Cold chain and virus‐free chloroplast‐made booster vaccine to confer immunity against different poliovirus serotypes

The WHO recommends complete withdrawal of oral polio vaccine (OPV) type 2 by April 2016 globally and replacing with at least one dose of inactivated poliovirus vaccine (IPV). However, high‐cost, limited supply of IPV, persistent circulating vaccine‐derived polioviruses transmission and need for subsequent boosters remain unresolved. To meet this critical need, a novel strategy of a low‐cost cold chain‐free plant‐made viral protein 1 (VP1) subunit oral booster vaccine after single IPV dose is reported. Codon optimization of the VP1 gene enhanced expression by 50‐fold in chloroplasts. Oral boosting of VP1 expressed in plant cells with plant‐derived adjuvants after single priming with IPV significantly increased VP1‐IgG1 and VP1‐IgA titres when compared to lower IgG1 or negligible IgA titres with IPV injections. IgA plays a pivotal role in polio eradication because of its transmission through contaminated water or sewer systems. Neutralizing antibody titres (~3.17–10.17 log₂ titre) and seropositivity (70–90%) against all three poliovirus Sabin serotypes were observed with two doses of IPV and plant‐cell oral boosters but single dose of IPV resulted in poor neutralization. Lyophilized plant cells expressing VP1 stored at ambient temperature maintained efficacy and preserved antigen folding/assembly indefinitely, thereby eliminating cold chain currently required for all vaccines. Replacement of OPV with this booster vaccine and the next steps in clinical translation of FDA‐approved antigens and adjuvants are discussed.     

Classification of Chinese herbs based on the cluster analysis of delayed luminescence

Traditional Chinese material medica are an important component of the Chinese pharmacopeia. According to the traditional Chinese medicinal concept, Chinese herbal medicines are classified into different categories based on their therapeutic effects, however, the bioactive principles cannot be solely explained by chemical analysis. The aim of this study is to classify different Chinese herbs based on their therapeutic effects by using delayed luminescence (DL). The DL of 56 Chinese herbs was measured using an ultra‐sensitive luminescence detection system. The different DL parameters were used to classify Chinese herbs according to a hierarchical cluster analysis. The samples were divided into two groups based on their DL kinetic parameters. Interestingly, the DL classification results were quite consistent with classification according to the Chinese medicinal concepts of ‘cold’ and ‘heat’ properties. In this paper, we show for the first time that by using DL technology, it is possible to classify Chinese herbs according to the Chinese medicinal concept and it may even be possible to predict their therapeutic properties. Copyright © 2015 John Wiley & Sons, Ltd.     

基于过氧化物同工酶分析月季种质资源的亲缘关系及杂种真实性

为了提高种质资源利用率,加速月季育种进程,对27份月季种质及3个杂交组合的8个杂交后代,采用过氧化物酶(POD)同工酶方法分析其亲缘关系并进行杂种真实性鉴定。结果表明:月季种质采用POD同工酶分析具有一定的可行性。酶谱分析中,在相对迁移率为0.264~0.858的位点处共获得7条酶带,其中共有酶带3条,特征酶带4条,表明不同月季种质间遗传多样性丰富,但又存在一定同源性。基于酶带特征进行聚类分析,在相似系数为0.57处,可将27份供试材料分为3个大组。合柱组与月季组材料聚在一个大组中,两个组在形态上的相似性再次得到确认。金樱子与硕苞蔷薇分别聚在两个不同的组中,表明二者之间的亲缘关系较远。供试的古老月季品种被聚在两个不同的大组中,与野生种聚成的一组呈平行关系,表明古老月季在起源上的差异较大,可利用其作为杂交亲本进行广泛杂交以选育具有丰富遗传多样性的杂交后代。根据有无父本特征酶带对杂种后代真实性进行鉴定,初步确定2个杂交组合的6个杂交后代中5个为真实杂种,1个为自交种。该研究结果为进一步开展月季遗传育种奠定了基础。     

Simulation of 3D tumor cell growth using nonlinear finite element method

We propose a novel parallel computing framework for a nonlinear finite element method (FEM)-based cell model and apply it to simulate avascular tumor growth. We derive computation formulas to simplify the simulation and design the basic algorithms. With the increment of the proliferation generations of tumor cells, the FEM elements may become larger and more distorted. Then, we describe a remesh and refinement processing of the distorted or over large finite elements and the parallel implementation based on Message Passing Interface to improve the accuracy and efficiency of the simulation. We demonstrate the feasibility and effectiveness of the FEM model and the parallelization methods in simulations of early tumor growth.     

The role of fish-poultry integration on fish growth performance,yields and economic benefits among smallholder farmers in sub-Saharan Africa,Tanzania

Aquaculture practices from sub-Saharan Africa are characterised by low production, owing to improper technology. Production can be increased through integrating fish farming with other existing on-farm activities, particularly livestock husbandry. We assessed the role of fish-poultry integration on all male Nile tilapia, Oreochromis niloticus growth performance, yields and economic benefits among smallholder farmers in sub-Saharan Africa, Tanzania. The study also compared phytoplankton species composition, abundance and biomass between the fish-poultry integration and non-integrated system. After 180 days of the experiment, all male O. niloticus cultured under fish-poultry integration exhibited significantly higher growth rates than those in the non-integrated system (p < 0.05). Gross fish yield (GFY), net fish yield (NFY) and net annual yields (NAY) obtained from fish-poultry integration were significantly higher than those from non-integrated system (p < 0.05). Partial enterprise budget analysis revealed that fish-poultry integration was more profitable than the non-integrated system. Moreover, fish-poultry integrated system produced significantly higher phytoplankton abundance and biomass than those from the non-integrated system. Results demonstrate that rural smallholder farmers can achieve higher growth rate, farm net yields and income by integrating all male O. niloticus with other on-farm activities than practising a stand-alone fish culture system.     

Health status of the lizard Podarcis siculus (Rafinesque-Schmaltz, 1810) subject to different anthropogenic pressures

The terrestrial lizard Podarcis siculus is the most abundant reptile in Italy, where is considered a ubiquitous species. This lizard is widely distributed from the islands to the Apennines, from cultivated fields to anthropized areas such as gardens and city parks. For this reason, these animals are exposed to extensive physical and chemical stresses, as well as to the possibility of coming into contact with industrial pollutants and substances used in agricultural practices. Here, we review the health status of lizard specimens inhabiting natural non-anthropized areas and fields devoted to organic farming, considering the condition of (1) liver, representing the main detoxifying organ, directly influenced by feeding, and (2) gonads, essential for reproduction and, therefore, for the survival of the species. The morphological and biomolecular condition of these organs was then compared with those obtained from lizard specimens experimentally treated with nonylphenol, a co-formulant of many insecticides and plant protection products widely used in conventional farming, known to have harmful estrogenic effects. Taken together, data demonstrate that lizards inhabiting manured soil are in good health status and show a regular morphology of liver, testis, and ovary. Animals are found to be less exposed to the toxic heavy metals cadmium and lead if compared with specimens collected in areas not devoted to agriculture, but probably more exposed to vehicular traffic. However, manure, as well as nonylphenol, exerts a xeno-estrogenic effect, particularly evident in male specimens, more sensitive to estrogenic contamination.     

Water footprint assessment of sheep farming systems based on farm survey data

Water scarcity is among the main challenges making vulnerable the livestock farming systems in drylands. The water footprint (WF) indicator was proposed as a metric to measure the impacts of livestock production on freshwater resources. Therefore, this study aimed to assess water use in five different Tunisian sheep production systems using the Water Footprint Network methodology. The primary data were obtained from 1050 sheep farms located in 13 Tunisian provinces. A multivariate analysis was performed to characterize the different farming systems. A validation step of the WF modeled values of sheep meat was conducted in 12 sheep farms belonging to two different farming systems. This was done through year-round monitoring of on-farm practices using water metres and recording equipment’s taking into account the direct and indirect water use. The typology analysis came up with five sheep farming systems that are the mixed sheep-cereal (MSC), the agro-sylvo-pastoral (ASP), the agro-pastoral (AP), the extensive agro-pastoral (EAP) and the mixed sheep-olive tree farming systems. The WF of sheep meat produced under the target farming systems ranged from 8654 to 13 056 l/kg live weight. The evaluation of WF of five different sheep production systems figured out that sheep raised under the EAP farming system had the greatest WF per ton of live animal. However, the ASP farming system exhibited the lowest WF. Water used to grow feedstuffs for sheep production accounts for 98% of the total WF of sheep. The green WF accounts for more than 92% of the total WF in all farming systems. Results of monitoring water use at farm scale show that the modeled values of WF are overestimated by an average of 23.3% and 24.1% for the selected farms assigned to the MSC and AP farming systems, respectively. Water use for sheep production is high in most of the Tunisian farms. Therefore, the general assumption that ‘meat production is a driver of water scarcity’ is supported and should be considered as an important focal point in agricultural and water policies. Particular attention should be given to forage crops with low WFs and high contribution to dry matter to provide ration with low WF. The efficient use of green water along the meat value chain is essential to minimize the depletion of blue water resources and to reduce the economic dependency on virtual water through the import of feedstuffs.     

Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning

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Spatiotemporal evaluation of trace elements in river water using multivariate methods

The multivariate statistical methods (cluster analysis and discriminant analysis [DA]) are used to evaluate the quality of water spatiotemporally in the Brahmani River basin. A total of 15 water quality indicators (pH, Chloramines, Sodium, Sulfate, Phosphate, Potassium, Boron, Fluoride, Cadmium, Copper, Lead, Nickel, Zinc, Iron, and Total Chromium) are collected for 13 years in two seasons (the dry and the wet season) from nine sampling stations. These stations are grouped into four clusters (Considerable [Co], Low Pollution [LP], Moderate Pollution [MP], and Extreme Pollution [(EP]) by hierarchical agglomerative cluster analysis based on the similarities of water quality characteristics. The nine important influencing discriminating water quality indicators are extracted by stepwise method of temporal DA,where as eight important influencing indicators for dry season and eight indicators (Potassium, Phosphate, Fluoride, Copper, Lead, Nickel, Iron, and Total Chromium) for wet season are found out by the spatial DA. The pollution status in the river basin was observed from overall trend in (Considerable) Co to (Extreme Pollution) EP regions. The study could be very useful in prioritizing the important sites for water resources and pollution management.     

Variation and inheritance of the Xanthomonas raxX-raxSTAB gene cluster required for activation of XA21-mediated immunity

The rice XA21-mediated immune response is activated on recognition of the RaxX peptide produced by the bacterium Xanthomonas oryzae pv. oryzae (Xoo). The 60-residue RaxX precursor is post-translationally modified to form a sulfated tyrosine peptide that shares sequence and functional similarity with the plant sulfated tyrosine (PSY) peptide hormones. The 5-kb raxX-raxSTAB gene cluster of Xoo encodes RaxX, the RaxST tyrosylprotein sulfotransferase, and the RaxA and RaxB components of a predicted type I secretion system. To assess raxX-raxSTAB gene cluster evolution and to determine its phylogenetic distribution, we first identified rax gene homologues in other genomes. We detected the complete raxX-raxSTAB gene cluster only in Xanthomonas spp., in five distinct lineages in addition to X. oryzae. The phylogenetic distribution of the raxX-raxSTAB gene cluster is consistent with the occurrence of multiple lateral (horizontal) gene transfer events during Xanthomonas speciation. RaxX natural variants contain a restricted set of missense substitutions, as expected if selection acts to maintain peptide hormone-like function. Indeed, eight RaxX variants tested all failed to activate the XA21-mediated immune response, yet retained peptide hormone activity. Together, these observations support the hypothesis that the XA21 receptor evolved specifically to recognize Xoo RaxX.