Automated in situ detection (AISD) of biomolecules

 In order to facilitate in situ detection of biomolecules in large sample series the processing of whole-mount specimens has been automated. A freely programmable liquid handling system is described by which embryos or similar biological materials are processed. Possible applications include in situ hybridization (ISH), immunocytochemistry (ICC) or reporter gene assays. Process times required for the preparation of whole-mount in situ hybridizations in Drosophila, Xenopus, Gallus and in hydroids were - in part - significantly reduced as compared with manual processing. Application of automated in situ detection (AISD) in random screening is demonstrated in hydroids. Potential further applications are discussed.

Deciphering the transcriptional regulation and spatiotemporal distribution of immunity response in barley to Pyrenophora graminea fungal invasion

BACKGROUND

Barley leaf stripe disease, caused by the fungus Pyrenophora graminea (Pg), is a worldwide crop disease that results in significant loss of barley yield. The purpose of the present work was to use transcriptomic profiling to highlight barley genes and metabolic pathways affected or altered in response to Pg infection and consequently elucidate their involvement and contribution in resistance to leaf stripe.

RESULTS

Our study examined and compared the transcriptomes of two barley genotypes using an established differential display reverse-transcription polymerase chain reaction (DDRT-PCR) strategy at 14 and 20 days post-inoculation (dpi). A total of 54 significantly modulated expressed sequence tags (ESTs) were identified. The analysis of gene expression changes during the course of infection with Pg suggested the involvement of 15 upregulated genes during the immunity response. By using network-based analyses, we could establish a significant correlation between genes expressed in response to Pg invasion. Microscopic analysis and quantitative PCR (qPCR) profiling of callose synthase and cellulose synthases revealed a direct involvement of cell wall reinforcement and callose deposition in the Pg-resistant phenotype.

CONCLUSIONS

We have identified a number of candidate genes possibly involved in the host-pathogen interactions between barley and Pg fungus, 15 of which are specifically expressed in Pg-resistant plants. Collectively, our results suggest that the resistance to leaf stripe in barley proceeds through callose deposition and different oxidation processes.

Response of Tradescantia plants to oxidative stress induced by heavy metal pollution of soils from industrial areas

Numerous investigations have demonstrated that even soil in which concentrations of individual elements do not exceed permissible limits can cause harmful effects in living organisms. In the present study, polluted-soil-induced oxidative stress was evaluated using Tradescantia clone 4430, which is widely used for genotoxicity evaluations, employing biochemical (superoxide dismutase (SOD), contents of ascorbic acid (AA), carotenoids (Car), hydrogen peroxide (H₂O₂), chlorophyll (Chl) a/b ratio), and molecular (RAPD and differential display (DD-PCR)) markers after long-term exposure. The activity (staining intensity) of SOD isoforms in Tradescantia leaves was higher in plants grown in all heavy-metal-polluted test soils compared to the control. No direct link between the soil pollution category and the contents of AA, Car, Chl a/b in Tradescantia leaves was revealed, but the concentration of H₂O₂ was shown to be a sensitive biochemical indicator that may appropriately reflect the soil contamination level. Both short-term (treatment of cuttings with H₂O extracts of soil) and long-term (0.5 and 1.0 year) exposure increased MN frequencies, but the coincidence of the MN induction and the soil pollution level was observed only in some cases of long-term exposure. Soil (geno)toxin-induced polymorphism in the RAPD profile was determined with two primers in plants after long-term exposure to soils of an extremely hazard category. Transcript profiling of plants after long-term cultivation in test soils using DD-PCR showed that the majority of differentially expressed transcript-derived fragments (TDFs) were homologous to genes directly or indirectly participating in photosynthesis, the abiotic stress response, and signal transduction cascades.

A proteomic study of rice cultivar TNG67 and its high aroma mutant SA0420

Fragrance is a very important economic trait for rice cultivars. To identify the aroma genes in rice, we performed a proteomics analysis of aroma-related proteins between Tainung 67 (TNG67) and its high aroma mutant SA0420. Seventeen of the differentially identified proteins were close related with the aroma phenotype of SA0420. Among them, 9 were found in leaves and 8 were found in grains. One protein (L3) was identified as the chloroplastic glyceraldehyde-3-phosphate dehydrogenase B (OsGAPDHB) which was less abundant in SA0420 than TNG67. Sequence analysis demonstrated that this protein in SA0420 carries a P425S mutation in the C-terminal extension domain, which might hinder the formation of holoenzyme, thereby changing the profile of aroma compounds. The protein profile of OsGAPDHB showed only a weak correlation to its transcription profile. This result indicated that the reduction of OsGAPDHB in SA0420 is regulated by post-translational processes and can only be analyzed by proteomics approach. Transgenic lines suppressing OsGAPDHB through RNAi harbored more fragrance than TNG67 but less than SA0420. With betaine-aldehyde dehydrogenase as the only fragrance gene identified in rice to date, OsGAPDHB may serve as the second protein known to contribute to the aroma phenotype.

Transient expression of a novel serine protease in the ectoderm of the ascidian Herdmania momus during development

 We have studied gene expression during ascidian embryonic development using the technique of differential display and isolated partial cDNA sequences of 12 genes. Developmental regulation of these genes has been confirmed by northern hybridization analysis. Further cDNA cloning and sequence analysis of an mRNA that is present during gastrulation, neurulation and tailbud formation reveals that it encodes a novel serine protease containing a single kringle motif and catalytic domain. The spatial expression of this gene, designated Hmserp1, is restricted to precursor cells of the epidermis. The structure and expression of Hmserp1 is discussed in relation to possible functions during development.

Isolation of a novel LPS-induced component of the ML superfamily in Ciona intestinalis

ML superfamily represents a group of proteins playing important roles in lipid metabolism and innate immune response. In this study, we report the identification of the first component of the ML superfamily in the invertebrate Ciona intestinalis by means of a subtractive hybridization strategy. Sequence homology and phylogenetic analysis showed that this protein forms a specific clade with vertebrate components of the Niemann-Pick type C2 protein and, for this reason, it has been named Ci-NPC2. The putative Ci-NPC2 is a 150 amino acids long protein with a short signal peptide, seven cysteine residues, three putative lipid binding site and a three-dimensional model showing a characteristic β-strand structure. Gene expression analysis demonstrated that the Ci-NPC2 protein is positively upregulated after LPS inoculum with a peak of expression 1 h after challenge. Finally, in-situ hybridization demonstrated that the Ci-NPC2 protein is preferentially expressed in hemocytes inside the vessel lumen.

Identification of genes involved in the drought adaptation and recovery in Portulaca oleracea by differential display

Portulaca oleracea is one of the richest plant sources of ω-3 and ω-6 fatty acids and other compounds potentially valuable for nutrition. It is broadly established in arid, semiarid and well-watered fields, thus making it a promising candidate for research on abiotic stress resistance mechanisms. It is capable of withstanding severe drought and then of recovering upon rehydration. Here, the adaptation to drought and the posterior recovery was evaluated at transcriptomic level by differential display validated by qRT-PCR. Of the 2279 transcript-derived fragments amplified, 202 presented differential expression. Ninety of them were successfully isolated and sequenced. Selected genes were tested against different abiotic stresses in P. oleracea and the behavior of their orthologous genes in Arabidopsis thaliana was also explored to seek for conserved response mechanisms. In drought adapted and in recovered plants changes in expression of many protein metabolism-, lipid metabolism- and stress-related genes were observed. Many genes with unknown function were detected, which also respond to other abiotic stresses. Some of them are also involved in the seed desiccation/imbibition process and thus would be of great interest for further research. The potential use of candidate genes to engineer drought tolerance improvement and recovery is discussed.

Identification of salinity responsive genes in lavender through cDNA-AFLP

Currently, a global demand exists forlavender as a significant medicinal plant and source of essential oils. Freshwater and arable lands are two major factors that inhibit extensive farming of medicinal plants in Iran. Saline water from seas and salty soil may be new resources for agricultural use, especially for medicinal plants. We sought to extend our knowledge of the Lavandula angustifolia genome and molecular basis of its salinity tolerance by using cDNA amplified fragment length polymorphism (cDNA-AFLP) to investigate the changes in plant transcriptomes in response to NaCl. All identified transcript derived fragments (TDF) were assigned as novel L. angustifolia genes related to signal transduction, regulation of gene expression, alternative splicing, autophagy, and secondary metabolite biosynthesis. qRT-PCR analysis of the TDFs in response to different concentrations of NaCl revealed various levels of mRNA of the identified genes in this plant. Our findings provided primary insights into the molecular response of L. angustifolia to salinity.

Analysis of Reverse Transcribed mRNA Using PCR and Polyacrylamide Gel Electrophoresis

The patterns of gene expression in the fission yeast Schizosaccharomyces pombe under various experimental conditions form the basis of any transcriptomic study. We describe a method involving reverse transcription of the mRNA, Polymerase Chain Reaction (PCR), and the subsequent separation of the products onto Urea-Polyacrylamide gel that can be used to study the gene expression patterns in the fission yeast. The method described is cost effective and reproducible with satisfactory resolution of expressed transcripts in the gel. The method has the following essential steps: total RNA isolation and purification, cDNA synthesis from mRNAs, PCR amplification of cDNAs, visualization of PCR products, re-amplification and cloning of the differentially expressed PCR products, sequencing the confirmed clones, and finally cDNA library screening to isolate the genes of interest. The technique is also popularly known as Differential Display Reverse Transcription (DDRT-PCR). After its invention in 1992, a number of modifications have been introduced to optimize the technique and specifically to reduce the major problem of "false positives." Since understanding of specific gene expression patterns that regulate developmental and stress responses is a major concern of biology, DDRT-PCR has become a very popular molecular technique during the past two decades.

What have we learned about non-involved psoriatic skin from large-scale gene expression studies?

Psoriasis is a chronic inflammatory skin disorder; its genetic background has been widely studied in recent decades. Recognition of novel factors contributing to the pathogenesis of this disorder was facilitated by potent molecular biology tools developed during the 1990s. Large-scale gene expression studies, including differential display and microarray, have been used in experimental dermatology to a great extent; moreover, skin was one of the first organs analyzed using these methods. We performed our first comprehensive gene expression analysis in 2000. With the help of differential display and microarray, we have discovered several novel factors contributing to the inherited susceptibility for psoriasis, including the EDA+ fibronectin splice variant and PRINS. The long non-coding PRINS RNA is expressed at higher levels in non-involved skin compared to healthy and involved psoriatic epidermis and might be a factor contributing cellular stress responses and, specifically, to the development of psoriatic symptoms. This review summarizes the most important results of our large-scale gene expression studies.

Effect of nitrate availability on expression of multi sensor histidine kinase gene in Spirulina platensis PCC 7345

Addition of nitrate (NO3 (-)) to a suspension of NO3 (-)-depleted Spirulina platensis PCC 7345 restored back the PSII reaction centre efficiency. Using RAPD/RT-PCR differential display, we have detected the upregulation of a novel gene in filaments starved of nitrogen when enriched with NO3 (-). Semiquantitative RT-PCR clearly shows that NO3 (-) repletion induces the expression of this gene. Its nucleotide sequence is homologous to multi sensor histidine kinase (hstk) from Spirulina platensis NIES-39 and Spirulina maxima CS-328 genes. The open reading frame of this gene encodes a protein of 98 amino acids contains sensory domain of PAS domain.

Differentially Expressed Nedd4-binding Protein Ndfip1 Protects Neurons Against Methamphetamine-induced Neurotoxicity

To identify factors involved in methamphetamine (METH) neurotoxicity, we comprehensively searched for genes which were differentially expressed in mouse striatum after METH administration using differential display (DD) reverse transcription-PCR method and sequent single-strand conformation polymorphism analysis, and found two DD cDNA fragments later identified as mRNA of Nedd4 (neural precursor cell expressed developmentally downregulated 4) WW domain-binding protein 5 (N4WBP5), later named Nedd4 family-interacting protein 1 (Ndfip1). It is an adaptor protein for the binding between Nedd4 of ubiquitin ligase (E3) and target substrate protein for ubiquitination. Northern blot analysis confirmed drastic increases in Ndfip1 mRNA in the striatum after METH injections, and in situ hybridization histochemistry showed that the mRNA expression was increased in the hippocampus and cerebellum at 2 h-2 days, in the cerebral cortex and striatum at 18 h-2 days after single METH administration. The knockdown of Ndfip1 expression with Ndfip1 siRNA significantly aggravated METH-induced neurotoxicity in the cultured monoaminergic neuronal cells. These results suggest that drastic increases in Ndfip1 mRNA is compensatory reaction to protect neurons against METH-induced neurotoxicity.