bluuebunny/crossref_metadata_2025 huggingface dataset:
Bap31 Is an Itinerant Protein That Moves between the Peripheral Endoplasmic Reticulum (ER) and a Juxtanuclear Compartment Related to ER-associated Degradation
Authors: Wakana Yuichi , Takai Sawako , Nakajima Ken-ichi , Tani Katsuko , Yamamoto Akitsugu , Watson Peter , Stephens David J. , Hauri Hans-Peter , Tagaya Mitsuo
Published: February 2008

Certain endoplasmic reticulum (ER)-associated degradation (ERAD) substrates with transmembrane domains are segregated from other ER proteins and sorted into a juxtanuclear subcompartment, known as the ER quality control compartment. Bap31 is an ER protein with three transmembrane domains, and it is assumed to be a cargo receptor for ER export of some transmembrane proteins, especially those prone to ERAD. Here, we show that Bap31 is a component of the ER quality control compartment and that it moves between the peripheral ER and a juxtanuclear ER or ER-related compartment distinct from the conventional ER–Golgi intermediate compartment. The third and second transmembrane domains of Bap31 are principally responsible for the movement to and recycling from the juxtanuclear region, respectively. This cycling was blocked by depolymerization of microtubules and disruption of dynein–dynactin function. Overexpression of Sar1p and Arf1 mutants affected Bap31 cycling, suggesting that this cycling pathway is related to the conventional vesicular transport pathways.
The Rim101 Pathway Is Involved in Rsb1 Expression Induced by Altered Lipid Asymmetry
Authors: Ikeda Mika , Kihara Akio , Denpoh Aki , Igarashi Yasuyuki
Published: February 2008

Biological membranes consist of lipid bilayers. The lipid compositions between the two leaflets of the plasma membrane differ, generating lipid asymmetry. Maintenance of proper lipid asymmetry is physiologically quite important, and its collapse induces several cellular responses including apoptosis and platelet coagulation. Thus, a change in lipid asymmetry must be restored to maintain “lipid asymmetry homeostasis.” However, to date no lipid asymmetry-sensing proteins or any related downstream signaling pathways have been identified. We recently demonstrated that expression of the putative yeast sphingoid long-chain base transporter/translocase Rsb1 is induced when glycerophospholipid asymmetry is altered. Using mutant screening, we determined that the pH-responsive Rim101 pathway, the protein kinase Mck1, and the transcription factor Mot3 all act in lipid asymmetry signaling, and that the Rim101 pathway was activated in response to a change in lipid asymmetry. The activated transcription factor Rim101 induces Rsb1 expression via repression of another transcription repressor, Nrg1. Changes in lipid asymmetry are accompanied by cell surface exposure of negatively charged phospholipids; we speculate that the Rim101 pathway recognizes the surface charges.
FBXO25-associated Nuclear Domains: A Novel Subnuclear Structure
Authors: Manfiolli Adriana O. , Maragno Ana Leticia G.C. , Baqui Munira M.A. , Yokoo Sami , Teixeira Felipe R. , Oliveira Eduardo B. , Gomes Marcelo D.
Published: February 2008

Skp1, Cul1, Rbx1, and the FBXO25 protein form a functional ubiquitin ligase complex. Here, we investigate the cellular distribution of FBXO25 and its colocalization with some nuclear proteins by using immunochemical and biochemical approaches. FBXO25 was monitored with affinity-purified antibodies raised against the recombinant fragment spanning residues 2-62 of the FBXO25 sequence. FBXO25 protein was expressed in all mouse tissues tested except striated muscle, as indicated by immunoblot analysis. Confocal analysis revealed that the endogenous FBXO25 was partially concentrated in a novel dot-like nuclear domain that is distinct from clastosomes and other well-characterized structures. These nuclear compartments contain a high concentration of ubiquitin conjugates and at least two other components of the ubiquitin-proteasome system: 20S proteasome and Skp1. We propose to name these compartments FBXO25-associated nuclear domains. Interestingly, inhibition of transcription by actinomycin D or heat-shock treatment drastically affected the nuclear organization of FBXO25-containing structures, indicating that they are dynamic compartments influenced by the transcriptional activity of the cell. Also, we present evidences that an FBXO25-dependent ubiquitin ligase activity prevents aggregation of recombinant polyglutamine-containing huntingtin protein in the nucleus of human embryonic kidney 293 cells, suggesting that this protein can be a target for the nuclear FBXO25 mediated ubiquitination.
Arp2 Links Autophagic Machinery with the Actin Cytoskeleton
Authors: Monastyrska Iryna , He Congcong , Geng Jiefei , Hoppe Adam D. , Li Zhijian , Klionsky Daniel J.
Published: February 2008

Macroautophagy involves lysosomal/vacuolar elimination of long-lived proteins and entire organelles from the cytosol. The process begins with formation of a double-membrane vesicle that sequesters bulk cytoplasm, or a specific cargo destined for lysosomal/vacuolar delivery. The completed vesicle fuses with the lysosome/vacuole limiting membrane, releasing its content into the organelle lumen for subsequent degradation and recycling of the resulting macromolecules. A majority of the autophagy-related (Atg) proteins are required at the step of vesicle formation. The integral membrane protein Atg9 cycles between certain intracellular compartments and the vesicle nucleation site, presumably to supply membranes necessary for macroautophagic vesicle formation. In this study we have tracked the movement of Atg9 over time in living cells by using real-time fluorescence microscopy. Our results reveal that an actin-related protein, Arp2, briefly colocalizes with Atg9 and directly regulates the dynamics of Atg9 movement. We propose that proteins of the Arp2/3 complex regulate Atg9 transport for specific types of autophagy.
Tight Junction Proteins Claudin-2 and -12 Are Critical for Vitamin D-dependent Ca2+ Absorption between Enterocytes
Authors: Fujita Hiroki , Sugimoto Kotaro , Inatomi Shuichiro , Maeda Toshihiro , Osanai Makoto , Uchiyama Yasushi , Yamamoto Yoko , Wada Takuro , Kojima Takashi , Yokozaki Hiroshi , Yamashita Toshihiko , Kato Shigeaki , Sawada Norimasa , Chiba Hideki
Published: February 2008

Ca2+ is absorbed across intestinal epithelial monolayers via transcellular and paracellular pathways, and an active form of vitamin D3, 1α,25-dihydroxyvitamin D3 [1α,25(OH)2D3], is known to promote intestinal Ca2+ absorption. However, the molecules driving the paracellular Ca2+ absorption and its vitamin D dependency remain obscure. Because the tight junction proteins claudins are suggested to form paracellular channels for selective ions between neighboring cells, we hypothesized that specific intestinal claudins might facilitate paracellular Ca2+ transport and that expression of these claudins could be induced by 1α,25(OH)2D3. Herein, we show, by using RNA interference and overexpression strategies, that claudin-2 and claudin-12 contribute to Ca2+ absorption in intestinal epithelial cells. We also provide evidence showing that expression of claudins-2 and -12 is up-regulated in enterocytes in vitro and in vivo by 1α,25(OH)2D3 through the vitamin D receptor. These findings strongly suggest that claudin-2- and/or claudin-12-based tight junctions form paracellular Ca2+ channels in intestinal epithelia, and they highlight a novel mechanism behind vitamin D-dependent calcium homeostasis.
The Mood Stabilizer Valproate Inhibits both Inositol- and Diacylglycerol-signaling Pathways inCaenorhabditis elegans
Authors: Tokuoka Suzumi M. , Saiardi Adolfo , Nurrish Stephen J.
Published: February 2008

The antiepileptic valproate (VPA) is widely used in the treatment of bipolar disorder, although the mechanism of its action in the disorder is unclear. We show here that VPA inhibits both inositol phosphate and diacylglycerol (DAG) signaling in Caenorhabditis elegans. VPA disrupts two behaviors regulated by the inositol-1,4,5-trisphosphate (IP3): defecation and ovulation. VPA also inhibits two activities regulated by DAG signaling: acetylcholine release and egg laying. The effects of VPA on DAG signaling are relieved by phorbol ester, a DAG analogue, suggesting that VPA acts to inhibit DAG production. VPA reduces levels of DAG and inositol-1-phosphate, but phosphatidylinositol-4,5-bisphosphate (PIP2) is slightly increased, suggesting that phospholipase C-mediated hydrolysis of PIP2to form DAG and IP3is defective in the presence of VPA.
Organization of the Pre-autophagosomal Structure Responsible for Autophagosome Formation
Authors: Kawamata Tomoko , Kamada Yoshiaki , Kabeya Yukiko , Sekito Takayuki , Ohsumi Yoshinori
Published: February 2008

Autophagy induced by nutrient depletion is involved in survival during starvation conditions. In addition to starvation-induced autophagy, the yeast Saccharomyces cerevisiae also has a constitutive autophagy-like system, the Cvt pathway. Among 31 autophagy-related (Atg) proteins, the function of Atg17, Atg29, and Atg31 is required specifically for autophagy. In this study, we investigated the role of autophagy-specific (i.e., non-Cvt) proteins under autophagy-inducing conditions. For this purpose, we used atg11Δ cells in which the Cvt pathway is abrogated. The autophagy-unique proteins are required for the localization of Atg proteins to the pre-autophagosomal structure (PAS), the putative site for autophagosome formation, under starvation condition. It is likely that these Atg proteins function as a ternary complex, because Atg29 and Atg31 bind to Atg17. The Atg1 kinase complex (Atg1–Atg13) is also essential for recruitment of Atg proteins to the PAS. The assembly of Atg proteins to the PAS is observed only under autophagy-inducing conditions, indicating that this structure is specifically involved in autophagosome formation. Our results suggest that Atg1 complex and the autophagy-unique Atg proteins cooperatively organize the PAS in response to starvation signals.
Protein Networks Supporting AP-3 Function in Targeting Lysosomal Membrane Proteins
Authors: Baust Thorsten , Anitei Mihaela , Czupalla Cornelia , Parshyna Iryna , Bourel Line , Thiele Christoph , Krause Eberhard , Hoflack Bernard
Published: February 2008

The AP-3 adaptor complex targets selected transmembrane proteins to lysosomes and lysosome-related organelles. We reconstituted its preferred interaction with liposomes containing the ADP ribosylation factor (ARF)-1 guanosine triphosphatase (GTPase), specific cargo tails, and phosphatidylinositol-3 phosphate, and then we performed a proteomic screen to identify new proteins supporting its sorting function. We identified ≈30 proteins belonging to three networks regulating either AP-3 coat assembly or septin polymerization or Rab7-dependent lysosomal transport. RNA interference shows that, among these proteins, the ARF-1 exchange factor brefeldin A-inhibited exchange factor 1, the ARF-1 GTPase-activating protein 1, the Cdc42-interacting Cdc42 effector protein 4, an effector of septin-polymerizing GTPases, and the phosphatidylinositol-3 kinase IIIC3 are key components regulating the targeting of lysosomal membrane proteins to lysosomes in vivo. This analysis reveals that these proteins, together with AP-3, play an essential role in protein sorting at early endosomes, thereby regulating the integrity of these organelles.
Black Cohosh Hepatic Safety: Follow-Up of 107 Patients Consuming a SpecialCimicifuga racemosa rhizomeHerbal Extract and Review of Literature
Authors: Firenzuoli Fabio , Gori Luigi , di Sarsina Paolo Roberti
Published: February 2008

European Medicines Agency (EMEA) and the Committee on Herbal Medicinal Products (HMPC) on July 2006 have released an alert to get European sanitary authorities aware of 42 cases of suspected hepatotoxic reactions in patients consumingCimicifuga racemosa rhizome. In the public statement EMEA itself considered reliable as hepatotoxic reactions only four cases, on the base of RUCAM score: two were considered possible and two probable. Lacking in almost all of them a precise description of cases, especially a botanical-chemical analysis of the suspected substance, we think there is no real proof of supposedC. racemosa rhizomehepatotoxicity. In our department we administer from about 10 yearsC. racemosaas special herbal dry extract as single substance or mixed with other medicinal plants at the dose of 500–1000 mg daily, for treatment of menopause related disorders without any reported adverse effect. After EMEA's official signal we have contacted all our patients using aC. racemosa rhizomeherbal extract continuously from more than 12 months to verify possible hepatotoxic effects. We followed-up 107 women, and asked them by telephone (33/107) and/or after anamnesis and clinical examination (74/107) to undergo a blood sample examination. In all the patients there was no sign of hepatic disease, or worsening of already altered but stable parameters. We think on the base of these data and current literatureC. racemosa rhizomeextract should not be considered a potential hepatotoxic substance.
A two-stage biomass dynamic model for Bay of Biscay anchovy: a Bayesian approach
Authors: Ibaibarriaga Leire , Fernández Carmen , Uriarte Andrés , Roel Beatriz A.
Published: February 2008

Ibaibarriaga, L., Fernández, C., Uriarte, A., and Roel, B. A. 2008. A two-stage biomass dynamic model for Bay of Biscay anchovy: a Bayesian approach. – ICES Journal of Marine Science, 65: 191–205. A two-stage biomass-based state-space model with stochastic recruitment processes and deterministic dynamics was developed for the Bay of Biscay anchovy population. It is fitted in a Bayesian context with posterior computations carried out using Markov chain Monte Carlo techniques. The model is tested first on a simulated dataset and the effects of different modelling assumptions and of missing values evaluated. Then, it is applied to a real historical series of commercial catch and survey data from 1987 to 2006. Results are compared with those obtained by the standard assessment model for this stock, integrated catch-at-age analysis (ICA). From the posterior distribution of biomass in the latest year (2006), the distribution of unexploited biomass in 2007 can be derived assuming the distribution of recruitment in 2007 to be a mixture of the posterior distributions of past series recruitment. Hence, the effect of different catch options on future biomass levels can be quantified in probabilistic terms. Finally, directions for possible further improvements are indicated.
Using acoustic backscatter from a sidescan sonar to explain fish and invertebrate distributions: a case study in Bristol Bay, Alaska
Authors: Yeung Cynthia , McConnaughey Robert A.
Published: February 2008

Yeung, C., and McConnaughey, R. A. 2008. Using acoustic backscatter from a sidescan sonar to explain fish and invertebrate distributions: a case study in Bristol Bay, Alaska. – ICES Journal of Marine Science, 65: 242–254. Environmental variables that are ecologically relevant and easily measured over large areas are useful for modelling species distributions and habitats. Continuous acoustic, sonar-backscatter data convey information about physical properties of the seabed, and hence could be a valuable addition to that suite of variables. We tested the potential utility of acoustic backscatter for improving habitat models of marine species using data from a pilot sidescan-sonar survey. Raw digital-backscatter data were processed with QTC SIDEVIEW and CLAMS software. Resultant acoustic variables—Q-values (Q1, Q2, and Q3), representing the first three principal components of the data derived from image analysis of backscatter echoes, and a complexity metric (compx) measuring the variance of Q-values in a geographic area—were used in multiple linear regression to model individual species abundance from bottom-trawl survey data. Habitat models for flathead sole (Hippoglossoides elassodon), Pacific cod (Gadus macrocephalus), walleye pollock (Theragra chalcogramma), red king crab (Paralithodes camtschaticus), basket star (Gorgonocephalus eucnemis), and sponges (Porifera) included acoustic variables as significant predictors. For these six taxa, full models explained 67–86% of variability in abundance, with 9–54% of that total contributed by the acoustic predictors, suggesting that acoustic data could advance habitat research for some bottom-associated marine species.
DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins
Authors: Song Young Hun , Yoo Cheol Min , Hong An Pio , Kim Seong Hee , Jeong Hee Jeong , Shin Su Young , Kim Hye Jin , Yun Dae-Jin , Lim Chae Oh , Bahk Jeong Dong , Lee Sang Yeol , Nagao Ron T. , Key Joe L. , Hong Jong Chan
Published: February 2008

LONG HYPOCOTYL5 (HY5) is a bZIP (basic leucine zipper) transcription factor that activates photomorphogenesis and root development in Arabidopsis (Arabidopsis thaliana). Previously, STF1 (soybean [Glycine max] TGACG-motif binding factor 1), a homologous legume protein with a RING-finger motif and a bZIP domain, was reported in soybean. To investigate the role of STF1, the phenotypes of transgenic Arabidopsis plants overexpressing STF1 and HY5 were compared. In addition, the DNA-binding properties of STF1 and HY5 were extensively studied using random binding site selection and electrophoretic mobility shift assay. Overexpression of STF1 in the hy5 mutant of Arabidopsis restored wild-type photomorphogenic and root development phenotypes of short hypocotyl, accumulation of chlorophyll, and root gravitropism with partial restoration of anthocyanin accumulation. This supports that STF1 is a homolog of HY5 with a role in light and hormone signaling. The DNA-binding properties of STF1 and HY5 are shown to be similar to each other in recognizing many ACGT-containing elements with a consensus sequence motif of 5′-(G/A)(G/A) TGACGT(C/G/A)(A/T/G)-3′. The motif represents a characteristically strong preference for flanking sequence to TGACGT and a larger sequence than the sequences recognized by the G-box binding factor and TGA protein families. The finding of C-box, hybrid C/G-, and C/A-boxes as high-affinity binding sites over the G-box and parameters associated with HY5 recognition define the criteria of HY5/STF1 protein-DNA interaction in the promoter regions. This study helps to predict the precise in vivo binding sites of the HY5 protein from the vast number of putative HY5 genomic binding sites analyzed by chromatin immunoprecipitation on chip.
Protein Diffusion and Macromolecular Crowding in Thylakoid Membranes
Authors: Kirchhoff Helmut , Haferkamp Silvia , Allen John F. , Epstein David B.A. , Mullineaux Conrad W.
Published: February 2008

The photosynthetic light reactions of green plants are mediated by chlorophyll-binding protein complexes located in the thylakoid membranes within the chloroplasts. Thylakoid membranes have a complex structure, with lateral segregation of protein complexes into distinct membrane regions known as the grana and the stroma lamellae. It has long been clear that some protein complexes can diffuse between the grana and the stroma lamellae, and that this movement is important for processes including membrane biogenesis, regulation of light harvesting, and turnover and repair of the photosynthetic complexes. In the grana membranes, diffusion may be problematic because the protein complexes are very densely packed (approximately 75% area occupation) and semicrystalline protein arrays are often observed. To date, direct measurements of protein diffusion in green plant thylakoids have been lacking. We have developed a form of fluorescence recovery after photobleaching that allows direct measurement of the diffusion of chlorophyll-protein complexes in isolated grana membranes from Spinacia oleracea. We show that about 75% of fluorophores are immobile within our measuring period of a few minutes. We suggest that this immobility is due to a protein network covering a whole grana disc. However, the remaining fraction is surprisingly mobile (diffusion coefficient 4.6 ± 0.4 × 10−11 cm2 s−1), which suggests that it is associated with mobile proteins that exchange between the grana and stroma lamellae within a few seconds. Manipulation of the protein-lipid ratio and the ionic strength of the buffer reveals the roles of macromolecular crowding and protein-protein interactions in restricting the mobility of grana proteins.
Systemic Signaling of the Plant Nitrogen Status Triggers Specific Transcriptome Responses Depending on the Nitrogen Source in Medicago truncatula
Authors: Ruffel Sandrine , Freixes Sandra , Balzergue Sandrine , Tillard Pascal , Jeudy Christian , Martin-Magniette Marie Laure , van der Merwe Margaretha J. , Kakar Klementina , Gouzy Jerôme , Fernie Alisdair R. , Udvardi Michael , Salon Christophe , Gojon Alain , Lepetit Marc
Published: February 2008

Legumes can acquire nitrogen (N) from NO3  −, NH4  +, and N2 (through symbiosis with Rhizobium bacteria); however, the mechanisms by which uptake and assimilation of these N forms are coordinately regulated to match the N demand of the plant are currently unknown. Here, we find by use of the split-root approach in Medicago truncatula plants that NO3  − uptake, NH4  + uptake, and N2 fixation are under general control by systemic signaling of plant N status. Indeed, irrespective of the nature of the N source, N acquisition by one side of the root system is repressed by high N supply to the other side. Transcriptome analysis facilitated the identification of over 3,000 genes that were regulated by systemic signaling of the plant N status. However, detailed scrutiny of the data revealed that the observation of differential gene expression was highly dependent on the N source. Localized N starvation results, in the unstarved roots of the same plant, in a strong compensatory up-regulation of NO3  − uptake but not of either NH4  + uptake or N2 fixation. This indicates that the three N acquisition pathways do not always respond similarly to a change in plant N status. When taken together, these data indicate that although systemic signals of N status control root N acquisition, the regulatory gene networks targeted by these signals, as well as the functional response of the N acquisition systems, are predominantly determined by the nature of the N source.
Control of Compound Leaf Development byFLORICAULA/LEAFYOrthologSINGLE LEAFLET1inMedicago truncatula
Authors: Wang Hongliang , Chen Jianghua , Wen Jiangqi , Tadege Million , Li Guangming , Liu Yu , Mysore Kirankumar S. , Ratet Pascal , Chen Rujin
Published: February 2008

Molecular genetic studies suggest that FLORICAULA (FLO)/LEAFY (LFY) orthologs function to control compound leaf development in some legume species. However, loss-of-function mutations in the FLO/LFY orthologs result in reduction of leaf complexity to different degrees in Pisum sativum and Lotus japonicus. To further understand the role of FLO/LFY orthologs in compound leaf development in legumes, we studied compound leaf developmental processes and characterized a leaf development mutant, single leaflet1 (sgl1), from the model legume Medicago truncatula. The sgl1 mutants exhibited strong defects in compound leaf development; all adult leaves in sgl1 mutants are simple due to failure in initiating lateral leaflet primordia. In addition, the sgl1 mutants are also defective in floral development, producing inflorescence-like structures. Molecular cloning of SGL1 revealed that it encodes the M. truncatula FLO/LFY ortholog. When properly expressed, LFY rescued both floral and compound leaf defects of sgl1 mutants, indicating that LFY can functionally substitute SGL1 in compound leaf and floral organ development in M. truncatula. We show that SGL1 and LFY differed in their promoter activities. Although the SGL1 genomic sequence completely rescued floral defects of lfy mutants, it failed to alter the simple leaf structure of the Arabidopsis thaliana plants. Collectively, our data strongly suggest that initiation of lateral leaflet primordia required for compound leaf development involves regulatory processes mediated by the SGL1 function in M. truncatula.
How to account for the lipid effect on carbon stable‐isotope ratio (δ13C): sample treatment effects and model bias
Authors: Mintenbeck K. , Brey T. , Jacob U. , Knust R. , Struck U.
Published: February 2008

This study investigated the impact of lipid extraction, CaCO3 removal and of both treatments combined on fish tissue δ13C, δ15N and C:N ratio. Furthermore, the suitability of empirical δ13C lipid normalization and correction models was examined. δ15N was affected by lipid extraction (increase of up to 1·65‰) and by the combination of both treatments, while acidification alone showed no effect. The observed shift in δ15N represents a significant bias in trophic level estimates, i.e. lipid‐extracted samples are not suitable for δ15N analysis. C:N and δ13C were significantly affected by lipid extraction, proportional to initial tissue lipid content. For both variables, rates of change with lipid content (ΔC:N and Δδ13C) were species specific. All tested lipid normalization and correction models produced biased estimates of fish tissue δ13C, probably due to a non‐representative database and incorrect assumptions and generalizations the models were based on. Improved models need a priori more extensive and detailed studies of the relationships between lipid content, C:N and δ13C, as well as of the underlying biochemical processes.
Cephalopod dietary specialization and ontogenetic partitioning of the Australian weasel shark Hemigaleus australiensis White, Last & Compagno
Authors: Taylor S. M. , Bennett M. B.
Published: February 2008

The diet and ontogenetic partitioning of the Australian weasel shark Hemigaleus australiensis was examined in Moreton Bay, south‐east Queensland, Australia. The index of relative importance (IRI) revealed a highly specialized diet, consisting entirely of cephalopod molluscs (99·6% IRI) and crustaceans (0·4% IRI). Benthic octopus (Octopoda) dominated the diet, accounting for 96·7% IRI. A highly significant difference was found between the stomach contents of juvenile and sub‐adult and adult Australian weasel sharks. Dietary specialization increased with ontogeny and fish ≥1000 mm in total length (LT) fed almost exclusively on octopus (98% IRI). A highly significant difference was found between the LT of Australian weasel sharks from coral and sand and seagrass sites. At the coral site 75·4% of fish were mature while at the sand and seagrass site only 16·1% were mature. This spatial segregation may be attributed to shifting energy requirements associated with ontogeny and the relative abundance of large octopus at the coral site. Hemigaleus australiensis resides in an area of high shark diversity and its specialized cephalopod diet may reduce competition for food with other Carcharhiniformes whose prey comprises predominantly teleosts.
First record of Barbonymus schwanenfeldii (Bleeker) in the Iberian Peninsula
Authors: Gante H. F. , Moreira da Costa L. , Micael J. , Alves M. J.
Published: February 2008

The South‐east Asian cyprinid Barbonymus schwanenfeldii is recorded for the first time in the Iberian Peninsula from two specimens collected in the Guadiana River Basin in 2005. Their presence is probably due to release from aquaria.
Records ofAustrolethops wardiWhitley (Teleostei: Gobiidae) as an inhabitant of burrows of the thalassinid shrimpNeaxius acanthusin tropical seagrass beds of the Spermonde Archipelago, Sulawesi, Indonesia
Authors: Kneer D. , Asmus H. , Ahnelt H. , Vonk J. A.
Published: February 2008

The occurrence of the gobiidAustrolethops wardiin seagrass beds at Bone Batang, a small island of the Spermonde Archipelago, south‐west Sulawesi, Indonesia, is reported; the first record ofA. wardiin Indonesia. All fish were found to be associated with burrows of the thalassinid shrimpNeaxius acanthus, where they were caught either as single specimens or as pairs. The main diagnostic characters of this rarely found gobiid are presented.
Retrospective approach to investigating the early life history of a diadromous fish: allis shad Alosa alosa (L.) in the Gironde–Garonne–Dordogne watershed
Authors: Lochet A. , Jatteau P. , Tomás J. , Rochard E.
Published: February 2008

In this study, the identification of major ontogenetic events and the duration of the fresh water and estuarine phases before the seaward exit of young allis shad Alosa alosa were investigated retrospectively, using the otoliths of spawners. Daily growth increment periodicity in the otoliths was validated with an accuracy of 4 days (9·4%) for fish >30 days. The specific limits of the Sr:Ca ratios in the otoliths, indicating fish movements between salinity ‘compartments’, were up to 1·1 ×10−3 for the freshwater phase, 1·1 to 1·9 × 10−3 for the estuarine phase and 1·9 × 10−3 for the marine phase. In early life history, a major event occured at 22 days, which was marked on the otoliths by a change in the direction of the otolith growth axis. This event was related to a change in larval swimming behaviour. Juvenile freshwater residence time was between 58 and 123 days, with a median duration of 88 days. Contrary to what has been estimated in previous studies, the present study showed that the estuarine phase lasted from 4 to 36 days, with a median value of 11 days. Seaward exit occurred in fish aged from 63 to 150 days, with a median age of 99 days. These results have important implications for the sustainable management of this species.
Survival and growth of brown troutSalmo truttaL. embryos and the timing of hatching and emergence in two boreal lake outlet streams
Authors: Syrjänen J. , Kiljunen M. , Karjalainen J. , Eloranta A. , Muotka T.
Published: February 2008

Survival, growth and hatching of brown troutSalmo truttaembryos were studied usingin situincubation experiments in two lake outlet streams in Finland. The experimental design in both streams included an outlet site and a reference site far downstream. The date of hatching was recorded and the Elliott–Hurley model was then used to predict the time of emergence based on water temperature. For data analyses, the incubation period was divided into ‘winter’ (from fertilization to mid March) and ‘spring’ (from mid March until the end of the experiment). Temperature of the large‐lake outlet remained at 1° C through the winter, while in other sites temperature was close to 0° C. In spring, temperature increased more slowly in the large‐lake outlet. The survival of embryos was overall very high, from 83 to 98%, and they were larger in the outlets than in the downstream sites. Embryos hatched at the large‐lake outlet in March, and 3–5 weeks later in the other sites. Although there were considerable between‐site differences in hatching intervals, difference in expected 50% emergence dates of the earliest and latest site was only 4 days. Thus, any growth advantage that the outlet embryos had in winter disappeared by the end of the alevin period. Lake outlets, however, may be important for age 0 year brown trout later during the summer when other stream habitats do not provide adequate food resources.
Temperature effects on metabolic rate, swimming performance and condition of Pacific cod Gadus macrocephalus Tilesius
Authors: Hanna S. K. , Haukenes A. H. , Foy R. J. , Buck C. L.
Published: February 2008

Critical swimming speed (Ucrit) and rate of oxygen consumption of Pacific cod Gadus macrocephalus acclimated to 4 and 11° C were determined to assess the influence of water temperature on performance. The physiological effect of exercise trials on fish held at two temperatures was also assessed by comparing haematocrit and plasma concentrations of cortisol, metabolites and ions collected from fish before and after testing. The Ucrit of fish acclimated and exercised at 4° C did not differ from those acclimated and exercised at 11° C [1·07 body lengths (total length) s−1]. While the standard metabolic rate of 11° C acclimated fish was 28% higher than that of 4° C fish, no significant difference was observed between fish acclimated at the two temperatures. Plasma concentrations of cortisol, glucose and lactate increased significantly from pre‐ to post‐swim in both groups, yet only concentrations of cortisol differed significantly between temperature treatments. Higher concentrations of cortisol in association with greater osmoregulatory disturbance in animals acclimated at the lower temperature indicate that the lower water temperature acted as an environmental stressor. Lack of significant differences in Ucrit between temperature treatments, however, suggests that Pacific cod have robust physiological resilience with respect to swimming performance within temperature changes from 4 to 11° C.
Chronic lymphocytic leukaemia cells are efficiently killed by an anti‐CD20 monoclonal antibody selected for improved engagement of FcγRIIIA/CD16
Authors: De Romeuf Christophe , Dutertre Charles‐Antoine , Le Garff‐Tavernier Magali , Fournier Nathalie , Gaucher Christine , Glacet Arnaud , Jorieux Sylvie , Bihoreau Nicolas , Behrens Christian K. , Béliard Roland , Vieillard Vincent , Cazin Bruno , Bourel Dominique , Prost Jean‐François , Teillaud Jean‐Luc , Merle‐Béral Hélène
Published: February 2008

Patients with chronic lymphocytic leukaemia (CLL) treated with a combination of fludarabine, cyclophosphamide and rituximab show a high response rate. However, only a poor response is observed following rituximab monotherapy. The use of chemo‐immunotherapy is often associated with haematological and infectious complications. Thus, an antibody with an enhanced ability to kill CLL cells could lead to better clinical responses to antibody monotherapy and the possibility of lowering drug doses during chemo‐immunotherapy. We generated a chimeric anti‐CD20 monoclonal antibody (mAb), EMAB‐6, which has a low fucose content. Apoptosis and complement activities for EMAB‐6 were similar to those seen for rituximab. By contrast, EMAB‐6 mAb showed improved Fcγ receptor IIIA (FcγRIIIA)/CD16 binding and FcγRIIIA‐dependent effector functions. It induced a higher in vitro antibody‐dependent cellular cytotoxicity against CLL cells and a higher FcγRIIIA‐mediated interleukin‐2 production by FcγRIIIA+ Jurkat cells in the presence of CLL cells at both low and maximally saturating concentrations. Comparative studies between CLL and lymphoma cells coated with EMAB‐6 or rituximab indicated that the difference of efficacy was more pronounced at low doses and when target cells expressed fewer CD20 molecules. Thus, EMAB‐6 mAb represents a promising drug candidate for the treatment of CLL by inducing a strong cytotoxicity against tumour cells that express low CD20 levels.
A polymorphism in the NPPA gene associates with asthma
Authors: Lima J. J. , Mohapatra S. , Feng H. , Lockey R. , Jena P. K. , Castro M. , Irvin C. , Johnson J. A. , Wang J. , Sylvester J. E.
Published: February 2008

Background
Atrial natriuretic peptide (ANP) plays an important role in the lung and in augmenting allergic inflammation in asthma. The gene encoding ANP, NPPA, is located on chromosome 1p36, a region that has been linked to asthma.

Objectives
Determine associations between asthma and four common SNPs on the NPPA gene: C/G (rs13305986) in the promoter; G/A (rs5063) in Exon 1 resulting in NPPAMet32→Val substitution; T/C (rs5065) in Exon 3 resulting in an Arg152→Ter substitution; and T/C in the 3′UT region (rs5067).

Methods
A case–control design was used in White participants. The screening cohort consisted of 336 asthmatic cases who participated in a large clinical trial and 154, non‐asthmatic controls. The replicate cohort consisted of 172 asthmatic cases from a second clinical trial and 115 healthy controls. Demographic characteristics were well matched for cases and controls in the screening cohort. Adjusted (age, gender, body mass index) odds ratio (OR) were calculated by χ2 and logistic regression; a P‐value of 0.0167 defined the threshold of significance.

Results
The C allele of rs5067 was associated with asthma in the screening and replicate cohorts: adjusted ORs (95% confidence intervals) 0.5 (0.29–0.84; P=0.009) and 0.24 (0.11–0.53; P<0.0001), respectively. The C allele of rs5065 was associated with asthma in the screening cohort but not in the replicate. The population‐attributable risk for asthma in carriers of the C allele for rs5067 was 23.3%.

Conclusions
For rs5067, the risks of asthma in carriers of the C allele in the screening and replicate cohorts were reduced by 50% and 76%, respectively. NPPA may be an important susceptibility gene for asthma.
Empirical modelling of lake water‐temperature relationships: a comparison of approaches
Authors: SHARMA SAPNA , WALKER STEVEN C. , JACKSON DONALD A.
Published: February 2008

1. As a result of the role that temperature plays in many aquatic processes, good predictive models of annual maximum near‐surface lake water temperature across large spatial scales are needed, particularly given concerns regarding climate change. Comparisons of suitable modelling approaches are required to determine their relative merit and suitability for providing good predictions of current conditions. We developed models predicting annual maximum near‐surface lake water temperatures for lakes across Canada using four statistical approaches: multiple regression, regression tree, artificial neural networks and Bayesian multiple regression.

2. Annual maximum near‐surface (from 0 to 2 m) lake water‐temperature data were obtained for more than 13 000 lakes and were matched to geographic, climatic, lake morphology, physical habitat and water chemistry data. We modelled 2348 lakes and three subsets thereof encompassing different spatial scales and predictor variables to identify the relative importance of these variables at predicting lake temperature.

3. Although artificial neural networks were marginally better for three of the four data sets, multiple regression was considered to provide the best solution based on the combination of model performance and computational complexity. Climatic variables and date of sampling were the most important variables for predicting water temperature in our models.

4. Lake morphology did not play a substantial role in predicting lake temperature across any of the spatial scales. Maximum near‐surface temperatures for Canadian lakes appeared to be dominated by large‐scale climatic and geographic patterns, rather than lake‐specific variables, such as lake morphology and water chemistry.
Sequential colonization by river periphyton analysed by microscopy and molecular fingerprinting
Authors: SZABÓ KATALIN É. , MAKK JUDIT , KISS KEVE TIHAMÉR , EILER ALEXANDER , ÁCS ÉVA , TÓTH BENCE , KISS ÁRON KEVE , BERTILSSON STEFAN
Published: February 2008

1. An artificial glass substratum was incubated in the River Danube for a period of 28 days in order to detect the sequential colonization of microorganisms.

2. Light and fluorescent microscopy showed that microalgae and the picoalgal fraction on the slides increased rapidly over the first 2 weeks of colonization. Diatoms were numerically the most abundant component of the periphyton and their species richness and diversity increased rapidly in the early phase of colonization whereas diversity subsequently increased moderately.

3. Evenness of the diatom community was initially high, lower in the intermediate phase and again higher later on. Succession involving early, intermediate and late colonizer species was observed. Community composition during the first 5 days of colonization was very different from later stages whereas there were only minor changes subsequently.

4. Molecular community analysis by means of terminal restriction fragment length polymorphism analysis of PCR amplified 16S rRNA and 18S rRNA genes pointed to even larger differences between the composition of samples obtained early and late in the period.

5. The number of 18S rRNA and 16S rRNA terminal restriction fragments (T‐RF‐s) was variable over the colonization period and the fragment patterns of both the bacterial and eukaryotic portion of the microbial community were variable, with most T‐RF‐s unique to a single sample, suggesting a wide diversity and dynamic properties of periphytic organisms.
Do stream macroinvertebrates use instream refugia in response to severe short‐term flow reduction in New Zealand streams?
Authors: JAMES ALEXANDER B.W. , DEWSON ZOË S. , DEATH RUSSELL G.
Published: February 2008

1. Demand for water is increasing and water managers need to know how much they can remove from a stream before there are significant detrimental effects on its biological integrity. Flow reduction alters a number of habitat variables known to be important to aquatic invertebrates such as depth, velocity, temperature and fine sediment accumulation. Some taxa may attempt to use instream refugia to mitigate the effects of flow reduction.

2. We experimentally manipulated flows by constructing weirs and diversions in three small New Zealand streams. Discharge was reduced by 88–96%. We tested the hypothesis that macroinvertebrates would use pools and the hyporheic zone as refugia during short‐term (1‐month) periods of reduced flow.

3. We sampled hyporheic invertebrates with colonization chambers and pool invertebrates with kick nets within a before‐after, control‐impact (BACI) experimental design. A suite of physicochemical parameters was measured concurrently including surface and hyporheic temperatures.

4. Flow reduction significantly decreased velocity (60–69%) in all streams. Depth (18–61%) and wetted width (24–31%) tended to decrease but these changes were not always significant. Sediment cover increased the most in farmland streams (10–80%). Apart from decreasing temperature range (18–26%), flow reduction had little impact on the surface water temperatures.

5. Flow reduction had no impact on the abundance of common pool macroinvertebrates or on the abundance, vertical distribution or community composition of hyporheic macroinvertebrates.

6. Our results suggest that aquatic macroinvertebrates are resistant to short‐term, severe flow reduction as long as some water remains.
Evaluation of Listeria innocua as a suitable indicator for replacing Listeria monocytogenes during ripening of Camembert cheese
Authors: Liu Shaowei , Puri Virenda M. , Demirci Ali
Published: February 2008

The suitability of Listeria innocua for use as an indicator for replacing Listeria monocytogenes during the cheese‐making and ripening of Camembert cheese was evaluated. Pasteurized whole milk inoculated with either L. innocua or L. monocytogenes was used to make Camembert cheese, which were ripened in three stages. All cheese was ripened in three stages: room temperature (∼20 °C) and relative humidity of 60% for 36 h; 12 °C and relative humidity of 93% for 2 weeks; and 7 °C and relative humidity of 85% for 3 weeks. Results showed that population values of L. innocua and L. monocytogenes on day 1 were 7.16 and 6.11 log10 CFU/g, respectively, which declined to 6.54 and 5.45 log10 CFU/g, respectively, during subsequent 20 days. Thereafter, L. innocua and L. monocytogenes populations increased to 7.38 and 6.06 log10 CFU/g on day 35 of ripening, respectively. During ripening, surface and interior of cheeses were analysed for populations of L. innocua and L. monocytogenes, respectively. The data were collected on day 1, 5, 10, 15, 20, 25, 30, and 35 of ripening. Generally, the growth of L. innocua and L. monocytogenes is faster in surface than in centre. Top centre, bottom centre and bottom surface locations had similar population values during ripening. There were no significant differences (P > 0.05) between batch and section of cheese. The ripening time and locations had significant effect (P < 0.05) on the survival and growth of L. innocua and L. monocytogenes. The trends of survival and growth of L. innocua and L. monocytogenes were similar. These results indicated that L. innocua can be considered as an indicator for L. monocytogenes during ripening of Camembert cheese.
Physicochemical, pasting and thermal properties of tuber starches as modified by guar gum and locust bean gum
Authors: Huang Chien‐Chun
Published: February 2008

This study was carried out in order to compare the functional characteristics of isolated starch from five tuber crops, yam, taro, sweet potato, yam bean and potato, as well as effect of guar gum (GG) and locust bean gum (LBG) on pasting and thermal properties of tuber starches. The results showed that total amylose content of five tested starches ranged from 17.85% to 30.36%. The results of pasting behaviour showed that potato starches exhibited the highest peak viscosity and yam starch presented a stable curve with little breakdown viscosity. Addition of GG and LBG resulted in a significant increase in peak, final viscosity, breakdown and setback viscosity for all tuber starches (P < 0.05), but a slight decrease in pasting temperature. The gelatinisation enthalpy (ΔH) for starches with GG and LBG was slightly lower than those of the starches alone in yam and sweet potato, but not in taro and yam bean.
A comparison of two instrumental techniques used to discriminate the cooking quality of spaghetti
Authors: Sissons Mike , Ames Nancy , Egan Narelle , Rhymer Camille
Published: February 2008

Pasta is a popular food whose quality can be measured by appearance, flavour and texture. Several instruments have been devised to measure texture but there is little comparative information. This study compared the TA.XT2i texture analyser with the viscoelastograph of thirty spaghetti samples. There was a high correlation between these instruments and good agreement in ranks. While both instruments provide comparable data it is not the same. Two laboratories used the texture analyser to measure cooked spaghetti firmness using their own procedures. There was good agreement in firmness, however; there were differences in the ranks for samples that fell between the extremes in firmness. We attributed these differences to variations in the instrument settings, cooking method and sample presentation used by the laboratories indicating the need to standardise the method. Using a standard method greatly improved the correspondence between the laboratories improving the r2 to 0.99 with excellent agreement in the ranking of ten samples.
Theory‐guided interventions for adaptation to heart failure
Authors: Bakan Gülcan , Akyol Asiye Durmaz
Published: February 2008

Title.  Theory‐guided interventions for adaptation to heart failure

Aim.  This paper is a report of a study to examine the effects of a Roy Adaptation Model‐based experimental education, exercise and social support programme on adaptation in persons with heart failure.

Background.  In the past 20 years, a large number of studies have evaluated heart failure. Several studies of other chronic diseases have been based on the Roy Adaptation Model and show that this approach is useful in promoting adaptation for patients.

Method.  A randomized, parallel, controlled clinical trial was conducted in 2005 with 43 patients (21 intervention and 22 control patients). A booklet for patient training was given to those in the intervention group. Participants received a patient identification form, assessment form for physiological data, the Minnesota Living with Heart Failure Questionnaire, Interpersonal Support Evaluation List and the 6‐Minute Walk Test.

Results.  Patients in the intervention group adapted well to their condition and the four adaptive modes of Roy Adaptation Model were interrelated. Patients’ quality of life was enhanced, their functional capacities increased and social support within the interdependence dimension improved in patients in the intervention group.

Conclusion.  This is the first study to use the Roy Adaptation Model in a study of patients with heart failure. Roy’s model is an effective guide for nursing practice when caring for patients with heart failure.