Enhanced nitrogen removal in constructed wetlands: Effects of dissolved oxygen and step-feeding

Four horizontal subsurface flow constructed wetlands (HSFCWs), named HSFCW1 (three-stage, without step-feeding), HSFCW2 (three-stage, with step-feeding), HSFCW3 (five-stage, without step-feeding) and HSFCW4 (five-stage, with step-feeding) were designed to investigate the effects of dissolved oxygen (DO) and step-feeding on nitrogen removal. High removal of 90.9% COD, 99.1% ammonium nitrogen and 88.1% total nitrogen (TN) were obtained simultaneously in HSFCW4 compared with HSFCW1-3. The excellent TN removal of HSFCW4 was due to artificial aeration provided sufficient DO for nitrification and the favorable anoxic environment created for denitrification. Step-feeding was a crucial factor because it provided sufficient carbon source (high COD: nitrate ratio of 14.3) for the denitrification process. Microbial activities and microbial abundance in HSFCW4 was found to be influenced by DO distribution and step-feeding, and thus improve TN removal. These results suggest that artificial aeration combined with step-feeding could achieve high nitrogen removal in HSFCWs. © 2014 Elsevier Ltd

Genomic and transcriptomic approaches towards the genetic improvement of an underutilised crops: the case of bambara groundnut

With the world population estimated to be nine billion by 2050, the need to exploit plant genetic diversity in order to increase and diversify global food supply, and minimise the over-reliance for food on a few staple crops is of the utmost importance. Bambara groundnut (Vigna subterranea (L) Verdc.), is underutilised legume indigenous to Africa, rich in carbohydrates, with reasonable amounts of protein. It is known to be drought tolerant, able to grow on marginal lands where other major crops cannot with minimal rainfall (<700 mm) and chemical inputs. Crop improvement for abiotic stress tolerance and increasing/stabilising yield have been difficult to achieve due to the complex nature of these stresses, and the genotype x environment interaction (GxE). This review paper highlights how a number of recent technologies and approaches used for major crop research, can be translated into use in research of minor crops, using bambara groundnut as an exemplar species. Using drought tolerance as a trait of interest in this crop, we will demonstrate how limitations can affect genomic approaches for understanding traits in bambara groundnut, and, how genomic and transcriptomic methodologies developed for major crops can be applied to underutilised crops for better understanding of the genetics governing important agronomic traits. Furthermore, such approaches will allow for cross species comparison between major and minor crops, exemplified by bambara groundnut leading to improved research in such crops. This will lead to a better understanding of the role of stress-responsive genes and drought adaptation in this underutilised legume. Avec la population mondiale estimée à neuf milliards de personnes à échéance 2050, il est impérieux d’exploiter la diversité génétique des plantes afin d’accroître et diversifier la production globale en aliments, mais aussi réduire la dépendance à outrance de peu d’ aliments de base pour l’alimentation humaine. Le vouandzou (Vigna subterranea (L) Verdc.), est une légumineuse indigène sous utilisée enAfrique, mais qui est riche en amidon, avec une quantité raisonnable de proteine. Il reconnu comme étant resistant à la sécheresse, il est capable de pousser et de réaliser un cycle végétatif et reproducteur parfait dans les zones marginales de basse pluiviométrie (<700 mm) où d’autres cultures majeures ne peuvent survivre. L’amélioration des cultures pour la tolérance face aux stress abiotiques et l’accroissement et la stabilization des rendements ont été difficiles à réaliser en raison de nature complexe de ces stress et l’influence de l’interaction genotype-environment (GxE). Cette revue de literature montre comment les nombreuses technologies et approaches récentes utilisées par la recherche sur les cultures majeures peuvent adaptées et utilisées dans la recherhe sur les cultures mineures, en se servant du bambara groundnut comme espèce modèle. En prenant la tolerance à la sécheresse comme caractère désiré pour cette culture, nous allons démontrer commnents les insuffisances des approches de génomique peuvent empêcher la maîtrise des caractères désirés chez le vouandzou et comment les techniques de génomique et de transcriptomique développées pour les cultures majeures peuvent être appliquées aux cultures sous utilisées afin de mieux comprendre les déterminants génétiques gouvernant les caractères agronomiques. De plus, de telles approaches permettra de comparer les cultures majeures et mineures, avec ici l’exemple du vouandzou qui permettra d’améliorer le niveau de recherche chez de telles cultures. Cela permettra de mieux comprendre le rôle des genes répondant au stress hydrique et l’adaptation à la sécheresse chez cette légumineuse sous utilisée

Effect of straw and polyacrylamide on the stability of land/water ecotone soil and the field implementation

© 2016 Elsevier B.V. Poor stability of land/water ecotone (L/WE) soil is a serious and increasing problem in the context of ecological restoration. Effective management by adding straw and polyacrylamide (PAM), i.e., SPAM, to soil may increase soil stability, including structure and fertility. Thus, it is important to explore the effects of SPAM on L/WE soil, as well as to determine the appropriate ratio of straw and PAM to achieve optimal increases. To investigate the soil properties and provide basis for ecological restoration, an indoor soil culture experiment, including nine straw and PAM combinations, was conducted. It was found that 3 g/kg straw with 1 g/kg PAM was optimal; thus, this scale was applied in engineering of Gonghu L/WE, which was turning Fishery to Lake. The survey explored changes in soil nutrients and structure, dry-sieved aggregate stability, and wet-sieved water aggregate stability under nine measures. Results indicated that the measurement of SPAM strongly affected soil properties, such as improvements in the fine sand and clay fraction, decreased coarse sand fraction and density, and enhanced content of the larger aggregates (>2 mm), organic matter (OM), availabl. e nitrogen (AN), available phosphorus (AP), and available potassium (AK). For soil nutrients, applying of Straw/PAM significantly improved the contents of OM/AN, respectively; showing an increasing trend with a dosage rate. Meanwhile, it was shown that SPAM was more effective than treating each individual component on AP and AK improvements. Regarding soil structure, application of PAM significantly increased contents of the dry-sieved aggregates and wet-sieved water-stable aggregates, especially aggregates >2 mm. Straw mulching only improved the content of dry-sieve medium size aggregates. However, when combining SPAM, the straw improved the medium particle size fraction, after which PAM converted a portion of the medium particles into >2.0 mm aggregates. Furthermore, the measure proved to be beneficial to land/water ecotone engineering

Enteric dysbiosis and fecal calprotectin expression in premature infants.

BackgroundPremature infants often develop enteric dysbiosis with a preponderance of Gammaproteobacteria, which has been related to adverse clinical outcomes. We investigated the relationship between increasing fecal Gammaproteobacteria and mucosal inflammation, measured by fecal calprotectin (FC).MethodsStool samples were collected from very-low-birth weight (VLBW) infants at ≤2, 3, and 4 weeks' postnatal age. Fecal microbiome was surveyed using polymerase chain reaction amplification of the V4 region of 16S ribosomal RNA, and FC was measured by enzyme immunoassay.ResultsWe enrolled 45 VLBW infants (gestation 27.9 ± 2.2 weeks, birth weight 1126 ± 208 g) and obtained stool samples at 9.9 ± 3, 20.7 ± 4.1, and 29.4 ± 4.9 days. FC was positively correlated with the genus Klebsiella (r = 0.207, p = 0.034) and its dominant amplicon sequence variant (r = 0.290, p = 0.003), but not with the relative abundance of total Gammaproteobacteria. Klebsiella colonized the gut in two distinct patterns: some infants started with low Klebsiella abundance and gained these bacteria over time, whereas others began with very high Klebsiella abundance.ConclusionIn premature infants, FC correlated with relative abundance of a specific pathobiont, Klebsiella, and not with that of the class Gammaproteobacteria. These findings indicate a need to define dysbiosis at genera or higher levels of resolution

High speed e-beam writing for large area photonic nanostructures-a choice of parameters

Photonic nanostructures are used for many optical systems and applications. However, some high-end applications require the use of electron-beam lithography (EBL) to generate such nanostructures. An important technological bottleneck is the exposure time of the EBL systems, which can exceed 24 hours per 1 cm2. Here, we have developed a method based on a target function to systematically increase the writing speed of EBL. As an example, we use as the target function the fidelity of the Fourier Transform spectra of nanostructures that are designed for thin film light trapping applications, and optimize the full parameter space of the lithography process. Finally, we are able to reduce the exposure time by a factor of 5.5 without loss of photonic performance. We show that the performances of the fastest written structures are identical to the original ones within experimental error. As the target function can be varied according to different purposes, the method is also applicable to guided mode resonant grating and many other areas. These findings contribute to the advancement of EBL and point towards making the technology more attractive for commercial applications

Comparison of contact patterns relevant for transmission of respiratory pathogens in Thailand and the Netherlands using respondent-driven sampling

Understanding infection dynamics of respiratory diseases requires the identification and quantification of behavioural, social and environmental factors that permit the transmission of these infections between humans. Little empirical information is available about contact patterns within real-world social networks, let alone on differences in these contact networks between populations that differ considerably on a socio-cultural level. Here we compared contact network data that were collected in the Netherlands and Thailand using a similar online respondent-driven method. By asking participants to recruit contact persons we studied network links relevant for the transmission of respiratory infections. We studied correlations between recruiter and recruited contacts to investigate mixing patterns in the observed social network components. In both countries, mixing patterns were assortative by demographic variables and random by total numbers of contacts. However, in Thailand participants reported overall more contacts which resulted in higher effective contact rates. Our findings provide new insights on numbers of contacts and mixing patterns in two different populations. These data could be used to improve parameterisation of mathematical models used to design control strategies. Although the spread of infections through populations depends on more factors, found similarities suggest that spread may be similar in the Netherlands and Thailand

Evolution favors protein mutational robustness in sufficiently large populations

BACKGROUND: An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual, but can influence the course of future evolution. Functionally similar proteins can differ substantially in their robustness to mutations and capacity to evolve new functions, but it has remained unclear whether any of these differences might be due to evolutionary selection for these properties. RESULTS: Here we use laboratory experiments to demonstrate that evolution favors protein mutational robustness if the evolving population is sufficiently large. We neutrally evolve cytochrome P450 proteins under identical selection pressures and mutation rates in populations of different sizes, and show that proteins from the larger and thus more polymorphic population tend towards higher mutational robustness. Proteins from the larger population also evolve greater stability, a biophysical property that is known to enhance both mutational robustness and evolvability. The excess mutational robustness and stability is well described by existing mathematical theories, and can be quantitatively related to the way that the proteins occupy their neutral network. CONCLUSIONS: Our work is the first experimental demonstration of the general tendency of evolution to favor mutational robustness and protein stability in highly polymorphic populations. We suggest that this phenomenon may contribute to the mutational robustness and evolvability of viruses and bacteria that exist in large populations

Statistical analysis and significance testing of serial analysis of gene expression data using a Poisson mixture model

<p>Abstract</p> <p>Background</p> <p>Serial analysis of gene expression (SAGE) is used to obtain quantitative snapshots of the transcriptome. These profiles are count-based and are assumed to follow a Binomial or Poisson distribution. However, tag counts observed across multiple libraries (for example, one or more groups of biological replicates) have additional variance that cannot be accommodated by this assumption alone. Several models have been proposed to account for this effect, all of which utilize a continuous prior distribution to explain the excess variance. Here, a Poisson mixture model, which assumes excess variability arises from sampling a mixture of distinct components, is proposed and the merits of this model are discussed and evaluated.</p> <p>Results</p> <p>The goodness of fit of the Poisson mixture model on 15 sets of biological SAGE replicates is compared to the previously proposed hierarchical gamma-Poisson (negative binomial) model, and a substantial improvement is seen. In further support of the mixture model, there is observed: 1) an increase in the number of mixture components needed to fit the expression of tags representing more than one transcript; and 2) a tendency for components to cluster libraries into the same groups. A confidence score is presented that can identify tags that are differentially expressed between groups of SAGE libraries. Several examples where this test outperforms those previously proposed are highlighted.</p> <p>Conclusion</p> <p>The Poisson mixture model performs well as a) a method to represent SAGE data from biological replicates, and b) a basis to assign significance when testing for differential expression between multiple groups of replicates. Code for the R statistical software package is included to assist investigators in applying this model to their own data.</p

Advanced Technologies for Oral Controlled Release: Cyclodextrins for oral controlled release

Cyclodextrins (CDs) are used in oral pharmaceutical formulations, by means of inclusion complexes formation, with the following advantages for the drugs: (1) solubility, dissolution rate, stability and bioavailability enhancement; (2) to modify the drug release site and/or time profile; and (3) to reduce or prevent gastrointestinal side effects and unpleasant smell or taste, to prevent drug-drug or drug-additive interactions, or even to convert oil and liquid drugs into microcrystalline or amorphous powders. A more recent trend focuses on the use of CDs as nanocarriers, a strategy that aims to design versatile delivery systems that can encapsulate drugs with better physicochemical properties for oral delivery. Thus, the aim of this work was to review the applications of the CDs and their hydrophilic derivatives on the solubility enhancement of poorly water soluble drugs in order to increase their dissolution rate and get immediate release, as well as their ability to control (to prolong or to delay) the release of drugs from solid dosage forms, either as complexes with the hydrophilic (e.g. as osmotic pumps) and/ or hydrophobic CDs. New controlled delivery systems based on nanotechonology carriers (nanoparticles and conjugates) have also been reviewed

Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome

Transposable elements (TEs) have no longer been totally considered as “junk DNA” for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C(chromosomeconformation capture) have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC: r=0.9, P<2.2×1016; IMR90 fibroblasts: r = 0.94, P < 2.2 × 1016) and also have a significant positive correlation withsomeremote functional DNA elements like enhancers and promoters (Enhancer: hESC: r=0.997, P=2.3×10−4; IMR90: r=0.934, P=2×10−2; Promoter: hESC: r = 0.995, P = 3.8 × 10−4; IMR90: r = 0.996, P = 3.2 × 10−4). Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes