bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regional and local drivers of macroinvertebrate assemblages in boreal springs
Authors: Ilmonen Jari , Paasivirta Lauri , Virtanen Risto , Muotka Timo 
Published: January 2009

AbstractAim  To identify the most important environmental drivers of benthic macroinvertebrate assemblages in boreal springs at different spatial scales, and to assess how well benthic assemblages correspond to terrestrially derived ecoregions.Location  Finland.Methods  Benthic invertebrates were sampled from 153 springs across four boreal ecoregions of Finland, and these data were used to analyse patterns in assemblage variation in relation to environmental factors. Species data were classified using hierarchical divisive clustering (twinspan) and ordinated using non‐metric multidimensional scaling. The prediction success of the species and environmental data into a priori (ecoregions) and a posteriori (twinspan) groups was compared using discriminant function analysis. Indicator species analysis was used to identify indicator taxa for both a priori and a posteriori assemblage types.Results  The main patterns in assemblage clusters were related to large‐scale geographical variation in temperature. A secondary gradient in species data reflected variation in local habitat structure, particularly abundance of minerogenic spring brooks. Water chemistry variables were only weakly related to assemblage variation. Several indicator species representing southern faunistic elements in boreal springs were identified. Discriminant function analysis showed poorer success in classifying sites into ecoregions based on environmental than on species data. Similarly, when classifying springs into the twinspan groups, classification based on species data vastly outperformed that based on environmental data.Main conclusions  A latitudinal zonation pattern of spring assemblages driven by regional thermal conditions is documented, closely paralleling corresponding latitudinal patterns in both terrestrial and freshwater assemblages in Fennoscandia. The importance of local‐scale environmental variables increased with decreasing spatial extent. Ecoregions provide an initial stratification scheme for the bioassessment of benthic macroinvertebrates of North European springs. Our results imply that climate warming, landscape disturbance and degradation of spring habitat pose serious threats to spring biodiversity in northern Europe, especially to its already threatened southern faunistic elements.
Association between folate, vitamin B6 and vitamin B12 intake and depression in the SUN cohort study
Authors: Sánchez‐Villegas A. , Doreste J. , Schlatter J. , Pla J. , Bes‐Rastrollo M. , Martínez‐González M. A. 
Published: January 2009

AbstractBackground:  An association between low blood levels of folate, vitamins B6 and B12 and a higher prevalence of depressive symptoms has been reported in several epidemiological studies. The present study aimed to assess the association between folate, vitamins B6 and B12 intake and depresion prevalence in the SUN cohort study.Methods:  The study comprised a cross‐sectional analysis of 9670 participants. A validated semi‐quantitative food frequency questionnaire was used to ascertain vitamin intake. The association between the baseline intake of folate, vitamins B6 and B12 categorised in quintiles and the prevalence of depression was assessed. The analyses were repeated after stratifying by smoking habits, alcohol intake, physical activity and personality traits.Results:  Among women, odds ratios (OR) [95% confidence interval (CI)] for the third to fifth quintile for vitamin B12 intake were 0.58 (0.41–0.84), 0.56 (0.38–0.82) and 0.68 (0.45–1.04), respectively. Among those men with a low level of anxiety and current smokers, a significant positive association between low folate intake and the prevalence of depression was found. The OR (95% CI) for the first quintile of intake was 2.85 (1.49–5.45) and 2.18 (1.08–4.38), respectively, compared to the upper quintiles of intake (Q2–Q5) considered as a group.Conclusion:  Low folate intake was associated with depression among currently smoking men and men with low anxiety levels. Low intake of vitamin B12 was associated with depression among women. No significant associations were found for vitamin B6 intake.
Levels of specificity of Xylaria species associated with fungus‐growing termites: a phylogenetic approach
Authors: VISSER A. A. , ROS V. I. D. , DE BEER Z. W. , DEBETS A. J. M. , HARTOG E. , KUYPER T. W. , LÆSSØE T. , SLIPPERS B. , AANEN D. K. 
Published: January 2009

AbstractFungus‐growing termites live in obligate mutualistic symbiosis with species of the basidiomycete genus Termitomyces, which are cultivated on a substrate of dead plant material. When the termite colony dies, or when nest material is incubated without termites in the laboratory, fruiting bodies of the ascomycete genus Xylaria appear and rapidly cover the fungus garden. This raises the question whether certain Xylaria species are specialised in occupying termite nests or whether they are just occasional visitors. We tested Xylaria specificity at four levels: (1) fungus‐growing termites, (2) termite genera, (3) termite species, and (4) colonies. In South Africa, 108 colonies of eight termite species from three termite genera were sampled for Xylaria. Xylaria was isolated from 69% of the sampled nests and from 57% of the incubated fungus comb samples, confirming high prevalence. Phylogenetic analysis of the ITS region revealed 16 operational taxonomic units of Xylaria, indicating high levels of Xylaria species richness. Not much of this variation was explained by termite genus, species, or colony; thus, at level 2–4 the specificity is low. Analysis of the large subunit rDNA region, showed that all termite‐associated Xylaria belong to a single clade, together with only three of the 26 non‐termite‐associated strains. Termite‐associated Xylaria thus show specificity for fungus‐growing termites (level 1). We did not find evidence for geographic or temporal structuring in these Xylaria phylogenies. Based on our results, we conclude that termite‐associated Xylaria are specific for fungus‐growing termites, without having specificity for lower taxonomic levels.
Cohesive molecular genetic data delineate species diversity in the dinoflagellate genus Symbiodinium
Authors: SAMPAYO E. M. , DOVE S. , LAJEUNESSE T. C. 
Published: January 2009

AbstractThe diversity of symbiotic dinoflagellates (Symbiodinium) in pocilloporid corals originating from various reef habitats surrounding Heron Island, southern Great Barrier Reef, was examined by targeting ribosomal, mitochondrial, and chloroplast genes using six methods that analyse for sequence differences. The ability of each of 13 genetic analyses to characterize eight ecologically distinct Symbiodinium spp. was dependent on the level of conservation of the gene region targeted and the technique used. Other than differences in resolution, phylogenetic reconstructions using nuclear and organelle gene sequences were complementary and when combined produced a well‐resolved phylogeny. Analysis of the ribosomal internal transcribed spacers using denaturing gradient gel electrophoresis fingerprinting in combination with sequencing of dominant bands provided a precise method for rapidly resolving and characterizing symbionts into ecologically and evolutionarily distinct units of diversity. Single‐stranded conformation polymorphisms of the nuclear ribosomal large subunit (D1/D2 domain) identified the same number of ecologically distinct Symbiodinium spp., but profiles were less distinctive. The repetitive sequencing of bacterially cloned ITS2 polymerase chain reaction amplifications generated numerous sequence variants that clustered together according to the symbiont under analysis. The phylogenetic relationships between these clusters show how intragenomic variation in the ribosomal array diverges among closely related eukaryotic genomes. The strong correlation between phylogenetically independent lineages with different ecological and physiological attributes establishes a clear basis for assigning species designations to members of the genus Symbiodinium.
Global population structure of the tope (Galeorhinus galeus) inferred by mitochondrial control region sequence data
Authors: CHABOT C. L. , ALLEN L. G. 
Published: January 2009

AbstractIn order to properly manage and conserve exploited shark species, detailed analyses of their population structure is needed. Global populations of Galeorhinus galeus are in decline due to the exploitation of the fishery over the past 80 years. Currently, the genetic structure of eastern Pacific populations of G. galeus is not known and recent observations in the northeastern Pacific suggest an increase in numbers. To evaluate gene flow among populations of G. galeus, 116 samples were collected and analysed from six geographically dispersed locations: Australia, North America, South Africa, South America (Argentina and Peru), and the UK. Analysis of 968 to 1006 bp of the 1068‐bp mitochondrial control region revealed 38 unique haplotypes that were largely restricted to their collecting locality. Significant genetic structure was detected among populations (ΦST = 0.84; P < 0.000001) and migration estimates were low (Nm = 0.05–0.97). Due to an apparent lack of migration, populations of G. galeus appear to be isolated from each other with little to no gene flow occurring among them. As a consequence of this isolation, increasing numbers of G. galeus in the northeastern Pacific can be best explained by local recruitment and not by input from geographically distant populations.
Arabidopsis ING and Alfin1‐like protein families localize to the nucleus and bind to H3K4me3/2 via plant homeodomain fingers
Authors: Lee Woo Yong , Lee Daeyoup , Chung Won‐Il , Kwon Chang Seob 
Published: January 2009

SummaryIn yeast and animals, tri‐ and dimethylation of histone H3 at lysine 4 (H3K4me3/2) are markers of transcriptionally active genes that have recently been shown to be primary ligands for the plant homeodomain (PHD) finger. However, PHD fingers able to bind to H3K4me3/2 have not been identified in plants. Here, we identify 83 canonical PHD fingers in the Arabidopsis proteome database that are supported by both SMART and Pfam prediction. Among these, we focus on PHD fingers in ING (inhibitor of growth) homologues (AtING) and Alfin1‐like (AL) proteins, which are highly similar to those in human ING2 and bromodomain PHD finger transcription factor (BPTF), based on predicted tertiary structures. ING proteins are found in yeast, animals and plants, whereas AL proteins exist only in plants. In vitro binding experiments indicated that PHD fingers in AtING and AL proteins in Arabidopsis can bind to H3K4me3, and, to a lesser extent, to H3K4me2. In addition, mutational analysis confirmed that a predicted aromatic cage and a specific conserved acidic residue are both crucial for binding to H3K4me3/2. Finally, we demonstrate that AtING and AL proteins are nuclear proteins that are expressed in various tissues of the Arabidopsis plant. Thus, we propose that ING and AL proteins are nuclear proteins that are involved in chromatin regulation by binding to H3K4me3/2, the active histone markers, in plants.
Characterization of genes in the ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES (AS2/LOB) family in Arabidopsis thaliana, and functional and molecular comparisons between AS2 and other family members
Authors: Matsumura Yoko , Iwakawa Hidekazu , Machida Yasunori , Machida Chiyoko 
Published: January 2009

SummaryThe ASYMMETRIC LEAVES2 (AS2) gene is required for the generation of the flat and symmetrical shape of the leaf lamina in Arabidopsis. AS2 encodes a plant‐specific protein with an AS2/LATERAL ORGAN BOUNDARIES (AS2/LOB) domain that includes a cysteine repeat, a conserved single glycine residue and a leucine‐zipper‐like sequence in its amino‐terminal half. The Arabidopsis genome contains 42 genes, including AS2, that encode proteins with an AS2/LOB domain in their amino‐terminal halves, and these genes constitute the AS2/LOB gene family. In the present study, we cloned and characterized cDNAs that covered the putative coding regions of all members of this family, and investigated patterns of transcription systematically in Arabidopsis plants. Comparisons among amino acid sequences that had been deduced from the cloned cDNAs revealed eight groups of genes, with two or three members each, and high degrees of identity among entire amino acid sequences, suggesting that some members of the AS2/LOB family might have redundant function(s). Moreover, no member of the family exhibited significant similarity, in terms of the deduced amino acid sequence of the carboxy‐terminal half, to AS2. Results of domain swapping between AS2 and other members of the family showed that the AS2/LOB domain of AS2 cannot be functionally replaced by those of other members of the family, and that only a few dissimilarities among respective amino acid residues of the AS2/LOB domain of AS2 and those of other members are important for the specific functions of AS2.
Wall‐modifying genes regulated by the Arabidopsis homolog of trithorax, ATX1: repression of theXTH33gene as a test case
Authors: Ndamukong Ivan , Chetram Anand , Saleh Abdelaty , Avramova Zoya 
Published: January 2009

SummaryThe plant cell wall is a dynamic structure playing important roles in the control of plant cell growth and differentiation. These processes involve global reprogramming of the genome driven by dynamic changes in chromatin structure. The chromatin modifier ARABIDOPSIS HOMOLOG OF TRITHORAX (ATX1) methylates lysine residue 4 on histone H3 (H3K4me), acting as an epigenetic mark on associated genes. The remarkable overrepresentation in the ATX1‐regulated gene fraction of genes encoding plasma membrane and cell wall‐remodeling activities suggested a link between two separate factors affecting growth, development and adaptation in Arabidopsis: the wall‐modifying activities regulating cell extension, growth and fate, and the epigenetic mechanisms regulating chromatin structure and gene expression. A co‐regulated fraction of specific wall‐modifying proteins suggests that they may function together. Here, we study the ATX1‐dependent expression of the gene encoding the wall‐loosening factor XTH33 as a test case for development‐ and tissue‐specific effects displayed by the chromatin modifier. In addition, we show that XTH33 is, most likely, an integral plasma membrane protein. A putative transmembrane domain is conserved in some, but not all, XTH family members, suggesting that they may be differently positioned when functioning as wall modifiers.
Short panicle1encodes a putative PTR family transporter and determines rice panicle size
Authors: Li Shengben , Qian Qian , Fu Zhiming , Zeng Dali , Meng Xiangbing , Kyozuka Junko , Maekawa Masahiko , Zhu Xudong , Zhang Jian , Li Jiayang , Wang Yonghong 
Published: January 2009

SummaryThe architecture of the rice inflorescence, which is determined mainly by the number and length of primary and secondary inflorescence branches, is of importance in both agronomy and developmental biology. The position and number of primary branches are established during the phase transition from vegetative to reproductive growth, and several of the genes identified as participating in this process do so by regulating the meristemic activities of inflorescence. However, little is known about the molecular mechanism that controls inflorescence branch elongation. Here, we report on a novel rice mutant,short panicle1(sp1), which is defective in rice panicle elongation, and thus leads to the short‐panicle phenotype. Gene cloning and characterization indicate thatSP1encodes a putative transporter that belongs to the peptide transporter (PTR) family. This conclusion is based on the findings that SP1 contains a conserved PTR2 domain consisting of 12 transmembrane domains, and that the SP1‐GFP fusion protein is localized in the plasma membrane. TheSP1gene is highly expressed in the phloem of the branches of young panicles, which is consistent with the predicted function of SP1 and thesp1phenotype. Phylogenetic analysis implies that SP1 might be a nitrate transporter. However, neither nitrate transporter activity nor any other compounds transported by known PTR proteins could be detected in either aXenopusoocyte or yeast system, in our study, suggesting that SP1 may need other component(s) to be able to function as a transporter, or that it transports unknown substrates in the monocotyledonous rice plant.
Extracellular cross‐linking of maize arabinoxylans by oxidation of feruloyl esters to form oligoferuloyl esters and ether‐like bonds
Authors: Burr Sally J. , Fry Stephen C. 
Published: January 2009

SummaryPrimary cell walls of grasses and cereals contain arabinoxylans with esterified ferulate side chains, which are proposed to cross‐link the polysaccharides during maturation by undergoing oxidative coupling. However, the mechanisms and control of arabinoxylan cross‐linking in vivo are unclear. Non‐lignifying maize (Zea mays L.) cell cultures were incubated with l‐[1‐3H]arabinose or (E)‐[U‐14C]cinnamate (radiolabelling the pentosyl and feruloyl groups of endogenous arabinoxylans, respectively), or with exogenous feruloyl‐[3H]arabinoxylans. The cross‐linking rate of soluble extracellular arabinoxylans, monitored on Sepharose CL‐2B, peaked suddenly and transiently, typically at ∼9 days after subculture. This peak was not associated with appreciable changes in peroxidase activity, and was probably governed by fluctuations in H2O2 and/or inhibitors. De‐esterified arabinoxylans failed to cross‐link, supporting a role for the feruloyl ester groups. The cross‐links were stable in vivo. Some of them also withstood mild alkaline conditions, indicating that they were not (only) based on ester bonds; however, most were cleaved by 6 m NaOH, which is a property of p‐hydroxybenzyl–sugar ether bonds. Cross‐linking of [14C]feruloyl‐arabinoxylans also occurred in vitro, in the presence of endogenous peroxidases plus exogenous H2O2. During cross‐linking, the feruloyl groups were oxidized, as shown by ultraviolet spectra and thin‐layer chromatography. Esterified diferulates were minor oxidation products; major products were: (i) esterified oligoferulates, released by treatment with mild alkali; and (ii) phenolic components attached to polysaccharides via relatively alkali‐stable (ether‐like) bonds. Thus, feruloyl esters participate in polysaccharide cross‐linking, but mainly by oligomerization rather than by dimerization. We propose that, after the oxidative coupling, strong p‐hydroxybenzyl–polysaccharide ether bonds are formed via quinone‐methide intermediates.
Immune response to measles vaccine in 6 month old infants in Papua New Guinea
Authors: Kurubi Jonah , Vince John , Ripa Paulus , Tefuarani Nakapi , Riddell Michaela , Duke Trevor 
Published: January 2009

SummaryObjective  To assess the efficacy of the current measles immunization schedule in Papua New Guinea, which is to give the first dose at 6 months of age and the second at 9 months.Methods  Humoral immune response study of 140 Papua New Guinean infants at 6 months of age, measuring measles IgG antibodies by enzyme immunoassay before and 85 days after the 6‐month dose of measles vaccine.Results  After vaccination at 6 months, 35.7% of infants developed a level of measles antibodies consistent with protection (IgG >330 IU/ml); 17.7% had an antibody response (150–330 IU/ml) that is likely to afford some protection; 46.8% had no detectable antibody response (IgG <150 IU/ml). Among 53 infants with no antibody response, 37 (69.5%) developed an antibody response, while 42.4% (37/87) of those with maternal antibodies sero‐converted (P = 0.002).Conclusions  Antibody response to measles vaccine was lower than expected at 6 months. While the presence of maternally derived antibodies accounted for some of the limited seroconversion in young infants, other factors are involved. Issues to be considered in determining the value of the first dose of measles vaccination in mid infancy in poor countries are complex and antibody responses are only one factor. Others, such as cell mediated immune responses, the non‐specific protective effect of measles vaccine in preventing illness and death and the practicalities of uptake of vaccines at different ages, are also important.
Individual efficacy of intermittent preventive treatment with sulfadoxine–pyrimethamine in primi‐ and secundigravidae in rural Burkina Faso: impact on parasitaemia, anaemia and birth weight
Authors: Gies Sabine , Coulibaly Sheick Oumar , Ouattara Florence Tiemegna , D’Alessandro Umberto 
Published: January 2009

SummaryObjective  To assess the efficacy at individual level of intermittent preventive treatment with sulfadoxine–pyrimethamine (IPTp‐SP) in primi‐ and secundigravidae in rural Burkina Faso.Methods  Data of 1441 women enrolled in a health centre randomized trial and delivering a live‐singleton between September 2004 and October 2006 were analysed at individual level. Prevalence of peripheral and placental parasitaemia, anaemia (PCV <33%), low‐birth weight (<2500 g; LBW), mean packed cell volume (PCV) and birth weight were compared in relation to the number of directly observed SP doses.Results  Two or more doses of SP significantly reduced the risk of placental parasitaemia [adjusted odds ratio (AOR) = 0.04, 95%CI = 0.003–0.60, P = 0.023] and anaemia at delivery (AOR = 0.31, 95%CI = 0.18–0.52, P < 0.001). IPTp was associated with reduced risk of LBW in primigravidae (AOR = 0.11, 95%CI = 0.07–0.17, P < 0.001) but not secundigravidae (AOR = 0.70, 95%CI = 0.26–1.91, P = 0.452). For each increment in number of SP doses mean PCV increased by 1.0% (95%CI = 0.4–1.7, P = 0.005) at 32 weeks gestation, by 1.2% (95%CI = 0.2–2.2, P = 0.025) at delivery and mean birth weight by 220 g (95%CI = 134–306 P < 0.001) in primigravidae and by 102 g (95%CI = 55–148, P = 0.001) in secundigravidae.Conclusion  The risk of malaria infection was significantly reduced by IPTp with SP in primi‐ and secundigravidae in rural Burkina Faso. The impact on clinical outcomes is lower and mainly limited to primigravidae for LBW. Incomplete uptake of IPTp‐SP and limited effect in low risk groups together may substantially dilute the measurable impact of effective interventions. This needs to be taken into account when evaluating interventions at community level.
Paraneoplastic pemphigus/paraneoplastic autoimmune multiorgan syndrome
Authors: Sehgal Virendra N. , Srivastava Govind 
Published: January 2009

AbstractParaneoplastic pemphigus is the term used for an exclusive subset of pemphigus. The clinical lesions may resemble pemphigus, pemphigoid, erythema multiforme, graft‐vs.‐host disease, or lichen planus. A common denominator in all patients is the concomitant occurrence of either occult or confirmed systemic neoplasm. It is imperative to confirm the diagnosis through microscopy, where intraepidermal suprabasal cleavage, epidermal acantholysis, dyskeratotic keratinocytes and vacuolar changes in the basal epidermis, interfacial dermatitis, and epidermal exocytosis can be seen. Furthermore, the deposition of immunoglobulin G (IgG) and complement in the epidermal intercellular spaces, detected by direct and/or indirect immunofluorescence, is equally crucial for confirming the diagnosis.