Comparative in situ analyses of cell wall matrix polysaccharide dynamics in developing rice and wheat grain

Cell wall polysaccharides of wheat and rice endosperm are an important source of dietary fibre. Monoclonal antibodies specific to cell wall polysaccharides were used to determine polysaccharide dynamics during the development of both wheat and rice grain. Wheat and rice grain present near synchronous developmental processes and significantly different endosperm cell wall compositions, allowing the localisation of these polysaccharides to be related to developmental changes. Arabinoxylan (AX) and mixed-linkage glucan (MLG) have analogous cellular locations in both species, with deposition of AX and MLG coinciding with the start of grain filling. A glucuronoxylan (GUX) epitope was detected in rice, but not wheat endosperm cell walls. Callose has been reported to be associated with the formation of cell wall outgrowths during endosperm cellularisation and xyloglucan is here shown to be a component of these anticlinal extensions, occurring transiently in both species. Pectic homogalacturonan (HG) was abundant in cell walls of maternal tissues of wheat and rice grain, but only detected in endosperm cell walls of rice in an unesterified HG form. A rhamnogalacturonan-I (RG-I) backbone epitope was observed to be temporally regulated in both species, detected in endosperm cell walls from 12 DAA in rice and 20 DAA in wheat grain. Detection of the LM5 galactan epitope showed a clear distinction between wheat and rice, being detected at the earliest stages of development in rice endosperm cell walls, but not detected in wheat endosperm cell walls, only in maternal tissues. In contrast, the LM6 arabinan epitope was detected in both species around 8 DAA and was transient in wheat grain, but persisted in rice until maturity.

Detecting regular sound changes in linguistics as events of concerted evolution

Background: Concerted evolution is normally used to describe parallel changes at different sites in a genome, but it is also observed in languages where a specific phoneme changes to the same other phoneme in many words in the lexicon—a phenomenon known as regular sound change. We develop a general statistical model that can detect concerted changes in aligned sequence data and apply it to study regular sound changes in the Turkic language family. Results: Linguistic evolution, unlike the genetic substitutional process, is dominated by events of concerted evolutionary change. Our model identified more than 70 historical events of regular sound change that occurred throughout the evolution of the Turkic language family, while simultaneously inferring a dated phylogenetic tree. Including regular sound changes yielded an approximately 4-fold improvement in the characterization of linguistic change over a simpler model of sporadic change, improved phylogenetic inference, and returned more reliable and plausible dates for events on the phylogenies. The historical timings of the concerted changes closely follow a Poisson process model, and the sound transition networks derived from our model mirror linguistic expectations. Conclusions: We demonstrate that a model with no prior knowledge of complex concerted or regular changes can nevertheless infer the historical timings and genealogical placements of events of concerted change from the signals left in contemporary data. Our model can be applied wherever discrete elements—such as genes, words, cultural trends, technologies, or morphological traits—can change in parallel within an organism or other evolving group.

Genome-wide mapping of 5-hydroxymethylcytosine in three rice cultivars reveals its preferential localization in transcriptionally silent transposable element genes

5-Hydroxymethylcytosine (5hmC), a modified form of cytosine that is considered the sixth nucleobase in DNA, has been detected in mammals and is believed to play an important role in gene regulation. In this study, 5hmC modification was detected in rice by employing a dot-blot assay, and its levels was further quantified in DNA from different rice tissues using liquid chromatography-multistage mass spectrometry (LC-MS/MS/MS). The results showed large intertissue variation in 5hmC levels. The genome-wide profiles of 5hmC modification in three different rice cultivars were also obtained using a sensitive chemical labelling followed by a next-generation sequencing method. Thousands of 5hmC peaks were identified, and a comparison of the distributions of 5hmC among different rice cultivars revealed the specificity and conservation of 5hmC modification. The identified 5hmC peaks were significantly enriched in heterochromatin regions,and mainly located in transposable element (TE) genes, especially around retrotransposons. The correlation analysis of 5hmC and gene expression data revealed a close association between 5hmC and silent TEs. These findings provide a resource for plant DNA 5hmC epigenetic studies and expand our knowledge of 5hmC modification.

The accuracy of HADS and GHQ-12 in detecting psychiatric morbidity in breast cancer patients

Objective: Psychological problems should be identified in breast cancer patients proactively if doctors and nurses are to help them cope with the challenges imposed by their illness. Screening is one possible way to identify emotional problems proactively. Self-report questionnaires can be useful alternatives to carrying out psychiatric interviews during screening, because interviewing a large number of patients can be impractical due to limited resources. Two such measures are the Hospital Anxiety and Depression Scale (HADS) and the General Health Questionnaire-12 (GHQ-12). Method: The present study aimed to compare the performance of the GHQ-12, and the HADS Unitary Scale and its subscales to that of the Schedule for Affective Disorders and Schizophrenia (SADS) in identifying patients with affective disorders, including DSM major depression and generalized anxiety disorder. The sample consisted of 296 female breast cancer patients who underwent surgery for breast cancer a year previously. Results: A small number of patients (11%) were identified as having DSM major depression or generalized anxiety disorder based on SADS score. The findings indicate that the optimal thresholds in detecting generalized anxiety disorder and DSM major depression with the HADS anxiety and depression subscales were ≥ 8 and ≥ 7, with 93.3% and 77.3% sensitivity, respectively, and 77.9% and 87.1% specificity, respectively. They also had a 21% and 36% positive predictive value, respectively. Using the HADS Unitary Scale the optimal threshold for detecting affective disorders was ≥ 12, with 88.9% sensitivity, 80.7% specificity, and a 35% positive predictive value. In detecting affective disorders, the optimal threshold on the GHQ-12 was ≥ 2, with 77.8% sensitivity and 70.2% specificity. This scale also had a 24% positive predictive value. In detecting generalized anxiety disorder and DSM major depression, the optimal thresholds on the GHQ-12 were ≥ 2 and ≥ 4 with 73.3% and 77.3% sensitivity, respectively, and 67.5% and 82% specificity, respectively. The scale also had 12% and 29% positive predictive values, respectively. Conclusion: The HADS Unitary Scale and its subscales were effective in identifying affective disorders. They can be used as screening measures in breast cancer patients. The GHQ-12 was less accurate in detecting affective disorders than the HADS, but it can also be used as a screening instrument to detect affective disorders, generalized anxiety disorder, and DSM major depression.

Detecting defects in UK new-build housing: a learning perspective

House builders play a key role in controlling the quality of new homes in the UK. The UK house building sector is, however, currently facing pressures to expand supply as well as conform to tougher low carbon planning and Building Regulation requirements; primarily in the areas of sustainability. There is growing evidence that the pressure the UK house building industry is currently under may be eroding build quality and causing an increase in defects. It is found that the prevailing defect literature is limited to the causes, pathology and statistical analysis of defects (and failures). The literature does not extend to examine how house builders individually and collectively, in practice, collect and learn from defects experience in order to reduce the prevalence of defects in future homes. The theoretical lens for the research is organisational learning. This paper contributes to our understanding of organisational learning in construction through a synthesis of current literature. Further, a suitable organisational learning model is adopted. The paper concludes by reporting the research design of an ongoing collaborative action research project with the National House Building Council (NHBC), focused on developing a better understanding of house builders’ localised defects analysis procedures and learning processes.

Evaluation of methods of detecting cell reactive oxygen species production for drug screening and cell cycle studies

Intracellular reactive oxygen species (ROS) production is essential to normal cell function. However, excessive ROS production causes oxidative damage and cell death. Many pharmacological compounds exert their effects on cell cycle progression by changing intracellular redox state and in many cases cause oxidative damage leading to drug cytotoxicity. Appropriate measurement of intracellular ROS levels during cell cycle progression is therefore crucial in understanding redox-regulation of cell function and drug toxicity and for the development of new drugs. However, due to the extremely short half-life of ROS, measuring the changes in intracellular ROS levels during a particular phase of cell cycle for drug intervention can be challenging. In this article, we have provided updated information on the rationale, the applications, the advantages and limitations of common methods for screening drug effects on intracellular ROS production linked to cell cycle study. Our aim is to facilitate biomedical scientists and researchers in the pharmaceutical industry in choosing or developing specific experimental regimens to suit their research needs.

Detecting abnormal and collusive bids in capped tendering

Recent developments in the area of Bid Tender Forecasting have enabled bidders to implement new types of easy-to-use tools for increasing their chances of winning contracts. Although these new tools (such as iso-Score Curve Graphs, Scoring Probability Graphs, and Position Probability Graphs) are designed for bidders in capped tendering (tenders with an upper price limit), some of their principles can also be applied by a Contracting Authority to detect which bidders do not follow a standard pattern, that is, their bids are extremely high or low. Since a collusive bid generally needs to be sufficiently high or low to make an impact on the bid distribution, any person in charge of supervising capped tenders can be alerted to any bidder that might be involved in a cartel after identifying the same abnormal behavior in a series of tenders through simple calculations and a new type of graph.

”Potato seeking rice”: language, culture, and identity in gay personal ads in Hong Kong

This paper examines the relationship between language, culture, and identity in a corpus of gay personal ads collected from two publications in Hong Kong in the three years before the 1997 transition of sovereignty. Gay personal ads are seen äs an "island of discourse," whose marginal nature is reflected in the use of language and in turn reflects issues of marginalization in the larger social context. Using Fairclough's (1992, 1993) three- dimensional model for critical discourse analysis, an attempt is made to uncover the relationship between text structure and issues ofpower/ideology in the society that produces the texts. On the level of text, it was found that structural components, particularly the degree of grammatical elaboration, differ according to the stated race or cultural background of the authors and their targets. On the level of discourse practice, authors were found to appropriate a variety of "voices"from the larger culture arena, the use of which amplifies or limits the participation of particular classes of individuals. Finally, on the level of social practice, the ads were found to reflect and re-create both the racial stereotypes and heterosexist ideology found in the dominant culture.

The effect of simulated flooding post-anthesis on pre-harvest sprouting and subsequent seed longevity in contrasting rice cultivars

Unpredictable flooding is a major constraint to rice production. It can occur at any growth stage. The effect of simulated flooding post-anthesis on yield and subsequent seed quality of pot-grown rice (Oryza sativa L.) plants was investigated in glasshouses and controlled-environment growth cabinets. Submergence post-anthesis (9-40 DAA) for 3 or 5 days reduced seed weight of japonica rice cv. Gleva, with considerable pre-harvest sprouting (up to 53%). The latter was greater the later in seed development and maturation that flooding occurred. Sprouted seed had poor ability to survive desiccation or germinate normally upon rehydration, whereas the effects of flooding on the subsequent air-dry seed storage longevity (p50) of the non-sprouted seed fraction was negligible. The indica rice cvs IR64 and IR64Sub1 (introgression of submergence tolerance gene Submergence1A-1) were both far more tolerant to flooding post-anthesis than cv. Gleva: four days’ submergence of these two near-isogenic cultivars at 10-40 DAA resulted less than 1% sprouted seeds. The presence of the Sub1A-1 allele in cv. IR64Sub1 was verified by gel electrophoresis and DNA sequencing. It had no harmful effect on loss in seed viability during storage compared with IR64 in both control and flooded environments. Moreover, the germinability and changes in dormancy during seed development and maturation were very similar to IR64. The efficiency of using chemical spray to increase seed dormancy was investigated in the pre-harvest sprouting susceptible rice cv. Gleva. Foliar application of molybdenum at 100 mg L-1 reduced sprouted seeds by 15-21% following 4 days’ submergence at 20-30 DAA. Analyses confirmed that the treatment did result in molybdenum uptake by the plants, and also tended to increase seed abscisic acid concentration. The latter was reduced by submergence and declined exponentially during grain ripening. The selection of submergence-tolerant varieties was more successful than application of molybdenum in reducing pre-harvest sprouting.

Detecting defects in the UK new-build housing sector: a learning perspective

Rapid growth in the production of new homes in the UK is putting build quality under pressure as evidenced by an increase in the number of defects. Housing associations (HAs) contribute approximately 20% of the UK’s new housing supply. HAs are currently experiencing central government funding cuts and rental revenue reductions. As part of HAs’ quest to ramp up supply despite tight budget conditions, they are reviewing how they learn from defects. Learning from defects is argued as a means of reducing the persistent defect problem within the UK housebuilding industry, yet how HAs learn from defects is under-researched. The aim of this research is to better understand how HAs, in practice, learn from past defects to reduce the prevalence of defects in future new homes. The theoretical lens for this research is organizational learning. The results drawn from 12 HA case studies indicate that effective organizational learning has the potential to reduce defects within the housing sector. The results further identify that HAs are restricting their learning to focus primarily on reducing defects through product and system adaptations. Focusing on product and system adaptations alone suppresses HAs’ abilities to reduce defects in the future.

Response surface methodology applied to the analysis of rice bran oil extraction process with ethanol

P>Vegetable oils can be extracted using ethanol as solvent. The main goal of this work was to evaluate the ethanol performance on the extraction process of rice bran oil. The influence of process variables, solvent hydration and temperature was evaluated using the response surface methodology, aiming to maximise the soluble substances and gamma-oryzanol transfer and minimise the free fatty acids extraction and the liquid content in the underflow solid. It can be noted that oil solubility in ethanol was highly affected by the water content. The free fatty acids extraction is improved by increasing the moisture content in the solvent. Regarding the gamma-oryzanol, it can be observed that its extraction is affected by temperature when low level of water is added to ethanol. On the other hand, the influence of temperature is minimised with high levels of water in the ethanol.

EVALUATION OF THE INTERACTION OF NUTRIENTS IN THE ZINC APPLICATION IN SEEDS OF THE RICE

The efficient fertilizer use contend micronutrient depends, also, of the interactions that occur with some nutrients. The objective was to study the interaction of zinc with the excessively nutrient ones in function of the application of different doses and sources of Zn saw seed in the culture of the rice. The experiment was carried through in conditions of vegetation house, in the FCAV/Unesp. The used experimental delineation was entirely cazualized, with three repetitions. The treatments had been five doses: 0; 1,0; 2,0; 4,0 and 8,0 g of Zn for kg of seed; e two zinc sources; sulphate of zinc (22% of Zn) and zinc oxide (50% of Zn). The experimental unit was a translucent polyethylene tray, filled with 5 washed thick sand, where 50 seeds of rice had been sown (to var. Caiapo). To the 30 days after the sowing, effected the cut of the plants, separating them in aerial part and roots. From the results of the dry substance and text of nutrients of the aerial part and root of the rice, the accumulation of the nutrients in the respective agencies of the plants was calculated. Becoming fullfilled it variance analysis and the when necessary unfoldings. It had effect of the interactions in distinguishing way between root and aerial part of rice, with regard to the doses and sources.

Use of PCR for detecting Aspergillus flavus in maize treated by gamma radiation process

The aim of this study was to verify the effects of gamma radiation process on the fungal DNA and the application of PCR in the detection of Aspergillus flavus in irradiated maize grains. The samples were inoculated with a toxigenic strain and incubated under controlled conditions of relative humidity, water activity, and temperature for 15 days. After incubation, the samples were treated with gamma radiation with doses of 5 and 10 kGy and individually analyzed. The use of PCR technique showed the presence of DNA bands of Aspergillus flavus in all irradiated samples that showed no fungal growth in agar medium.

Beyond the average: Detecting global singular nodes from local features in complex networks

Deviations from the average can provide valuable insights about the organization of natural systems. The present article extends this important principle to the systematic identification and analysis of singular motifs in complex networks. Six measurements quantifying different and complementary features of the connectivity around each node of a network were calculated, and multivariate statistical methods applied to identify singular nodes. The potential of the presented concepts and methodology was illustrated with respect to different types of complex real-world networks, namely the US air transportation network, the protein-protein interactions of the yeast Saccharomyces cerevisiae and the Roget thesaurus networks. The obtained singular motifs possessed unique functional roles in the networks. Three classic theoretical network models were also investigated, with the Barabasi-Albert model resulting in singular motifs corresponding to hubs, confirming the potential of the approach. Interestingly, the number of different types of singular node motifs as well as the number of their instances were found to be considerably higher in the real-world networks than in any of the benchmark networks. Copyright (C) EPLA, 2009