymphocytes from Aire−/− or wild‐type donors to Aire+/+ lymphopenic recipients, which allowed us to gauge the autoreactivity inherent in the cells originating in an Aire−/− thymus. In the ensuing lymphopenia‐induced proliferation (LIP), the recipients of cells from Aire−/− showed definite T cell hyperproliferation and developed autoantibodies at a higher frequency than the recipients of wild‐type cells. However, neither of the recipient groups developed clinical symptoms, and pathological tissue infiltrates were also absent. The recipients of Aire−/− cells showed hyperproliferation and increased accumulation of regulatory T cells (Tregs), especially in tissues susceptible to inflammation triggered by LIP. These data are consistent with the view that T cells developing in the absence of Aire are autoreactive. However, overt autoimmunity was prevented, most likely by the suppressive function of Treg cells in the Aire‐sufficient recipients. Our results support the importance of the peripheral AIRE expression in the maintenance of immunological tolerance.
The Long‐Term Survival of Plasma Cells
Authors: Chu V. T. , Beller A. , Nguyen T. T. N. , Steinhauser G. , Berek C.
Published: February 2011

Plasma cells sustain antibody production and hence are an essential part of immune protection. In the mucosa‐associated lymphoid tissues plasma cells secrete IgA antibodies which protect the organism from invasion by pathogenic bacteria while in the bone marrow they produce the antibodies which guarantee long‐term humoral immune protection. The various lymphoid organs provide specific microenvironments which support plasma cell survival. In particular, in the bone marrow, highly specialized survival niches are established by the underlying stromal reticular cells which permit plasma cells to survive for years. In some situations, however, the antibody may be detrimental to the organism. In those auto immune diseases, where plasma cells play a pathological role by producing the auto antibodies, new strategies are needed to interfere with the lifespan of plasma cells and thus to diminish their numbers. The recent finding that eosinophils are essential for the long‐term survival of plasma cells in the bone marrow provides a new therapeutic target to modulate the plasma cell survival niche.
Carbonate facies patterns in surface sediments of upwelling and non‐upwelling shelf environments (Panama, East Pacific)
Authors: REIJMER JOHN J. G. , BAUCH THORSTEN , SCHÄFER PRISKA
Published: February 2011

In this study two carbonate environments are compared and contrasted; the Gulf of Panama and the Gulf of Chiriquí on the Pacific side of Panama. These two embayments are in close geographic proximity at latitudes between 7° N and 9° N. The Gulf of Panama and the Gulf of Chiriquí are characterized by contrasting oceanographic conditions with year‐round stable non‐upwelling conditions in the Gulf of Chiriquí and strong seasonal upwelling in the dry season (December to April) in the Gulf of Panama. The upwelling variations only have a limited influence on the amount of carbonate produced; however, they do have a major impact on the occurrence of specific carbonate producing biota. In addition, carbonate production and distribution is influenced in both gulfs by the occurrence of islands and by terrigenous input. Terrigenous material is found mainly in the smaller grain sizes (<63 to 250 μm) that can be transported easily by currents and waves. Carbonate dominant sediments (carbonate sands and mixed carbonate–siliciclastic sands) mainly occur around the islands and are dominated by larger grain‐sizes (>500 μm). The Gulf of Panama and the Gulf of Chiriquí both show warm and temperate carbonate‐producing biota, with carbonate producers from tropical (corals) to mixed tropical to cool‐water (coralline red algae) and cold‐water (balanids) environments. The Gulf of Chiriquí is characterized by oligotrophic to mesotrophic conditions resulting in a photozoan (coral) and/or rhodolith‐facies in shallow‐water areas surrounding the islands and a mollusc‐dominated facies in deeper waters towards the shelf edge. Seasonal upwelling causes temporary eutrophic conditions in the Gulf of Panama, which results in a heterozoan facies around the islands dominated by balanids, echinoderms and molluscs. Thus a ‘cool‐water’ carbonate fauna and eutrophic conditions can exist in the tropics within an area prone to seasonal upwelling. The distinct facies differences found on the Pacific shelf of Panama stress the importance of variations in oceanographic conditions, upwelling versus non‐upwelling, in determining carbonate production and associated facies patterns in the tropics.
Experimental evidence for rapid biotic and abiotic reduction of Fe (III) at low temperatures in salt marsh sediments: a possible mechanism for formation of modern sedimentary siderite concretions
Authors: MORTIMER ROBERT J. G. , GALSWORTHY AMANDA M. J. , BOTTRELL SIMON H. , WILMOT LUCY E. , NEWTON ROBERT J.
Published: February 2011

Fe (III) reduction is a key component of the global iron cycle, and an important control on carbon mineralization. However, little is known about the relative roles and rates of microbial (biotic) iron reduction, which utilizes organic matter, versus abiotic iron reduction, which occurs without carbon mineralization. This paper reports on the capacity for salt marsh sediments, which typically are rich in iron, to support abiotic reduction of mineral Fe (III) driven by oxidation of sulphide. Sediment was reacted with amorphous FeS under strictly anaerobic conditions at a range of temperatures in biotic and abiotic microcosm experiments. Fe (III) reduction driven by sulphide oxidation occurs abiotically at all temperatures, leading to Fe (II) and elemental sulphur production in all abiotic experiments. In biotic experiments elemental sulphur is also the oxidized sulphur product but higher bicarbonate production leads to FeCO3 precipitation. Abiotic reduction of Fe (III) occurs at rates that are significant compared with microbial Fe (III) reduction in salt marsh sediments. The solid phases produced by coupled abiotic and biotic reactions, namely elemental sulphur and FeCO3, are comparable to those seen in nature at Warham, Norfolk, UK. Furthermore, the rates of these processes measured in the microcosm experiments are sufficient to generate siderite concretions on the rapid time scales observed in the field. This work highlights the importance of abiotic Fe (III) reduction alongside heterotrophic reduction, which has implications for iron cycling and carbon mineralization in modern and ancient sediments.
Exhumation controlled by transcurrent tectonics: the Argentera–Mercantour massif (SW Alps)
Authors: Sanchez Guillaume , Rolland Yann , Jolivet Marc , Brichau Stéphanie , Corsini Michel , Carter Andrew
Published: February 2011

Terra Nova, 23, 116–126, 2011

New apatite fission track (AFT) and (U‐Th)/He ages from the Argentera–Mercantour External Crystalline Massif of the SW Alps document an exhumation history along transcurrent dextral faults. Significant AFT age differences across the strikes of the main faults have been obtained from the NE (12.9 Ma) to the SW (5.2 Ma) and are linked to vertical uplifts along these right‐lateral transpressional structures. Such segmentation is not observed in AHe ages. AHe ages have preserved younger ages (4–5 Ma) on the eastern hangingwall side of the High Durance extensional system. Such an exhumation history is interpreted to result from a transition of transpressional to transtensional regimes at 8–5 Ma during continuing Adria–Europe convergence. These data show that recent extensional deformation in the SW Alps can be related to the development of a transtensional domain in the Ubaye–Embrunais depression linked to ongoing strike‐slip deformation along the Argentera–Mercantour.