Group-wise ANOVA simultaneous component analysis for designed <Emphasis Type="Italic">omics</Emphasis> experiments

Introduction

Modern omics experiments pertain not only to the measurement of many variables but also follow complex experimental designs where many factors are manipulated at the same time. This data can be conveniently analyzed using multivariate tools like ANOVA-simultaneous component analysis (ASCA) which allows interpretation of the variation induced by the different factors in a principal component analysis fashion. However, while in general only a subset of the measured variables may be related to the problem studied, all variables contribute to the final model and this may hamper interpretation.

Objectives

We introduce here a sparse implementation of ASCA termed group-wise ANOVA-simultaneous component analysis (GASCA) with the aim of obtaining models that are easier to interpret.

Methods

GASCA is based on the concept of group-wise sparsity introduced in group-wise principal components analysis where structure to impose sparsity is defined in terms of groups of correlated variables found in the correlation matrices calculated from the effect matrices.

Results

The GASCA model, containing only selected subsets of the original variables, is easier to interpret and describes relevant biological processes.

Conclusions

GASCA is applicable to any kind of omics data obtained through designed experiments such as, but not limited to, metabolomic, proteomic and gene expression data.

     

Life cycle assessment of chitosan production in India and Europe

Purpose

The aim of this article is to present the first life cycle assessment of chitosan production based on data from two real producers located in India and Europe. The goal of the life cycle assessment (LCA) was to understand the main hot spots in the two supply chains, which are substantially different in terms of raw materials and production locations.

Methods

The LCA is based on consequential modelling principles, whereby allocation is avoided by means of substitution, and market mixes include only flexible, i.e. non-constrained suppliers. The product system is cradle to gate and includes the production of raw materials, namely waste shells from snow crab and shrimp in Canada and India, respectively, the processing of these in China and India and the manufacture of chitosan in Europe and India. Primary data for chitin and chitosan production were obtained from the actual producers, whereas raw material acquisition as well as waste management activities were based on literature sources. The effects of indirect land use change (iLUC) were also included. Impact assessment was carried out at midpoint level by means of the recommended methods in the International Life Cycle Data (ILCD) handbook.

Results and discussion

In the Indian supply chain, the production of chemicals (HCl and NaOH) appears as an important hot spot. The use of shrimp shells as raw material affects the market for animal feed, resulting in a credit in many impact indicators, especially in water use. The use of protein waste as fertilizer is also an important source of greenhouse-gas and ammonia emissions. In the European supply chain, energy use is the key driver for environmental impacts, namely heat production based on coal in China and electricity production in China and Europe. The use of crab shells as raw material avoids the composting process they would be otherwise subject to, leading to a saving in composting emissions, especially ammonia. In the Indian supply chain, the effect of iLUC is relevant, whereas in the European one, it is negligible.

Conclusions

Even though we assessed two products from the same family, the results show that they have very different environmental profiles, reflecting their substantially different supply chains in terms of raw material (shrimp shells vs. crab shells), production locations (locally produced vs. a global supply chain involving three continents) and the different applications (general-purpose chitosan vs. chitosan for the medical sector).

     

Life cycle inventory modeling of phosphorus substitution,losses and crop uptake after land application of organic waste products

Purpose

Life cycle assessments (LCAs) that attempt to provide advice on treatment options for phosphorus (P) containing organic waste products encounter problems related to the quantification of mineral P fertilizer substitution, P loss and crop P uptake after land application. The purpose of this study was to develop a relatively easy to use life cycle inventory model, known as PLCI, that could be used to estimate these values.

Methods

A life cycle inventory model for P was developed, which estimates the effect of an application of organic waste followed by ordinary fertilizer management in the modeling period. This was compared with a simulation without the initial waste application. The difference in mineral P fertilizer application (substitution), P loss and crop P uptake was then calculated and expressed as a proportion of the amount of waste applied. As an example, the effect of an initial application of mineral fertilizer, sewage sludge and ash on two farm types was simulated. These results were applied in an LCA case study of different sewage sludge treatment options.

Results and discussion

Farm type influenced the P fertilizer substitution, loss and crop uptake factors. The application on an arable farm showed a substitution of 28 to 31%, relatively low P loss and a large spread in crop P uptake for the different P sources, compared with the pig farm. Application on a pig farm showed no mineral P substitution. For substitution, mineral fertilizer outperformed waste product fertilizer with a short modeling period, due to higher immediate P availability, which was not the case with a long period. The LCA case study showed that the P substitution factor had an influence on the environmental impact categories climate change and depletion of reserve-based abiotic resources while the P loss factor influenced freshwater eutrophication. Application of the P loss and substitution factors generated from the PLCI model resulted in higher environmental burdens and lower savings than using conventional factors.

Conclusions

The soil P status mainly affected P substitution and loss, with the fertilizer type only having a small influence when soils had a low P status. The PLCI model can facilitate more coherent and rigorous estimates of P substitution and loss to be used in LCA studies involving application of waste products on agricultural land. This is important since P substitution and loss can have an important influence on impact categories, such as freshwater eutrophication and resource depletion.

     

Graphene Doping Induced Tunability of Nanoparticles Plasmonic Resonances

Interest in graphene has been widely increasing since its discovery in 2004. Research on graphene for plasmonic applications has also boomed due to the high potential of these systems. In this article, we discuss the possible interaction between metallic NPs and graphene monolayer. We show how the contact between metallic NPs and graphene results in graphene doping. More importantly, we experimentally put into evidence the possible modulation of the plasmonic resonance of NPs by graphene doping. Understanding and evidencing this interaction is highly important both from a fundamental point of view and for specific applications such as active plasmonic devices.

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Enhanced production of pharmaceutically important isoflavones from hairy root rhizoclones of <Emphasis Type="Italic">Trifolium pratense</Emphasis> L.

These studies report the development of an efficient technique for large-scale cultivation of fast-growing hairy root culture systems for production of bioactive isoflavones. Trifolium pratense L. is an important source of pharmaceutically important isoflavones with immense health care applications. Trifolium pratense was transformed using different strains of Agrobacterium rhizogenes for hairy root induction and establishment of hairy root rhizoclones. Selected fast-growing rhizoclones of T. pratense were evaluated for their growth and isoflavone production. This study is the first report of stable production of isoflavones through successive culture passages from transformed hairy-root rhizoclones of T. pratense. One of the fast-growing hairy-root rhizoclones 2364A displayed significantly higher accumulation of all four pharmaceutically important isoflavones, 8.56 mg (gdw)^?1 of daidzein, 2.45 mg (gdw)^?1 of genistein, 15.23 mg (gdw)^?1 of formononetin, and 1.10 mg (gdw)^?1 of biochanin A, compared to other rhizoclones.     

Development of an <Emphasis Type="Italic">Agrobacterium</Emphasis>-mediated transformation method for <Emphasis Type="Italic">Taxus</Emphasis> suspension cultures

The FDA-approved anti-cancer compound paclitaxel is currently produced commercially by Taxus plant cell suspension cultures. One major limitation to the use of plant cell culture as a production platform is the low and variable product yields. Therefore, methods to increase and stabilize paclitaxel production are necessary to ensure product security, especially as the demand for paclitaxel continues to rise. Although a stable transformation method for Taxus suspension cultures has been developed, stable transformant yields are low (around 1% of experiments) and the method does not translate to the Taxus cuspidata Siebold and Zucc. and Taxus canadensis Marshall cell lines utilized in this study. Therefore, a new method for Agrobacterium-mediated transformation of Taxus callus and suspension cultures was developed through identification of the optimal Agrobacterium strain, inclusion of an anti-necrotic cocktail (silver nitrate, cysteine, and ascorbic acid) and increased recovery time for cells after cocultivation, the time following infection with Agrobacterium tumefaciens. Application of the increased recovery time to transformation of T. cuspidata line PO93XC resulted in 200 calluses staining positive for GUS. Additionally, two transgenic lines have been maintained with stable transgene expression for over 5 yr. This method represents an improvement over existing transformation methods for Taxus cultures and can be applied for future metabolic engineering efforts.     

Efficient direct plant regeneration from immature leaf roll explants of sugarcane (<Emphasis Type="Italic">Saccharum officinarum</Emphasis> L.) using polyamines and assessment of genetic fidelity by SCoT markers

A rapid and efficient method for in vitro direct plant regeneration from immature leaf roll explants of Saccharum officinarum L. (sugarcane) cv. Co 86032 was developed by the application of exogenous polyamines (PA). The effect of explant source from apical meristems and pre-culture of explants in the dark on shoot regeneration was studied. Adventitious shoot regeneration occurred on the proximal regions of immature leaf roll explants when pre-incubated in the dark for 2 wk and the regeneration response was decreased from the middle to distal end. A higher number of direct shoots (130 primary shoots explant^?1) and multiple shoots (657 secondary shoots explant^?1), were obtained with a combination of spermidine (103.27 μM), spermine (49.42 μM), and putrescine (31.04 μM) along with plant growth regulators. Shoot induction was increased up to twofold and multiplication was increased up to threefold in the medium supplemented with PA. Profuse rooting was observed in putrescine (93.12 μM), spermidine (68.84 μM), and spermine (24.71 μM), with mean number of 57 roots. A twofold increase in the number of roots was observed in medium supplemented with PA with respect to control cultures, which facilitated the successful transplantation and acclimatization process of in vitro propagated sugarcane plants. Histology and scanning electron microscopy analyses supported adventitious direct shoot regeneration from immature leaf roll explants. The genetic stability of in vitro regenerated plants was confirmed using start codon targeted polymorphism marker system.     

Interaction of boron and aluminum on the physiological characteristics of rape (<Emphasis Type="Italic">Brassica napus</Emphasis> L.) seedlings

It has been reported that aluminum (Al) toxicity is a major limiting factor for plant growth and production on acidic soils. Boron (B) is indispensable micronutrient for normal growth of higher plants, and its addition could alleviate Al toxicity. The rape seedlings were grown under three B (0.25, 25 and 500 μM) and two Al concentrations [0 (?Al) and 100 μM (+Al) as AlCl₃·6H₂O]. The results indicated that Al stress severely hampered root elongation and root activity at 0.25 μM B while the normal (25 μM) and excess (500 μM) B improved the biomass of rape seedlings under Al exposure. Additionally, normal and excess B treatment reduced accumulation of Al in the roots and leaves under Al toxicity, which was also confirmed by hematoxylin with light staining. This indicates that both normal and excess B could alleviate Al toxicity. Furthermore, it also decreased the contents of malondialdehyde and soluble protein under Al toxicity. Likewise, superoxide dismutase activity (SOD) improved by 97.82 and 131.96% in the roots, and 168 and 119.88% in the leaves at 25 and 500 µM B, respectively, while the peroxidase and catalase activities dropped as a result of Al stress. The study results demonstrated that appropriate B application is necessary to avoid the harmful consequences of Al toxicity in rape seedlings.