Molecular tools to investigate Rhizoctonia solani distribution in soil

Real-time PCR protocols were developed to detect and discriminate 11 anastomosis groups (AGs) of Rhizoctonia solani using ribosomal internal transcribed spacer (ITS) regions (AG-1-IA, AG-1-IC, AG-2-1, AG-2-2, AG-4HGI+II, AG-4HGIII, AG-8) or beta-tubulin (AG-3, AG-4HGII, AG-5 and AG-9) sequences. All real-time assays were target group specific, except AG-2-2, which showed a weak cross-reaction with AG-2tabac. In addition, methods were developed for the high throughput extraction of DNA from soil and compost samples. The DNA extraction method was used with the AG-2-1 assay and shown to be quantitative with a detection threshold of 10-7 g of R. solani per g of soil. A similar DNA extraction efficiency was observed for samples from three contrasting soil types. The developed methods were then used to investigate the spatial distribution of R. solani AG-2-1 in field soils. Soil from shallow depths of a field planted with Brassica oleracea tested positive for R. solani AG-2-1 more frequently than soil collected from greater depths. Quantification of R. solani inoculum in field samples proved challenging due to low levels of inoculum in naturally occurring soils. The potential uses of real-time PCR and DNA extraction protocols to investigate the epidemiology of R. solani are discussed.

The amphioxus FoxQ1 gene is expressed in the developing endostyle

The FoxQ1 genes form a distinct group within the Fox (also known as forkhead) gene family. We have isolated a gene from the amphioxus Branchiostoma floridae that encodes a forkhead domain with high identity to FoxQ1 genes in other chordates. Molecular phylogenetic analysis places AmphiFoxQ1 in a robust grouping with vertebrate FoxQ1 genes and with Ciona intestinalis Ci-FoxQ1. This group is separate from that containing AmphiFoxQ2, which instead groups with other invertebrate Fox genes. The expression of AmphiFoxQ1 was analysed by whole mount in situ hybridisation. The results show that AmphiFoxQ1 expression is confined to the developing endoderm, and specifically marks the endostyle and associated peripharyngeal bands of amphioxus larvae. Ci-FoxQ1 is also expressed in the endostyle, highlighting this as a conserved site of FoxQ1 gene expression in basal chordates. (C) 2004 Elsevier B.V. All rights reserved.

Oestrogenic activity of p-hydroxybenzoic acid (common metabolite of paraben esters) and methylparaben in human breast cancer cell lines

This paper addresses the question of whether p-hydroxybenzoic acid, the common metabolite of parabens, possesses oestrogenic activity in human breast cancer cell lines. The alkyl esters of p-hydroxybenzoic acid (parabens) are used widely as preservatives in consumer products to which the human population is exposed and have been shown previously to possess oestrogenic activity and to be present in human breast tumour tissue, which is an oestrogen-responsive tissue. Recent work has shown p-hydroxybenzoic acid to give an oestrogenic response in the rodent uterotrophic assay. We report here that p-hydroxybenzoic acid possesses oestrogenic activity in a panel of assays in human breast cancer cell lines. p-Hydroxybenzoic acid was able to displace [H-3]oestradiol from cytosolic oestrogen receptor of MCF7 human breast cancer cells by 54% at 5 x 10(6)-fold molar excess and by 99% at 10(7)-fold molar excess. It was able to increase the expression of a stably integrated oestrogen responsive reporter gene (ERE-CAT) at a concentration of 5 x 10(-4) M in MCF7 cells after 24 h and 7 days, which could be inhibited by the anti-oestrogen ICI 182 780 (Faslodex, fulvestrant). Proliferation of two human breast cancer cell lines (MCF7, ZR-75-1) could be increased by 10(-5) M p-hydroxybenzoic acid. Following on from previous studies showing a decrease in oestrogenic activity of parabens with shortening of the linear alkyl chain length, this study has compared the oestrogenic activity of p-hydroxybenzoic acid where the alkyl grouping is no longer present with methylparaben, which has the shortest alkyl group. Intrinsic oestrogenic activity of p-hydroxybenzoic acid was similar to that of methylparaben in terms of relative binding to the oestrogen receptor but its oestrogenic activity on gene expression and cell proliferation was lower than that of methylparaben. It can be concluded that removal of the ester group from parabens does not abrogate its oestrogenic activity and that p-hydroxybenzoic acid can give oestrogenic responses in human breast cancer cells. Copyright (C) 2005 John Wiley & Sons, Ltd.

Phylogenetic relationships within the moss family Bryaceae based on chloroplast DNA evidence

The Bryaceae are a large cosmopolitan family of mosses containing genera of considerable taxonomic difficulty. Phylogenetic relationships within the family were inferred using data from chloroplast DNA sequences (rps4 and trnL-trnF region). Parsimony and maximum likelihood optimality criteria, and Bayesian phylogenetic inference procedures were employed to reconstruct relationships. The genera Bryum and Brachymenium are not monophyletic groups. A clade comprising Plagiobryum, Acidodontium, Mielichhoferia macrocarpa, Bryum sects. Bryum, Apalodictyon, Limbata, Leucodontium, Caespiticia, Capillaria (in part: sect. Capillaria), and Brachymenium sect. Dicranobryum, is well supported in all analyses and represents a major lineage within the family. Section Dicranobryum of Brachymenium is more closely related to section Bryum than to the other sections of Brachymenium, as are Mielichhoferia macrocarpa and M. himalayana. Species of Acidodontium form a clade with Anomobryum julaceum. The grouping of species with a rosulate gametophytic growth form suggests the presence of a 'rosulate' clade similar in circumscription to the genus Rosulabryum. Mielichhoferia macrocarpa and M. himalayana are transferred to Bryum as B. porsildii and B. caucasicum, respectively.

Oestrogenic activity of benzylparaben

Previous work has demonstrated that the alkyl esters of p-hydroxybenzoic acid (parabens) possess oestrogenic activity, which increases with length of alkyl chain from methylparaben to n-butylparaben and with branching in the alkyl chain from n-butylparaben to isobutylparaben. This study reports on the oestrogenic activity of benzylparaben in a variety of assays in vitro and in vivo. Benzylparaben was able to displace [H-3]oestradiol from cytosolic oestrogen receptor (ER) of MCF7 human breast cancer cells by 22% at 1000-fold molar excess, by 40% at 10000-fold molar excess, by 57% at 100000-fold molar excess and by 100% at 1000000-fold molar excess. It was able to increase expression of a stably transfected oestrogen responsive reporter gene (ERE-CAT) in MCF7 cells after 24 h at 10(-5)M/10(-4)M and after 7 days at 10(-6)M/10(-5)M/10(-4)M. Proliferation of MCF7 cells could be increased by 10(-6)M/10(-5)M benzylparaben and this could be inhibited by 10(-7)M pure anti-oestrogen ICI 182,780, indicating that growth effects were ER mediated. Further evidence for ER-mediation was provided from the ability of benzylparaben to increase the growth of a second oestrogen-dependent human breast cancer cell line ZR-75-1, but not the oestrogen-insensitive NIDA-MB-231 cell line. When tested in the presence of 10(-10)M 17beta-oestradiol, benzylparaben gave no antagonist response on the growth of either MCF7 or ZR-75-1 cells. Finally, benzylparaben could increase uterine weight in the immature mouse following topical application of three daily doses of 33 mg to dorsal skin. These results demonstrate that the oestrogenicity of methylparaben can be increased by the addition of an aryl group as well as by lengthening or branching the alkyl grouping. Copyright (C) 2003 John Wiley Sons, Ltd.

Formate-dependent growth and homoacetogenic fermentation by a bacterium from human feces: Description of Bryantella formatexigens gen. nov., sp nov.

Formate stimulates growth of a new bacterium from human feces. With high formate, it ferments glucose to acetate via the Wood-Ljungdahl pathway. The original isolate fermented vegetable cellulose and carboxymethylcellulose, but it lost this ability after storage at -76degreesC. 16S rRNA gene sequencing identifies it as a distinct line within the Clostridium coccoides supra-generic rRNA grouping. We propose naming it Bryantella formatexigens gen. nov., sp. nov.

Hespellia stercorisuis gen. nov., sp nov and Hespellia porcina sp nov., isolated from swine manure storage pits

Four Gram-positive-staining, strictly anaerobic, non-spore-forming, rod-shaped organisms were isolated from a pig manure storage pit. Comparative 16S rRNA gene sequence analysis revealed that the isolates belonged to two related but distinct groups. Sequence analysis showed that the two groups of isolates were highly related to each other (approx. 97% 16S rRNA gene sequence similarity), forming a distinct cluster within the Clostridium coccoides suprageneric rDNA grouping. Biochemical and physiological studies confirmed the division of the isolates into two related, albeit distinct, groups. Based on both phenotypic and phylogenetic evidence, it is proposed that the unidentified rod-shaped isolates from pig manure should be classified in a novel genus, Hespellia gen. nov., as Hespellia stercorisuis sp. nov. and Hespellia porcina sp. nov. The type species of the novel genus is H. stercorisuis (type strain, PC18(T) = NRRL B-23456(T) = CCUG 46279(T) = ATCC BAA-677(T)) and the type strain of H. porcina is PC80(T) (= NRRL B-23458(T) = ATCC BAA-674(T)).

Colonic microbiota signatures across five northern European countries

The composition of the colonic microbiota of 91 northern Europeans was characterized by fluorescent in situ hybridization using 18 phylogenetic probes. On average 75% of the bacteria were identified, and large interindividual variations were observed. Clostridium coccoides and Clostridium leptum were the dominant groups (28.0% and 25.2%), followed by the Bacteroides (8.5%). According to principal component analysis, no significant grouping with respect to geographic origin, age, or gender was observed.

Fastidiosipila sanguinis gen. nov., sp nov., a new Gram-positive, coccus-shaped organism from human blood

Phenotypic and phylogenetic studies were performed on two strains of an unidentified Gram-positive, fastidious, non-spore-forming, coccus-shaped bacterium recovered from human blood. The organism was catalase-negative and grew under strictly anaerobic conditions and in the presence of 2 and 6% O-2. Comparative 16S rRNA gene sequencing demonstrated that the unidentified bacterium was, phylogenetically, far removed from peptostreptococci and related Gram-positive coccus-shaped organisms, but exhibited a phylogenetic association with Clostridium rRNA cluster III [as defined by Collins et al, Int J Syst Bacteriol 44 (1994), 812-826]. Sequence divergence values of 15% or more were observed between the unidentified bacterium and all other recognized species within this and related rRINIA clostridial clusters. Treeing analysis showed that the unknown bacterium formed a deep line branching at the periphery of rRNA cluster III and represents a hitherto unknown genus within this supra-generic grouping. On the basis of both phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from blood be classified in a new genus, Fastidiosipila gen. nov., as Fastidiosipila sanguinis sp, nov. The type strain of Fastidiosipila sanguinis is CCUG 47711(T) (= CIP 108292(T)).

Example uses of a learning object

A self study course for learning to program using the C programming language has been developed. A Learning Object approach was used in the design of the course. One of the benefits of the Learning Object approach is that the learning material can be reused for different purposes. 'Me course developed is designed so that learners can choose the pedagogical approach most suited to their personal learning requirements. For all learning approaches a set of common Assessment Learning Objects (ALOs or tests) have been created. The design of formative assessments with ALOs can be carried out by the Instructional Designer grouping ALOs to correspond to a specific assessment intention. The course is non-credit earning, so there is no summative assessment, all assessment is formative. In this paper examples of ALOs and their uses is presented together with their uses as decided by the Instructional Designer and learner. Personalisation of the formative assessment of skills can be decided by the Instructional Designer or the learner using a repository of pre-designed ALOs. The process of combining ALOs can be carried out manually or in a semi-automated way using metadata that describes the ALO and the skill it is designed to assess.

Room reflections and constancy in speech-like sounds: within-band effects

The experiment asks whether constancy in hearing precedes or follows grouping. Listeners heard speech-like sounds comprising 8 auditory-filter shaped noise-bands that had temporal envelopes corresponding to those arising in these filters when a speech message is played. The „context‟ words in the message were “next you‟ll get _to click on”, into which a “sir” or “stir” test word was inserted. These test words were from an 11-step continuum that was formed by amplitude modulation. Listeners identified the test words appropriately and quite consistently, even though they had the „robotic‟ quality typical of this type of 8-band speech. The speech-like effects of these sounds appears to be a consequence of auditory grouping. Constancy was assessed by comparing the influence of room reflections on the test word across conditions where the context had either the same level of reflections, or where it had a much lower level. Constancy effects were obtained with these 8-band sounds, but only in „matched‟ conditions, where the room reflections were in the same bands in both the context and the test word. This was not the case in a comparison „mismatched‟ condition, and here, no constancy effects were found. It would appear that this type of constancy in hearing precedes the across-channel grouping whose effects are so apparent in these sounds. This result is discussed in terms of the ubiquity of grouping across different levels of representation.

A three-shot improvement scheme for hard-decision based linear decorrelating detector in DS/CDMA

This paper proposes a three-shot improvement scheme for the hard-decision based method (HDM), an implementation solution for linear decorrelating detector (LDD) in asynchronous DS/CDMA systems. By taking advantage of the preceding (already reconstructed) bit and the matched filter output for the following two bits, the coupling between temporally adjacent bits (TABs), which always exists for asynchronous systems, is greatly suppressed and the performance of the original HDM is substantially improved. This new scheme requires no signaling overhead yet offers nearly the same performance as those more complicated methods. Also, it can easily accommodate the change in the number of active users in the channel, as no symbol/bit grouping is involved. Finally, the influence of synchronisation errors is investigated.

Keyphrase extraction by synonym analysis of n-grams for e-journals categorisation

Automatic keyword or keyphrase extraction is concerned with assigning keyphrases to documents based on words from within the document. Previous studies have shown that in a significant number of cases author-supplied keywords are not appropriate for the document to which they are attached. This can either be because they represent what the author believes the paper is about not what it actually is, or because they include keyphrases which are more classificatory than explanatory e.g., “University of Poppleton” instead of “Knowledge Discovery in Databases”. Thus, there is a need for a system that can generate appropriate and diverse range of keyphrases that reflect the document. This paper proposes a solution that examines the synonyms of words and phrases in the document to find the underlying themes, and presents these as appropriate keyphrases. The primary method explores taking n-grams of the source document phrases, and examining the synonyms of these, while the secondary considers grouping outputs by their synonyms. The experiments undertaken show the primary method produces good results and that the secondary method produces both good results and potential for future work.

Caste, livelihoods and livestock: an exploration of the uptake of livestock vaccination adoption among poor farmers in India

The study explores the uptake of livestock vaccination among poor farming communities in Tamil Nadu State, India by revisiting innovation diffusion theory. Overall, 601 farmers participated in the study. We found the adoption of particular vaccines was strongly influenced by socio-cultural grouping i.e. caste, rather than other factors such as income, age, education-level or gender. Adoption was also related to specific knowledge frames regarding disease causality, rather than any wider ethno-veterinary beliefs. Thus, the adoption of livestock vaccination is unlikely to improve without knowledge transfer activities, which acknowledge both social divisions and local epistemologies regarding animal health. Copyright © 2010 John Wiley & Sons, Ltd.

Temporal-envelope constancy of speech in rooms and the perceptual weighting of frequency bands

Three experiments measured constancy in speech perception, using natural-speech messages or noise-band vocoder versions of them. The eight vocoder-bands had equally log-spaced center-frequencies and the shapes of corresponding “auditory” filters. Consequently, the bands had the temporal envelopes that arise in these auditory filters when the speech is played. The “sir” or “stir” test-words were distinguished by degrees of amplitude modulation, and played in the context; “next you’ll get _ to click on.” Listeners identified test-words appropriately, even in the vocoder conditions where the speech had a “noise-like” quality. Constancy was assessed by comparing the identification of test-words with low or high levels of room reflections across conditions where the context had either a low or a high level of reflections. Constancy was obtained with both the natural and the vocoded speech, indicating that the effect arises through temporal-envelope processing. Two further experiments assessed perceptual weighting of the different bands, both in the test word and in the context. The resulting weighting functions both increase monotonically with frequency, following the spectral characteristics of the test-word’s [s]. It is suggested that these two weighting functions are similar because they both come about through the perceptual grouping of the test-word’s bands.