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.     

Forest Regeneration from Pasture in the Dry Tropics of Panama: Effects of Cattle, Exotic Grass, and Forested Riparia

We currently have the opportunity to restore one of the most threatened tropical ecosystems on the Pacific coast of Panama as a consequence of land use change. Factors that influence succession must be understood in order to capitalize on natural regeneration mechanisms. In this study, we determined the effects of exotic grass removal, cattle removal, proximity to forested riparian zones, and topography (upslope vs. downslope) on the initial stages of forest regeneration from pasture in a dry tropical region. After 3 years, basal area, stem density, and species richness of plants (trees, shrubs, vines, and herbs) were significantly and positively affected by exclusion of cattle, presence of exotic grass (no herbicide application), and presence of adjacent forested riparian zones ( p < 0.01). Interactions between factors were not significant. Cattle foraged and stomped on vegetation, whereas herbicide application, although effectively removing grass, also killed tree and shrub sprouts, the major source of regrowth. Proximity to forested riparian zones had the greatest effect on species diversity. Shannon's index for diversity ( H ) equaled 3.23 in plots adjacent to forested riparian zones as compared to 2.78 in plots not associated with these areas. Our recommendations during the early stages of forest succession are to (1) exclude cattle, (2) make site-specific decisions about herbicide application based on the presence or absence of forested riparia and prevalence of coppicing, and (3) actively conserve and protect riparian zones, which function as a critical source of diverse propagules.     

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.     

Development of the ��Three-step MACS��: a Novel Strategy for Isolating Rare Cell Populations in the Absence of Known Cell Surface Markers from Complex Animal Tissue

To circumvent the difficulty of isolating specific cell populations by MACS from dissociated complex animal tissue, when their proportions reached levels similar to that of the background, we developed the “Three-step MACS” strategy. Cells of interest are defined by their expression of a particular gene(s) of interest rather by than their natural cell surface markers or size. A two-component transgenic cell surface protein, for two sequential rounds of MACS, is expressed under the promoter control of the endogenous gene of interest by means of gene targeting and the generation of transgenic tissue. An initial step to remove dead cells is also used. Here, we describe proof-of-concept experiments, using the biotin acceptor peptide (BAP)-low-affinity nerve growth factor receptor as the two-component protein. The first component, the BAP, can be biotinylated in specific subsets of cells expressing a particular gene by expressing the biotinylating enzyme, hBirA = humanized BirA (hBirA), under the promoter control of another gene defining the specific subpopulation. We showed that a rare population of cells (1.1% of the 13.5 days postcoital mouse embryo) could be enriched to a sufficiently high purity (84.4%). From another sample with 0.1% of our cells of interest, we achieved a 40.3% pure sample. The low cost, speed, and technical ease of the Three-step MACS also make it scalable and hence, an ideal method for preparing sufficient quantities of biological samples for sensitive, high-throughput assays.     

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.     

Tenebrio molitor抗冻蛋白基因家族cDNA片段的克隆、序列分析及原核表达

利用反转录-多聚酶链式反应(RT-PCR)的方法, 克隆黄粉甲虫(Tenebrio molitor)抗冻蛋白基因cDNA片段并进行序列分析和原核表达。同源性分析表明, 获得9条新cDNA片段, 与黄粉甲虫抗冻蛋白基因家族的其他基因序列具有较高的同源性。重组质粒pGEX-4T-1-tmafp-XJ430, 转化E.coli BL21进行原核表达, SDS-PAGE分析结果表明, 抗冻蛋白基因以可溶性融合蛋白表达, 相对分子量为38 kDa。构建真核表达载体pCDNA3-tmafp-XJ430, 免疫小鼠, 获得的抗血清滴度为1:2 000。Western blotting 结果为单一的条带, 证明该抗血清具有针对抗冻蛋白TmAFP-XJ430抗原的专一性。     

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.