An ordered EST catalogue and gene expression profiles of cassava (<Emphasis Type="Italic">Manihot esculenta</Emphasis>) at key growth stages

A cDNA library was constructed from the root tissues of cassava variety Huanan 124 at the root bulking stage. A total of 9,600 cDNA clones from the library were sequenced with single-pass from the 5′-terminus to establish a catalogue of expressed sequence tags (ESTs). Assembly of the resulting EST sequences resulted in 2,878 putative unigenes. Blastn analysis showed that 62.6% of the unigenes matched with known cassava ESTs and the rest had no ‘hits’ against the cassava database in the integrative PlantGDB database. Blastx analysis showed that 1,715 (59.59%) of the unigenes matched with one or more GenBank protein entries and 1,163 (40.41%) had no ‘hits’. A cDNA microarray with 2,878 unigenes was developed and used to analyze gene expression profiling of Huanan 124 at key growth stages including seedling, formation of root system, root bulking, and starch maturity. Array data analysis revealed that (1) the higher ratio of up-regulated ribosome-related genes was accompanied by a high ratio of up-regulated ubiquitin, proteasome-related and protease genes in cassava roots; (2) starch formation and degradation simultaneously occur at the early stages of root development but starch degradation is declined partially due to decrease in UDP-glucose dehydrogenase activity with root maturity; (3) starch may also be synthesized in situ in roots; (4) starch synthesis, translocation, and accumulation are also associated probably with signaling pathways that parallel Wnt, LAM, TCS and ErbB signaling pathways in animals; (5) constitutive expression of stress-responsive genes may be due to the adaptation of cassava to harsh environments during long-term evolution.     

Effects of enhanced atmospheric ammonia on photosynthetic characteristics of two maize (<Emphasis Type=Italic>Zea mays</Emphasis> L.) cultivars with various nitrogen supply across long-term growth period and their diurnal change patterns

We investigated the effect of enhanced atmospheric ammonia (NH₃) in combination with low and high nitrogen (LN and HN, respectively) growth medium on photosynthetic characteristics of two maize (Zea mays L.) cultivars (NE5 with high- and SD19 with low N-use efficiency) across long-term growth period and their diurnal change patterns exposed to 10 nl l⁻¹ and 1,000 nl l⁻¹ NH₃ fumigation in open-top chambers (OTCs). Regardless of the level of N in medium, increased NH₃ concentration promoted maximum net photosynthetic rate (P _max) and apparent quantum yield (AQY) of both cultivars at earlier growth stages, but inhibited P _max of NE5 from silking to maturity stage and that of SD19 at maturity stage only above the ambient concentration. Greater positive/less negative responses were predominant in the LN than in the HN treatment, especially for SD19. Dark respiration rate (R _D) remained more enhanced in the LN than in the HN treatment for SD19 as well as increased in the LN while decreased in the HN treatment for NE5 at their silking stage, following exposure to elevated NH₃ concentration. Additionally, enhanced atmospheric NH₃ increased net photosynthetic rate (P _N) and stomatal conductance (g _s) but reduced intercellular CO₂ concentration (C _i) of both cultivars with either the LN or HN treatment during the diurnal period at tasseling stage. The diurnal change patterns of P _N and g _s showed bimodal curve type and those of C _i presented single W-curve type for NE5, when NH₃ concentration was enhanced. As for SD19, single-peak curve type was showed for both P _N and g _s while single V-curve type for C _i. All results supported the hypothesis that appropriately enhanced atmospheric NH₃ can increase assimilation of CO₂ by improving photosynthesis of maize plant, especially at earlier growth stages and after photosynthetic “noon-break” point. These impacts of elevated NH₃ concentration were more beneficial for SD19 as compared to those for NE5, especially in the LN supply environment.     

The role of the soil seed and seedling bank in the regeneration of diverse plant communities in the subtropical Ailao Mountains,Southwest China

We compared species composition and diversity of the soil seed and seedling banks in three secondary vegetation types (shrubland, Populus bonatii forest, Lithocarpus regrowth forest) and a primary old-growth forest in the subtropical Ailao Mountains of southwestern China to clarify the importance of seed and seedling banks for forest dynamics. The average species richness was the highest in soil samples from the shrubland (26.80 ± 1.98), and the lowest from the primary forest (9.93 ± 0.50). The density of germinable tree seeds increased from the secondary vegetation to the primary forest, and the density of shrub, forb, and graminoid seeds decreased significantly. The most abundant seedlings recorded in soil samples were light-demanding species in the shrubland and Populus bonatii forest. For ground flora, the number of shrub seedlings strongly decreased with the increase in stand age, and shade-tolerant tree seedlings tended to increase. The species similarity between the seed bank and the aboveground vegetation in all sites was low (Sørensen’s index = 0.11–0.33), however, the shrubland had higher similarity compared with the other three plant communities. In the primary forest, light-demanding woody species dominated in soil seed banks, while shade-tolerant species dominated in the overstory and the forest floor. In the primary forest, seedlings of dominant tree species were rare in the understory, and no seeds of the dominant species were found in the soil. Results indicated that the early stages of vegetation recovery should take into account the possibility of recovering soil seed bank processes. However, colonization and establishment of tree seedlings will be difficult once a primary forest is destroyed.     

Overexpression of malate dehydrogenase in transgenic tobacco leaves: enhanced malate synthesis and augmented Al-resistance

Numerous studies with transgenic plants have demonstrated that overexpression of enzymes related to organic acid metabolism under the control of CaMV 35S promoter increased organic acid exudation and Al-resistance. The synthesis of organic acids requires a large carbon skeleton supply from leaf photosynthesis. Thus, we produced transgenic tobacco overexpressing cytosolic malate dehydrogenase (MDH) cDNA from Arabidopsis thaliana (amdh) and the MDH gene from Escherichia coli (emdh), respectively, under the control of a leaf-specific light-inducible promoter (Rubisco small subunit promoter, PrbcS) in the present study. Our data indicated that an increase (120–130%) in MDH-specific activity in leaves led to an increase in malate content in the transgenic tobacco leaves and roots as well as a significant increase in root malate exudation compared with the WT plants under the acidic (pH 4.5) conditions irrespective of 300 μM Al³⁺ stress absence or presence. After being exposed to 25 μM Al³⁺ in a hydroponic solution, the transgenic plants exhibited stronger Al-tolerance than WT plants and the degree of A1 tolerance in the transgenic plants corresponded with the amount of malate secretion. When grown in an Al-stress perlite medium, the transgenic tobacco lines showed better growth than the WT plants. The results suggested that overexpression of MDH driven by the PrbcS promoter in transgenic plant leaves enhanced malate synthesis and improved Al-resistance.     

Plasma Neutrophil Elastase and Elafin Imbalance Is Associated with Acute Respiratory Distress Syndrome (ARDS) Development

Background

We conducted an exploratory study of genome-wide gene expression in whole blood and found that the expression of neutrophil elastase inhibitor (PI3, elafin) was down-regulated during the early phase of ARDS. Further analyses of plasma PI3 levels revealed a rapid decrease during early ARDS development. PI3 and secretory leukocyte proteinase inhibitor (SLPI) are important low-molecular-weight proteinase inhibitors produced locally at neutrophil infiltration site in the lung. In this study, we tested the hypothesis that an imbalance between neutrophil elastase (HNE) and its inhibitors in blood is related to the development of ARDS.

Methodology/Principal Findings

PI3, SLPI, and HNE were measured in plasma samples collected from 148 ARDS patients and 63 critical ill patients at risk for ARDS (controls). Compared with the controls, the ARDS patients had higher HNE, but lower PI3, at the onset of ARDS, resulting in increased HNE/PI3 ratio (mean = 14.5; 95% CI, 10.9–19.4, P<0.0001), whereas plasma SLPI was not associated with the risk of ARDS development. Although the controls had elevated plasma PI3 and HNE, their HNE/PI3 ratio (mean = 6.5; 95% CI, 4.9–8.8) was not significantly different from the healthy individuals (mean = 3.9; 95% CI, 2.7–5.9). Before the onset (7-days period prior to ARDS diagnosis), we only observed significantly elevated HNE, but the HNE-PI3 balance remained normal. With the progress from prior to the onset of ARDS, the plasma level of PI3 declined, whereas HNE was maintained at a higher level, tilting the balance toward more HNE in the circulation as characterized by an increased HNE/PI3 ratio. In contrast, three days after ICU admission, there was a significant drop of HNE/PI3 ratio in the at-risk controls.

Conclusions/Significance

Plasma profiles of PI3, HNE, and HNE/PI3 may be useful clinical biomarkers in monitoring the development of ARDS.     

Boule Is Present in Fish and Bisexually Expressed in Adult and Embryonic Germ Cells of Medaka

Background

The DAZ family genes boule, daz and dazl encode RNA binding proteins essential for fertility of diverse animals including human. dazl has bisexual expression in both mitotic and meiotic germ cells, whereas daz has male premeiotic expression, and boule is largely a unisexual meiotic regulator. Although boule has been proposed as the ancestor for dazl/daz by gene duplication, it has been identified only in invertebrates and mammals. It has, however, remained unclear when and how the DAZ family has evolved in vertebrates.

Methodology and Principal Findings

This study was aimed at identifying and characterizing the DAZ family genes in fish as the basal vertebrate. We show that boule and dazl coexist in medaka and stickleback. Similar to the medaka dazl (Odazl), the medaka boule (Obol) is maternally supplied and segregates with primordial germ cells. Surprisingly, Obol is expressed in adult germ cells at pre-meiotic and meiotic stages of spermatogenesis and oogenesis. However, the maximal meiotic Obol expression in spermatocytes contrasts with the predominant pre-meiotic Odazl expression in spermatogonia, and the diffuse cytoplasmic Obol distribution in early oocytes contrasts with the Odazl concentration in the Balbinani''s body.

Conclusions

The identification of fish boule and dazl genes provides direct evidence for the early gene duplication during vertebrate evolution. Our finding that Obol exhibits bisexual expression in both embryonic and adult germ cells considerably extends the diversity of boule expression patterns and offers a new insight into the evolutions of DAZ family members, expression patterns and functions in animal fertility.     

Transgene Expression Is Associated with Copy Number and Cytomegalovirus Promoter Methylation in Transgenic Pigs

Transgenic animals have been used for years to study gene function, produce important proteins, and generate models for the study of human diseases. However, inheritance and expression instability of the transgene in transgenic animals is a major limitation. Copy number and promoter methylation are known to regulate gene expression, but no report has systematically examined their effect on transgene expression. In the study, we generated two transgenic pigs by somatic cell nuclear transfer (SCNT) that express green fluorescent protein (GFP) driven by cytomegalovirus (CMV). Absolute quantitative real-time PCR and bisulfite sequencing were performed to determine transgene copy number and promoter methylation level. The correlation of transgene expression with copy number and promoter methylation was analyzed in individual development, fibroblast cells, various tissues, and offspring of the transgenic pigs. Our results demonstrate that transgene expression is associated with copy number and CMV promoter methylation in transgenic pigs.     

Exploring the structural requirements for jasmonates and related compounds as novel plant growth regulators: A current computational perspective

Jasmonates and related compounds have been highlighted recently in the field of plant physiology and plant molecular biology due to their significant regulatory roles in the signaling pathway for the diverse aspects of plant development and survival. Though a considerable amount of studies concerning their biological effects in different plants have been widely reported, the molecular details of the signaling mechanism are still poorly understood. This review sheds new light on the structural requirements for the bioactivity/property of jasmonic acid derivatives in current computational perspective, which differs from previous research that mainly focus on their biological evaluation, gene and metabolic regulation and the enzymes in their biosynthesis. The computational results may contribute to further understanding the mechanism of drug-receptor interactions in their signaling pathway and designing novel plant growth regulators as high effective ecological pesticides.Key words: jasmonates, amino acid conjugates of jasmonic acid, plant growth regulators, quantitative structure-activity relationship, quantitative structure-property relationship, a mini-review     

Ecological restoration design of a stream on a college campus in central Ohio

Straightened stream channels and altered and drained wetlands have adversely impacted streams and rivers throughout Midwestern USA, where some of the most dense drainage and riparian ecosystem alteration in the world have occurred. A segment of Grave Creek on The Ohio State University's Marion (OSU Marion) campus in Ohio, USA, with its lack of riparian ecosystems, illustrates the transformation of a natural fluvial ecosystem to an unstable and “simplified” aquatic environment that requires continued maintenance and provides little value to the surrounding landscape or to the university. However, the straight ditch, available adjacent riparian land and existing hydric soil give OSU Marion a great opportunity to demonstrate a project of stream and wetland restoration on a college campus. To restore the natural ecological stability of OSU Marion's “back yard” and to provide habitat improvement to Grave Creek and its surrounding landscape on the OSU Marion campus, we have designed a restoration of 1.1 km of Grave Creek meandering to the east of the existing sewer, using the two-stage channel techniques, and about 0.6–0.8 ha of adjacent wetland. We estimate that restoration on this scale will cost about US$ 200,000–300,000, not including monitoring of the results. To fulfill this project, it is likely that an opportunity for using this restoration in a stream/wetland loss mitigation will present itself in this region of Ohio while a long-term pre- and post-construction monitoring plan and more detailed design would be expected as the next step.