High throughput nano-liter RT-qPCR to classify soil contamination using a soil arthropod

Background  

To incorporate genomics data into environmental assessments a mechanistic perspective of interactions between chemicals and induced biological processes needs to be developed. Since chemical compounds with structural similarity often induce comparable biological responses in exposed animals, gene expression signatures can serve as a starting point for the assessment of chemicals and their toxicity, but only when relevant and stable gene panels are available. To design such a panel, we isolated differentially expressed gene fragments from the soil arthropod Folsomia candida, a species often used for ecotoxicological testing. Animals were exposed to two chemically distinct compounds, being a metal (cadmium) and a polycyclic aromatic hydrocarbon (phenanthrene). We investigated the affected molecular responses resulting from either treatment and developed and validated 44 qPCR assays for their responses using a high throughput nano-liter RT-qPCR platform for the analysis of the samples.     

Design and evaluation of 16S rRNA sequence based oligonucleotide probes for the detection and quantification of Comamonas testosteroni in mixed microbial communities

Background  

The β-proteobacterial species Comamonas testosteroni is capable of biotransformation and also biodegradation of a range of chemical compounds and thus potentially useful in chemical manufacturing and bioremediation. The ability to detect and quantify members of this species in mixed microbial communities thus may be desirable.     

Underwater light attenuation inhibits native submerged plants and facilitates the invasive co-occurring plant Cabomba caroliniana

Aim

Decreasing in the diversity and distribution of native submerged plants have been widely observed in recent decades. Global underwater darkening, which is mainly caused by radiation dimming and a decrease in transparency due to, e.g. eutrophication, has emerged as a general trend that strongly hampers the growth of submerged plants in lakes by decreasing the light available for photosynthesis. However, few studies have attempted to compare the responses of native and invasive submerged plants to underwater darkening. In this study, we aimed to compare the effects of light attenuation on the growth and photosynthesis traits of native and invasive submerged plants.

Location

East China.

Method

Through field investigations and a mesocosm experiment, the responses of functional traits of two representative native [water thyme (Hydrilla verticillata), Eurasian watermilfoil (Myriophyllum spicatum)] and one invasive [Carolina fanwort (Cabomba caroliniana)] plant species to various environmental factors, notably to underwater light attenuation, were studied.

Results

Underwater photosynthetically active radiation (PAR) exerted a substantial effect on the relative coverage and abundance of the three studied submerged plants in their natural freshwater habitats. Invasive C. caroliniana showed relatively superior growth (total biomass and relative growth rate) and photosynthesis traits (maximum quantum yield of photosystem II F_v/F_m, chlorophyll a content, chlorophyll b content and the ratio of Chl a and b contents) compared to the two native plants under low underwater PAR conditions. In contrast, under high underwater PAR conditions, C. caroliniana showed the opposite response.

Main Conclusions

Light attenuation inhibits the growth of native submerged plants but facilitates the growth of invasive plant species. Restoration of freshwater lakes by reducing deterioration from underwater darkening (for instance, by reducing of external nutrients loading) may therefore constrain the growth and spread of the invasive C. caroliniana.     

Cloning and characterization of a 9-lipoxygenase gene induced by pathogen attack from <Emphasis Type="Italic">Nicotiana benthamiana</Emphasis>for biotechnological application

Background  

Plant lipoxygenases (LOXs) have been proposed to form biologically active compounds both during normal developmental stages such as germination or growth as well as during responses to environmental stress such as wounding or pathogen attack. In our previous study, we found that enzyme activity of endogenous 9-LOX in Nicotiana benthamiana was highly induced by agroinfiltration using a tobacco mosaic virus (TMV) based vector system.     

UreB immunodominant epitope-specific CD8+ T-cell responses were beneficial in reducing gastric symptoms in Helicobacter pylori-infected individuals

Background and aims

Although Helicobacter pylori is recognized as an extracellular infection bacterium, it can lead to an increase in the number of CD8⁺ T cells after infection. At present, the characteristics of H. pylori antigen-specific CD8⁺ T cells and the epitope response have not been elucidated. This study was focused on putative protective antigen UreB to detect specific CD8⁺ T-cell responses in vitro and screen for predominant response epitopes.

Methods

The PBMCs collected from H. pylori-infected individuals were stimulated by UreB peptide pools in vitro to identify the immunodominant CD8⁺ T-cell epitopes. Furthermore, their HLA restriction characteristics were detected accordingly by NGS. Finally, the relationship between immunodominant responses and appearance of gastric symptoms after H. pylori infection was conducted.

Results

UreB-specific CD8⁺ T-cell responses were detected in H. pylori-infected individuals. Three of UreB dominant epitopes (A-2 (UreB_443–451: GVKPNMIIK), B-4 (UreB_420–428: SEYVGSVEV), and C-1 (UreB_5–13: SRKEYVSMY)) were firstly identified and mainly presented by HLA-A*1101, HLA-B*4001 and HLA-C*0702 alleles, respectively. C-1 responses were mostly occurred in H. pylori-infected subjects without gastric symptoms and may alleviate the degree of gastric inflammation.

Conclusions

The UreB dominant epitope-specific CD8⁺ T-cell response was closely related to the gastric symptoms after H. pylori infection, and the C-1 (UreB_5-13) dominant peptides may be protective epitopes.     

Impact of receptor clustering on ligand binding

Background  

Cellular response to changes in the concentration of different chemical species in the extracellular medium is induced by ligand binding to dedicated transmembrane receptors. Receptor density, distribution, and clustering may be key spatial features that influence effective and proper physical and biochemical cellular responses to many regulatory signals. Classical equations describing this kind of binding kinetics assume the distributions of interacting species to be homogeneous, neglecting by doing so the impact of clustering. As there is experimental evidence that receptors tend to group in clusters inside membrane domains, we investigated the effects of receptor clustering on cellular receptor ligand binding.     

A tritrophic signal that attracts parasitoids to host-damaged plants withstands disruption by non-host herbivores

Background  

Volatiles emitted by herbivore-infested plants are highly attractive to parasitoids and therefore have been proposed to be part of an indirect plant defense strategy. However, this proposed function of the plant-provided signals remains controversial, and it is unclear how specific and reliable the signals are under natural conditions with simultaneous feeding by multiple herbivores. Phloem feeders in particular are assumed to interfere with plant defense responses. Therefore, we investigated how attack by the piercing-sucking cicadellid Euscelidius variegatus influences signaling by maize plants in response to the chewing herbivore Spodoptera littoralis.     

Introgression of Swertia mussotii gene into Bupleurum scorzonerifolium via somatic hybridization

Background  

The wild herb Swertia mussotii is a source of the anti-hepatitis compounds swertiamarin, mangiferin and gentiopicroside. Its over-exploitation has raised the priority of producing these compounds heterologously. Somatic hybridization represents a novel approach for introgressing Swertia mussotii genes into a less endangered species.     

Homologous high-throughput expression and purification of highly conserved <Emphasis Type="Italic">E coli</Emphasis> proteins

Background  

Genetic factors and a dysregulated immune response towards commensal bacteria contribute to the pathogenesis of Inflammatory Bowel Disease (IBD). Animal models demonstrated that the normal intestinal flora is crucial for the development of intestinal inflammation. However, due to the complexity of the intestinal flora, it has been difficult to design experiments for detection of proinflammatory bacterial antigen(s) involved in the pathogenesis of the disease. Several studies indicated a potential association of E. coli with IBD. In addition, T cell clones of IBD patients were shown to cross react towards antigens from different enteric bacterial species and thus likely responded to conserved bacterial antigens. We therefore chose highly conserved E. coli proteins as candidate antigens for abnormal T cell responses in IBD and used high-throughput techniques for cloning, expression and purification under native conditions of a set of 271 conserved E. coli proteins for downstream immunologic studies.     

Inhibitory effects of Eucalyptus globulus on understorey plant growth and species richness are greater in non‐native regions

Aim

We studied the novel weapons hypothesis in the context of the broadly distributed tree species Eucalyptus globulus. We evaluated the hypothesis that this Australian species would produce stronger inhibitory effects on species from its non‐native range than on species from its native range.

Location

We worked in four countries where this species is exotic (U.S.A., Chile, India, Portugal) and one country where it is native (Australia).

Time period

2009–2012.

Major taxa studied

Plants.

Methods

We compared species composition, richness and height of plant communities in 20 paired plots underneath E. globulus individuals and open areas in two sites within its native range and each non‐native region. We also compared effects of litter leachates of E. globulus on root growth of seedlings in species from Australia, Chile, the U.S.A. and India.

Results

In all sites and countries, the plant community under E. globulus canopies had lower species richness than did the plant community in open areas. However, the reduction was much greater in the non‐native ranges: species richness declined by an average of 51% in the eight non‐native sites versus 8% in the two native Australian sites. The root growth of 15 out of 21 species from the non‐native range were highly suppressed by E. globulus litter leachates, whereas the effect of litter leachate varied from facilitation to suppression for six species native to Australia. The mean reduction in root growth for Australian plants was significantly lower than for plants from the U.S.A., Chile and India.

Main conclusions

Our results show biogeographical differences in the impact of an exotic species on understorey plant communities. Consistent with the novel weapons hypothesis, our findings suggest that different adaptations of species from the native and non‐native ranges to biochemical compounds produced by an exotic species may play a role in these biogeographical differences.     

Characterization of Vitis vinifera NPR1 homologs involved in the regulation of Pathogenesis-Related gene expression

Background  

Grapevine protection against diseases needs alternative strategies to the use of phytochemicals, implying a thorough knowledge of innate defense mechanisms. However, signalling pathways and regulatory elements leading to induction of defense responses have yet to be characterized in this species. In order to study defense response signalling to pathogens in Vitis vinifera, we took advantage of its recently completed genome sequence to characterize two putative orthologs of NPR1, a key player in salicylic acid (SA)-mediated resistance to biotrophic pathogens in Arabidopsis thaliana.     

The isolation and mapping of a novel hydroxycinnamoyltransferase in the globe artichoke chlorogenic acid pathway

Background  

The leaves of globe artichoke and cultivated cardoon (Cynara cardunculus L.) have significant pharmaceutical properties, which mainly result from their high content of polyphenolic compounds such as monocaffeoylquinic and dicaffeoylquinic acid (DCQ), and a range of flavonoid compounds.     

Vitamin B6 deficient plants display increased sensitivity to high light and photo-oxidative stress

Background  

Vitamin B6 is a collective term for a group of six interconvertible compounds: pyridoxine, pyridoxal, pyridoxamine and their phosphorylated derivatives. Vitamin B6 plays essential roles as a cofactor in a range of biochemical reactions. In addition, vitamin B6 is able to quench reactive oxygen species in vitro, and exogenously applied vitamin B6 protects plant cells against cell death induced by singlet oxygen (¹O₂). These results raise the important question as to whether plants employ vitamin B6 as an antioxidant to protect themselves against reactive oxygen species.     

Aquaporins in the wild: natural genetic diversity and selective pressure in the PIP gene family in five Neotropical tree species

Background  

Tropical trees undergo severe stress through seasonal drought and flooding, and the ability of these species to respond may be a major factor in their survival in tropical ecosystems, particularly in relation to global climate change. Aquaporins are involved in the regulation of water flow and have been shown to be involved in drought response; they may therefore play a major adaptive role in these species. We describe genetic diversity in the PIP sub-family of the widespread gene family of Aquaporins in five Neotropical tree species covering four botanical families.     

Plant-like substitutions in the large-subunit carboxy terminus of <Emphasis Type="Italic">Chlamydomonas</Emphasis> Rubisco increase CO<Subscript>2</Subscript>/O<Subscript>2</Subscript> Specificity

Background  

Ribulose-1,5-bisphosphate is the rate-limiting enzyme in photosynthesis. The catalytic large subunit of the green-algal enzyme from Chlamydomonas reinhardtii is ~90% identical to the flowering-plant sequences, although they confer diverse kinetic properties. To identify the regions that may account for species variation in kinetic properties, directed mutagenesis and chloroplast transformation were used to create four amino-acid substitutions in the carboxy terminus of the Chlamydomonas large subunit to mimic the sequence of higher-specificity plant enzymes.     

SuperSAGE analysis of the <Emphasis Type="Italic">Nicotiana attenuata</Emphasis> transcriptome after fatty acid-amino acid elicitation (FAC): identification of early mediators of insect responses

Background  

Plants trigger and tailor defense responses after perception of the oral secretions (OS) of attacking specialist lepidopteran larvae. Fatty acid-amino acid conjugates (FACs) in the OS of the Manduca sexta larvae are necessary and sufficient to elicit the herbivory-specific responses in Nicotiana attenuata, an annual wild tobacco species. How FACs are perceived and activate signal transduction mechanisms is unknown.     

Volatile induction of infected and neighbouring uninfected plants potentially influence attraction/repellence of a cereal herbivore

Pathogen infection can induce plant volatile organic compounds (VOCs). We infected ‘McNeal’ wheat and ‘Harrington’ barley with a Fusarium spp. blend (F. graminearum,F. avenaceum and F. culmorum). Both cereals had the greatest VOC induction 14 days after pathogen innoculation, only slightly lower induction occurred at 7 days, but displayed no induction at 1 days. The induced VOC bouquet for both cereals included six green leaf volatiles (GLVs; e.g. (Z)‐3‐hexenol and (Z)‐3‐hexenyl acetate), four terpenes (linalool, linalool oxide, (Z)‐β‐ocimene and (E)‐β‐caryophyllene) and benzyl acetate. Neighbouring, uninfected individuals of both cereals had significant VOC induction when exposed to an infected, conspecific plant. The temporal pattern and VOC blend were qualitatively similar to infected plants but with quantitative reductions for all induced VOCs. The degree of neighbouring, uninfected plant induction was negatively related to distance from an infected plant. Plant VOC induction in response to pathogen infection potentially influences herbivore attraction or repellency. Y‐tube tests showed that herbivorous female and male Oulema cyanella Voet. (Chrysomelidae: Coleoptera) were significantly attracted to (Z)‐3‐hexenal and (Z)‐3‐hexenyl acetate at 300 and 1500 ng/h but were repelled by both GLVs as well as (Z)‐β‐ocimene and linalool at 7500 ng/h. These O. cyanella behavioural responses were significantly at higher concentrations than those emitted by single plants with pathogen‐induced VOCs, so adults might only be able to respond to a dense group of infected plants. Also, O. cyanella dose responses differ from the previously tested congeneric O. melanopus (cereal leaf beetle), which was attracted to three VOCs induced by Fusarium infection of maize, barley and wheat. Future behavioural tests may indicate whether different herbivore dose responses measured with each VOC singly can help to predict attraction or repellency to injured and uninjured VOC bouquets from different host plant species.