Evaluation of the Use of the Polyubiquitin Genes,Ubi4 and Ubi10 as Reference Genes for Expression Studies in Brachypodium distachyon

Background

Brachypodium distachyon is emerging as the model plant for temperate grass research and the genome of the community line Bd21 has been sequenced. Additionally, techniques have been developed for Agrobacterium-mediated transformation for the generation of T-DNA insertional lines. Recently, it was reported that expression of the polyubiquitin genes, Ubi4 and Ubi10 are stable in different tissues and growth hormone-treated plant samples, leading to the conclusion that both Ubi4 and Ubi10 are good reference genes for normalization of gene expression data using real-time, quantitative PCR (qPCR).

Principal Findings

Mining of the Joint Genome Institute (JGI) 8X Brachypodium distachyon genome assembly showed that Ubi4 and Ubi10 share a high level of sequence identity (89%), and in silico analyses of the sequences of Ubi4 (Bradi3g04730) and Ubi10 (Bradi1g32860) showed that the primers used previously exhibit multiple binding sites within the coding sequences arising from the presence of tandem repeats of the coding regions. This can potentially result in over-estimation of steady-state levels of Ubi4 and Ubi10. Additionally, due to the high level of sequence identity between both genes, primers used previously for amplification of Ubi4 can bind to Ubi10 and vice versa, resulting in the formation of non-specific amplification products.

Conclusions

The results from this study indicate that the primers used previously were not sufficiently robust and specific. Additionally, their use would result in over-estimation of the steady-state expression levels of Ubi4. Our results question the validity of using the previously proposed primer sets for qPCR amplification of Ubi4 and Ubi10. We demonstrate that primers designed to target the 3′-UTRs of Ubi4 and Ubi10 are better suited for real-time normalization of steady-state expression levels in Brachypodium distachyon.     

Use of Biometric Characteristics of Major Salivary Glands as a Baseline to Develop a Formula for the Quantitative Estimation of Posttraumatic Regeneration of Glandular Tissue

In experiments conducted on 903 rats, we studied the biometric characteristics of the major salivary glands (parotid, submandibular, and sublingual glands) during ontogenesis. We calculated the indices of nondirectional fluctuation asymmetry for the submandibular and sublingual glands and determined correlation coefficients and the coefficients of linear regression between salivary glands, rat body weight, and the weight of the femoral bone (the largest bone in the rat). The strongest correlation was found between the dry weight of the submandibular gland and the rat body weight. Mathematical analysis of the growth of the submandibular gland after sialotomy allowed us to derive a formula for the quantitative estimation of regeneration, taking into account the natural growth of the rat.     

Stab Wound Injury of the Zebrafish Adult Telencephalon: A Method to Investigate Vertebrate Brain Neurogenesis and Regeneration

Adult zebrafish have an amazing capacity to regenerate their central nervous system after injury. To investigate the cellular response and the molecular mechanisms involved in zebrafish adult central nervous system (CNS) regeneration and repair, we developed a zebrafish model of adult telencephalic injury.In this approach, we manually generate an injury by pushing an insulin syringe needle into the zebrafish adult telencephalon. At different post injury days, fish are sacrificed, their brains are dissected out and stained by immunohistochemistry and/or in situ hybridization (ISH) with appropriate markers to observe cell proliferation, gliogenesis, and neurogenesis. The contralateral unlesioned hemisphere serves as an internal control. This method combined for example with RNA deep sequencing can help to screen for new genes with a role in zebrafish adult telencephalon neurogenesis, regeneration, and repair.     

Aerosolization of Respirable Droplets from a Domestic Spa Pool and the Use of MS-2 Coliphage and Pseudomonas aeruginosa as Markers for Legionella pneumophila

Legionnaires'' disease can result when droplets or aerosols containing legionella bacteria are inhaled and deposited in the lungs. A number of outbreaks have been associated with the use of a spa pool where aeration, a high water temperature, and a large and variable organic load make disinfectant levels difficult to maintain. Spa pool ownership is increasing, and the aim of this study, using two surrogate organisms (MS-2 coliphage and Pseudomonas aeruginosa [a natural contaminant]), was to assess the potential risk to domestic users when disinfection fails. A representative “entry level” domestic spa pool was installed in an outdoor courtyard. The manufacturer''s instructions for spa pool maintenance were not followed. A cyclone sampler was used to sample the aerosols released from the spa pool with and without activation of the air injection system. Samples were taken at increasing heights and distances from the pool. An aerodynamic particle sizer was used to measure the water droplet size distribution at each sample point. When the air injection system was inactivated, neither surrogate organism was recovered from the air. On activation of the air injection system, the mean mass of droplets within the respirable range (10 cm above the water line) was 36.8 μg cm⁻³. This corresponded to a mean air concentration of P. aeruginosa of 350 CFU m⁻³. From extrapolation from animal data, the estimated risk of infection from aerosols contaminated with similar concentrations of Legionella pneumophila was 0.76 (males) and 0.65 (females). At 1 m above and/or beyond the pool, the mean aerosol mass decreased to 0.04 μg cm⁻³ and corresponded to a 100-fold reduction in mean microbial air concentration. The estimated risk of infection at this distance was negligible.     

Cloning of cDNAs for Cecropins A and B,and Expression of the Genes in the Silkworm,Bombyx mori

cDNA clones coding cecropins A and B were isolated from a cDNA library constructed from the fat body of immunized Bombyx mori larvae. The cloned cDNAs had an open reading frame of 63 amino acids, indicating the primary translated peptides were processed to form mature cecropins of 35 amino acid residues. The homology in the coding regions of cecropins A and B was 73%.

In immunized fat body, the expression of both cecropin A and B genes reached the maximal level 5 h after the injection of soluble peptidoglycan, and the high level was maintained until 9 h after immunization. The cecropin A and B genes were expressed at high levels in fat body and hemocytes, at lower but significant levels in malpighian tube, slightly in midgut, and none in silk gland.     

The Sequence and Expression of the {gamma}-VPE Gene, One Member of a Family of Three Genes for Vacuolar Processing Enzymes in Arabidopsis thaliana

Vacuolar processing enzymes (VPEs) are responsible for the maturationof seed proteins. Southern blot analysis showed that a familyof genes for VPEs in Arabidopsis thaliana was composed of threegenes, for      

Suppressors, Screens, and Genes: An Educational Primer for Use with "A Network of Genes Antagonistic to the LIN-35 Retinoblastoma Protein of Caenorhabditis elegans"

An article by Polley and Fay in this issue of GENETICS provides an excellent opportunity to introduce or reinforce concepts of reverse genetics and RNA interference, suppressor screens, synthetic phenotypes, and phenocopy. Necessary background, explanations of these concepts, and a sample approach to classroom use of the original article, including discussion questions, are provided.     

A simple and rapid procedure to establish embryogenic cell suspensions as a source of protoplasts for efficient plant regeneration from two Chinese commercial rice cultivars

An efficient and rapid procedure has been developed to establish embryogenic cell suspension cultures of two Japonica Chinese commercial rice cultivars, Zhonghua 8 and Eryi 105. Embryogenic cell suspensions of both varieties were established from 0.5–1.0 g fresh weight of embryogenic callus in AA medium within 2.5 months of the initiation of callus from sterilised seeds. The previously reported subculture of callus on semi-solid medium for 4–8 weeks prior to transfer into liquid medium was unnecessary and caused delay in the establishment of embryogenic cell suspensions. Protoplasts were isolated reproducibly from cell suspensions up to 18 months after their initiation, with protoplast plating efficiencies attaining 0.15–0.37%. Reproducible plant regeneration from 14–26% of the protoplast-derived tissues was achieved without the requirement for nurse cells. This revised version was published online in June 2006 with corrections to the Cover Date.     

Use of Synthetic Genes for Cloning,Production and Functional Expression of the Bacteriocins Enterocin A and Bacteriocin E 50-52 by Pichia pastoris and Kluyveromyces lactis

The use of synthetic genes may constitute a successful approach for the heterologous production and functional expression of bacterial antimicrobial peptides (bacteriocins) by recombinant yeasts. In this work, synthetic genes with adapted codon usage designed from the mature amino acid sequence of the bacteriocin enterocin A (EntA), produced by Enterococcus faecium T136, and the mature bacteriocin E 50-52 (BacE50-52), produced by E. faecium NRRL B-32746, were synthesized. The synthetic entA and bacE50-52 were cloned into the protein expression vectors pPICZαA and pKLAC2 for transformation of derived vectors into Pichia pastoris X-33 and Kluyveromyces lactis GG799, respectively. The recombinant vectors were linearized and transformed into competent cells selecting for P. pastoris X-33EAS (entA), P. pastoris X-33BE50-52S (bacE50-52), K. lactis GG799EAS (entA), and K. lactis GG799BE50-52S (bacE50-52). P. pastoris X-33EAS and K. lactis GG799EAS, but not P. pastoris X-33BE50-52S and K. lactis GG799BE50-52S, showed antimicrobial activity in their supernatants. However, purification of the supernatants of the producer yeasts permitted recovery of the bacteriocins EntA and BacE50-52. Both purified bacteriocins were active against Gram-positive bacteria such as Listeria monocytogenes but not against Gram-negative bacteria, including Campylobacter jejuni.     

Advances in Development of a Genetic System for Thermoanaerobacterium spp.: Expression of Genes Encoding Hydrolytic Enzymes, Development of a Second Shuttle Vector, and Integration of Genes into the Chromosome

Despite recent success in transforming various thermophilic gram-type-positive anaerobes with plasmid DNA, use of shuttle vectors for the expression of genes other than antibiotic resistance markers has not previously been described. We constructed new vectors in order to express heterologous hydrolytic enzymes in our model system, Thermoanaerobacterium saccharolyticum JW/SL-YS485. Transformed Thermoanaerobacterium expressed active enzyme, indicating that this system may function as an alternate expression host, especially for genes with a thermophilic origin. To develop further the genetic system for T. saccharolyticum JW/SL-YS485, two improved Escherichia coli-Thermoanaerobacterium shuttle vectors, pRKM1 and pRUKM, were constructed. Furthermore, the kanamycin resistance cassette alone and the kanamycin resistance cassette plus the cellobiohydrolase gene (cbhA) from Clostridium thermocellum JW20 were integrated into the xylanase gene (xynA) region of the Thermoanaerobacterium chromosome via homologous recombination using pUC-based suicide vectors pUXK and pUXKC.     

Synthesis,Crystal Structure,and in Vitro Biological Evaluation of C-6 Pyrimidine Derivatives: New Lead Structures for Monitoring Gene Expression in Vivo

Novel C-6 substituted pyrimidine derivatives are good substrates of herpes simplex virus type 1 thymidine kinase (HSV1-TK). Enzyme kinetic experiments showed that our lead compound, N-methyl DHBT (N-methyl-6-(1,3-dihydroxyisobutyl) thymine; N-Me DHBT), is phosphorylated at a similar rate compared to “gold standard” 9-[4-fluoro-3-(hydroxymethyl)butyl]guanine, FHBG, (K _m = 10 ± 0.3 μM; k _cat = 0.036 ± 0.015 sec^?1). Additionally, it does not show cytotoxic properties on B16F1 cells up to a concentration of 10 mM. The x-ray analysis of the crystal structures of HSV1-TK with N-Me DHBT and of HSV1-TK with the fluorinated derivative N-Me FHBT confirmed the binding mode predicted by docking studies and their substrate characteristics. Moreover, the crystal structure of HSV1-TK with N-Me DHBT revealed an additional water-mediated H-bond interesting for the design of further analogues.     

Peeling as a novel, simple, and effective method for isolation of apical membrane from intact polarized epithelial cells

Apical membrane of polarized epithelial cells is generally isolated by physicochemical methods, that is, precipitation with polyethylene glycol (PEG) or MgCl₂ followed by differential centrifugation or sucrose density gradient centrifugation. However, these protocols are considerably sophisticated and frequently accompanied by impurities (e.g., contaminations of basolateral membrane and intracellular organelles), particularly by inexperienced investigators. We have developed a simple and effective method for isolation of apical membrane from intact polarized renal tubular epithelial cells. On the basis of hydrous affinity and/or ionic interaction, the apical membrane could be efficiently peeled from the cells by four different materials—Whatman filter paper, nitrocellulose membrane, cellophane, and glass coverslip—all of which are available in most research laboratories. Phase-contrast and laser-scanning confocal microscopic examinations using anti-ZO-1 antibody showed that other parts of the cells, particularly tight junction complex, remained intact after peeling by all four of these surfaces. Western blot analyses of gp135 (apical membrane marker) and of Na⁺/K⁺-ATPase, LAMP-2, COX-4, and calpain-1 (markers of basolateral membrane, lysosome, mitochondria, and cytosolic compartment, respectively) revealed that peeling with Whatman filter paper and glass coverslip was most and second-most effective, respectively, without any contaminations from basolateral membrane and other intracellular organelles that could be detected in the samples isolated by peeling with nitrocellulose membrane and cellophane and by conventional methods (i.e., precipitation with PEG or MgCl₂ followed by differential centrifugation or sucrose density gradient centrifugation). Our physical method is very simple, easy to follow (even by inexperienced investigators), time-saving, and cost-effective with a higher efficiency (as compared with conventional methods) for isolation of apical membrane from polarized epithelial cells.     

A sustainable process for adsorptive removal of methylene blue onto a food grade mucilage: kinetics,thermodynamics, and equilibrium evaluation

Abstract

Adsorption of dyes onto natural materials like polysaccharides is considered a green chemistry approach for remediation of wastewater. In this work, the polysaccharide isolated from the corm of Colocasia esculenta (L.) Schott or taro tuber (CEM) was utilized for removing methylene blue (MB) from aqueous solution by batch adsorption method. The CEM adsorbent was characterized by FTIR spectroscopy, Brunauer–Emmett–Teller (BET), and scanning electron microscopy (SEM). The solution pH and adsorbent dose have been found to have a significant positive correlation with the adsorptive removal efficiency of CEM for MB dye. The removal efficiency of CEM was found to be 72.35% under the optimum conditions; 20?mg/L initial concentration of dye, 120?mg of adsorbent dose, solution pH 8.5, 311.2?K temperature and 80?min contact time. The adsorption of MB onto CEM followed best the Freundlich isotherm and pseudo-second-order kinetics. The adsorption was thermodynamically favorable and was endothermic in nature. The desorption/adsorption data justifiably indicated the reuse capability of CEM adsorbent for MB adsorption. Hence, CEM may be regarded as an eco-friendly and cost-effective natural adsorbent for MB dye removal from aqueous solution.     

A New Tool for Routine Testing of Cellular Protein Expression: Integration of Cell Staining and Analysis of Protein Expression on a Microfluidic Chip-Based System

The key benefits of Lab-on-a-Chip technology are substantial time savings via an automation of lab processes, and a reduction in sample and reagent volumes required to perform analysis. In this article we present a new implementation of cell assays on disposable microfluidic chips. The applications are based on the controlled movement of cells by pressure-driven flow in microfluidic channels and two-color fluorescence detection of single cells. This new technology allows for simple flow cytometric studies of cells in a microfluidic chip-based system. In addition, we developed staining procedures that work “on-chip,” thus eliminating time-consuming washing steps. Cells and staining-reagents are loaded directly onto the microfluidic chip and analysis can start after a short incubation time. These procedures require only a fraction of the staining reagents generally needed for flow cytometry and only 30,000 cells per sample, demonstrating the advantages of microfluidic technology. The specific advantage of an on-chip staining reaction is the amount of time, cells, and reagents saved, which is of great importance when working with limited numbers of cells, e.g., primary cells or when needing to perform routine tests of cell cultures as a quality control step. Applications of this technology are antibody staining of proteins and determination of cell transfection efficiency by GFP expression. Results obtained with microfluidic chips, using standard cell lines and primary cells, show good correlation with data obtained using a conventional flow cytometer.